The Brassicaceae family displays divergent, shoot-skewed NLR … · 2017-12-01 · 131 revealed stable root to shoot NLR gene expression ratios within species, with all monocot and

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1

The Brassicaceae family displays divergent, shoot-skewed NLR resistance gene expression 2

3

4

David Munch1, Vikas Gupta

1, Asger Bachmann

1, Wolfgang Busch

2, Simon Kelly

1, Terry Mun

1, and 5

Stig Uggerhøj Andersen1*

6

7

8

1: Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10, 8000 9

Aarhus C, Denmark. 10

2: Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N 11

Torrey Pines Rd, La Jolla, CA 92037, USA 12

13

Arabidopsis, AM, CC, CNL, ETI, Lotus, LRR, MAMP, Medicago, NB-ARC, NBD, NF, NLR, 14

PRRs, RNL, TIR, TNL, XNL. 15

16

Stig Uggerhøj Andersen, [email protected]. 17

18

Resistance genes, NB-LRR, NLR, plant immunity, Brassicaceae, Arabidopsis, Lotus 19

Plant Physiology Preview. Published on December 1, 2017, as DOI:10.1104/pp.17.01606

Copyright 2017 by the American Society of Plant Biologists

www.plantphysiol.orgon October 14, 2020 - Published by Downloaded from Copyright © 2017 American Society of Plant Biologists. All rights reserved.

http://www.plantphysiol.org

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Nucleotide-binding site leucine-rich repeat resistance genes (NLRs) allow plants to detect microbial 21

effectors. We hypothesized that NLR expression patterns could reflect organ-specific differences in 22

effector challenge and tested this by carrying out a meta-analysis of expression data for 1,235 NLRs 23

from 9 plant species. We found stable NLR root/shoot expression ratios within species, suggesting 24

organ-specific hardwiring of NLR expression patterns in anticipation of distinct challenges. Most 25

monocot and dicot plant species preferentially expressed NLRs in roots. In contrast, Brassicaceae 26

species, including oilseed rape and the model plant Arabidopsis thaliana, were unique in showing 27

NLR expression skewed towards the shoot across multiple phylogenetically distinct groups of 28

NLRs. The Brassicaceae are also outliers in the sense that they have lost the common symbiosis 29

signaling pathway, which enables intracellular infection by root symbionts. While it is unclear if 30

these two events are related, the NLR expression shift identified here suggests that the Brassicaceae 31

may have evolved unique PRRs and antimicrobial root metabolites to substitute for NLR protection. 32

Such innovations in root protection could potentially be exploited in crop rotation schemes or for 33

enhancing root defense systems of non-Brassicaceae crops. 34

35

36

The sessile nature of vascular plants has spurred development of mechanisms for coping 37

with biotic and abiotic stresses and for optimizing uptake of inorganic compounds under low 38

nutrient availability. In response to these challenges, plant roots and shoots have evolved 39

specialized functions above and below ground, where they have also adapted to interact with the 40

distinct microbial communities of the phyllo- or rhizosphere. These diverse plant-microbe 41



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interactions range from symbiosis over parasitism to pathogenic infection (Bulgarelli et al. 2013; 42

Fatima et al. 2015; Vandenkoornhuyse et al. 2015). 43

Reflecting the different characteristics of plant roots and shoots, distinct host-microbe 44

combinations have been used to unravel the molecular components required for trans-species 45

interaction and communication. In plant shoots, the focus has almost exclusively been on 46

pathogenic interactions, where work in the model plant Arabidopsis thaliana (Arabidopsis) from the 47

Brassicaceae family has provided great insight into plant immunity (Jones and Dangl 2006; 48

Nishimura et al. 2010). Passive defences, such as the waxy cuticle on epidermal cells, cell walls and 49

preformed anti-microbial chemicals form the first barriers for microbes and are often sufficient for 50

deterring would-be pathogens (Thordal-Christensen 2003). Microbes that successfully evade these 51

obstacles encounter a large repertoire of resistance (R) proteins in the form of trans-membrane 52

receptor-like proteins and receptor-like kinases on the surface of plant cells, which recognize 53

conserved microbe-associated molecular patterns (MAMPs). Upon activation, these pattern-54

recognition receptors (PRRs) trigger complex intracellular signalling cascades, such as 55

phytohormone perturbations, accumulation of ions, mitogen-activated protein kinase activation and 56

production of reactive oxygen species, ultimately leading to transcriptional and translational 57

changes that promote the production of defence compounds (Pel et al. 2012; Muthamilarasan et al. 58

2013). 59

To escape this MAMP-triggered immunity (MTI), microbes have evolved effectors that are 60

injected into the plant cell cytoplasm using specialized secretion systems that penetrate the plant 61

cell membrane. Upon translocation, these effectors target components of the defence machinery, 62

suppressing immune signalling and gene expression through degradation, allosteric or covalent 63

modification of host molecules, thus adapting the local environment to be more suitable for 64

microbial growth and improving the chances of successful tissue colonization (Jones and Dangl 65



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2006; Xin et al. 2013; Le Fevre et al. 2015). In response, plant cells employ a family of intracellular 66

R proteins that recognize effectors either by direct interaction, or indirectly through detection of 67

modifications made to host proteins (Khan et al. 2015). Effector-triggered immunity (ETI) 68

activation by an intracellular R protein leads to a stronger immune response than that of MTI and is 69

often associated with localized cell death to limit the spread of biotrophic pathogens (Jones and 70

Dangl 2006; Hofius et al. 2007). 71

The majority of intracellular R proteins share a similar structure with an amino-terminal 72

signalling domain followed by a highly conserved nucleotide binding domain (NBD) and a 73

carboxy-terminal leucine-rich repeat (LRR) domain of variable length (van der Biezen et al. 1998; 74

Takken et al. 2012). This class of R proteins is referred to as nucleotide-binding site leucine-rich 75

repeat (NLR) proteins. The NBD is shared by Apaf1, plant R proteins and CED4 (NB-ARC) and is 76

highly conserved among all NLR proteins. It acts as a molecular switch, and cycles between active 77

ATP-bound and inactive ADP-bound states depending on the activity of the LRR domain. The LRR 78

domain is believed to be directly involved in protein-protein interactions with microbial effectors or 79

host proteins and to function by auto-suppressing the NBD of the NLR (Jones and Jones 1997; 80

Takken et al. 2006; Marquenet et al. 2007; Lukasik et al. 2009; Takken et al. 2012). The amino-81

terminal signalling domain is generally divided into two separate classes based on homology to 82

either the signalling domain of Toll/Interleukin-1 Receptors (TIR) or the presence of a coiled-coil 83

(CC) domain. These two distinct signalling components share common downstream signalling 84

pathways, however both classes have also been observed to activate separate downstream 85

components (Aarts et al. 1998; Falk et al. 1999; Meyers et al. 1999; Pan et al. 2000; Takken et al. 86

2006; Hofius et al. 2009). While both CC and TIR type NLRs (CNLs and TNLs, respectively) are 87

widely distributed in dicots, canonical TNLs appear to be absent in monocots (Meyers et al. 1999; 88

Pan et al. 2000; Meyers et al. 2002; Tarr et al. 2009). In addition, variations of the signalling 89

domain-NBD-LRR (NLR) structure can be found in most plant species, with NBD-containing 90



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proteins lacking either the amino-terminal signalling domain or the carboxy-terminal LRR domain, 91

or having juxtaposed non-canonical domains, extending their flexibility as signalling components or 92

effector decoys for host proteins (Bonardi et al. 2012; Kroj et al. 2016). 93

Whilst many NLRs play important roles in Arabidopsis shoot immunity, little is known 94

about how Arabidopsis roots mount immune response against microbes, or what role NLRs play. 95

However, the PRR FLAGELLIN-SENSITIVE2 is fully functional in roots and activates similar 96

downstream MAP-kinase cascades in both root and shoot (Millet et al. 2010). There are reported 97

differences between roots and shoots for the phytohormone salicylic acid, which is considered a 98

requirement for basal defence in leaves against biotrophic pathogens, but does not appear to be as 99

important in root immune responses (Jones and Dangl 2006; Millet et al. 2010). 100

Unlike the work on Arabidopsis pathogen responses, studies of root-microbe interactions have 101

focused on endosymbiosis with nitrogen fixing rhizobia and mycorrhizal fungi. Up to 90% of all 102

terrestrial plants are believed to associate with arbuscular mycorrhizal (AM) fungi to enhance their 103

acquisition of phosphorus and other nutrients. Plant associations with nitrogen-fixing bacteria 104

contained within root nodules is restricted to around 10 families, including the agriculturally 105

important Fabaceae (legume) family (Doyle 1998; Gualtieri et al. 2000; Parniske 2008). 106

Arabidopsis belongs to the Brassicaceae family which is one of the few plant families that has lost 107

the capacity for root endosymbiosis with mycorrhizal fungi that is ancestral to the Angiospermae 108

(flowering plants) (Gualtieri et al. 2000; Smith et al. 2010; Delaux et al. 2014). Two model plants 109

from the legume family, Lotus japonicus (Lotus) and Medicago truncatula (Medicago), have been 110

extensively used for unravelling the genetic pathways required for root nodulation through their 111

symbiotic association nitrogen fixing rhizobia (Barker et al. 1990; Handberg and Stougaard 1992). 112

This work has led to the discovery of nodulation factors (NF), a key signal molecule secreted by 113

rhizobia, and several host receptors that perceive and transduce the signal through regulatory 114



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components to modulate downstream transcriptional regulation and coordinate nodule 115

organogenesis and infection of these by nitrogen-fixing rhizobia (Long 1989; Schauser et al. 1999; 116

Limpens et al. 2003; E. B. Madsen et al. 2003; Radutoiu et al. 2003; Lévy et al. 2004; Kalo et al. 117

2005; Smit et al. 2005; Tirichine et al. 2006; Kouchi et al. 2010; Madsen et al. 2010). Similar to NF 118

produced by rhizobia, AM fungi secrete Myc factors to activate symbiotic signalling in the host. 119

Despite their distinct phenotypic characteristics, AM and nodulation pathways share a core of 120

signaling components known as the common symbiosis signaling pathway, likely owing to their 121

common evolutionary origin (Oldroyd and Downie 2006; Parniske 2008; Banba et al. 2008; Singh 122

and Parniske 2012; Guillotin, Couzigou, and Combier 2016). 123

Despite the history of focusing on pathogenic plant-microbe interactions in plant shoots and on 124

symbiotic interactions in roots, both organs are prone to pathogen infection and would presumably 125

be protected by NLR proteins present in cells subject to effector challenge. Currently, little is 126

known about the expression characteristics of NLRs and, unless they are ubiquitously expressed 127

across all plant organs, NLR gene expression patterns could provide indications about differences in 128

pathogen effector pressures between plant tissues and across plant species. Here we present a meta-129

analysis of NLR gene expression data, including both monocot and dicot plant species. Our analysis 130

revealed stable root to shoot NLR gene expression ratios within species, with all monocot and 131

legume plant species examined predominantly expressing NLRs in roots. In contrast, members of 132

the Brassicaceae family displayed an aberrant shoot-skewed NLR expression, which suggested an 133

unusual mode of plant-microbe interaction for this plant family. 134

135



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136

137

Individual plant organs have evolved to function in specific environments, where they 138

interact with distinct microbiota (Vandenkoornhuyse et al. 2015). In addition, plant species, 139

including Lotus, which partake in symbiosis with rhizobia and mycorrhizal fungi, harbour 140

microbiota that diverge greatly from those of non-symbiotic species like Arabidopsis (Zgadzaj et 141

al., 2016). To investigate if NLR expression patterns reflected these cross-tissue and -species 142

differences, we analysed data from Lotus and Arabidopsis, which differ in symbiotic status and 143

have microarray expression atlas data available for multiple tissues (Schmid et al. 2005; Høgslund 144

et al. 2009; Verdier et al. 2013) (Supplemental table 1-2 and Supplemental file 1). We identified 145

all putative NLRs in Lotus and Arabidopsis based on the presence of an NBD and at least one other 146

NLR-associated domain and then classified genes by enriched expression in reproductive, shoot, 147

root or root nodule tissues. NLR expression in Lotus shoot and nodule tissues did not show 148

significant differences compared to overall gene expression, but reproductive tissues showed strong 149

depletion of NLR expression and Lotus roots displayed a significant enrichment of NLR expression 150

(Figure 1A-B). For Arabidopsis, reproductive tissues also showed a significant depletion of 151

expressed NLR genes, but Arabidopsis roots did not show enriched NLR gene expression. Instead, 152

Arabidopsis shoots displayed a significant enrichment of NLR gene expression (Figure 1C-D). 153

To investigate if the contrasting root/shoot NLR gene expression ratios were general for the two 154

species, we studied additional data sets. For Arabidopsis, we examined two recent RNA-seq 155

experiments including both root and shoot samples in the same experimental series (van Veen et al. 156

2016; Liu et al. 2016). Since no equivalent data sets were available for Lotus, we carried out an 157

RNA-seq experiment including mock and rhizobium inoculated root and shoot samples. Transcript 158



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quantification by RNA-seq is based on digital read counts, which provide a large dynamic range. 159

The methodology can, however, cause issues with normalization between samples because of 160

compositional bias effects, where a pronounced increase in the expression of a few genes reduces 161

the number of reads allocated to other transcripts in the same library (Li et al., 2012). Comparisons 162

between root and shoot samples, which have different expression profiles, could be subject to such 163

biases. We therefore evaluated four different normalization methods – total library read count, 164

Trimmed Means of M-values (TMM), PoissonSeq (PSS) and voom (Robinson et al., 2010; Li et al., 165

2012; Ritchie et al., 2015) – for their efficacy in controlling for compositional bias effects on 166

root/shoot gene expression ratios. To compare the methods, we simulated compositional biases in 167

the RNA-seq data by randomly elevating the expression of 100 genes 10,000 fold, followed by 168

scaling back expression of the remaining genes to retain the same overall library size. 169

Normalization of the simulated data using voom or total read counts produced erratic root/shoot 170

expression ratios, which depended on the direction of the introduced bias. In contrast, TMM and 171

PoissonSeq normalization both performed well, with PSS-based root/shoot ratios slightly more 172

robust to the introduced biases (Supplemental table 3). We therefore used PSS normalized data for 173

downstream analysis. 174

Both Arabidopsis RNA-seq data sets showed a clear shoot skew for NLRs relative to the average 175

expression ratio for all genes (Figure 1E and Supplemental table 4), and the NLR expression 176

ratios were strongly correlated across array and RNA-seq experiments (Figure 1F). For Lotus, the 177

RNA-seq data was consistent with the array data in showing a pronounced root skewed NLR 178

expression (Figure 1G-H and Supplemental table 4). 179

Bacterial inoculation is another factor that could potentially influence NLR root/shoot expression 180

ratios. We compared Lotus inoculated and uninoculated samples, but found no significant 181

differences in the root/shoot NLR expression ratios for neither the array nor the RNA-seq 182

experiment (Supplemental figure 1). NLR root/shoot expression ratios thus showed clear 183



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differences between Lotus and Arabidopsis, and these differences were consistent across 184

independent experiments carried out using either array or RNA-seq methodology for transcript 185

quantification, indicating that regulation of NLR gene expression varied between organs in a 186

species-specific manner. 187

188

To determine which of these contrasting patterns of NLR gene expression was predominant among 189

flowering plants, we analysed additional species for which root and shoot tissues had been 190

subjected to global expression profiling in the same experiment. These included three legume 191

species (Medicago, Glycine max, Lupinus albus), two Brassicaceae family members (Brassica rapa 192

ssp. pekinensis, Brassica napus) and two monocots (Zea mays, Oryza sativa) (Figure 1I, 193

Supplemental figure 2 and Supplemental figure 3). We calculated root/shoot expression ratios 194

for all genes, including only samples where root and shoot tissues had been analysed in the same 195

experimental series (Supplemental tables 1-2). We identified a total of 2,167 NLR genes across 196

the selected species, and expression data was available for 1,235 of these (Supplemental table 5). 197

Like Lotus, the three other dicot legumes and the two monocots displayed NLR gene expression 198

skewed towards the root when compared to the overall gene expression pattern (Figure 1I, 199

Supplemental figure 2, Supplemental figure 3 and Supplemental table 4). In comparison, the 200

three Brassicaceae species stood out by displaying shoot-skewed NLR gene expression (Figure 1I, 201

Supplemental figure 2, Supplemental figure 3 and Supplemental table 4). Comparisons within 202

either the legume, Brassicaceae or monocot groups showed very few statistically significant 203

differences. However, when we compared between species groups, many comparisons showed 204

significant differences, with the overall differences between Brassicaceae versus both legumes and 205

monocots highly significant (p<1e-04) (Figure 1I and Supplemental table 6). Among the 206

flowering plants investigated, shoot-skewed expression of NLR genes was a feature exclusive to the 207



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dicot Brassicaceae family, while the remaining monocots and dicot species all displayed root-208

skewed expression. 209

210

211

We speculated that the Brassicaceae expression shift could have been caused by the loss of a 212

specialized set of phylogenetically related NLRs evolved specifically to guard root specific 213

components. To test this hypothesis, we categorized all identified NLRs by aligning their NBDs and 214

constructing a phylogenetic tree based on 2,033 sequences (Figure 2A and Figure 2B). In addition 215

to the previously mentioned species, we included the carnivorous and submerged aquatic 216

bladderwort Utricularia gibba from the Asterids clade, which lacks a true root (Ibarra-Laclette et al. 217

2013). The phylogenetic analysis allowed us to identify five well-supported major NLR clades 218

(Figure 2B, Supplemental file 2, and Supplemental table 7). To investigate if the Brassicaceae 219

expression shift was correlated with a specific NLR subtype, we also classified all NLRs according 220

to domain composition, initially identifying TIR and CC domains, and compared these results to 221

our phylogenetic analysis (Supplemental figure 4 and Supplemental table 7). We found that 222

several of the sequences in our initially identified set of NLRs from all eight species contained a 223

specific subtype of the CC domain, the CCR domain, which shows high sequence similarity to the 224

amino terminal domain of the non-NBD-LRR R gene RPW8 (RESISTANCE TO POWDERY 225

MILDEW 8) (Xiao et al. 1997; Xiao et al. 2001; Collier and Moffett 2009; Collier, Hamel, and 226

Moffett 2011; Bonardi et al. 2011; Shao et al. 2016). We therefore included the CCR domain 227

proteins as a separate group in the analysis (Xiao et al. 2001; Meyers et al. 2003; Shao et al. 2016). 228

Hereafter, we refer to NLRs containing TIR, CC and CCR domains as TNLs, CNLs and RNLs, 229

respectively. NLRs containing neither of the three described domains are referred to as XNLs. We 230

performed a stringent search against the NCBI conserved domain database CDD (Marchler-Bauer 231



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et al. 2011) for identification of canonical CC and TIR domains. We did not classify as many NLRs 232

into TNL, and especially CNL groups, as in previous studies (Supplemental table 7; Monosi et al. 233

2004; Ameline-Torregrosa et al. 2008; J. Kim et al. 2012; Shao et al. 2014; Yu et al. 2014; Song et 234

al. 2015; Sarris et al. 2016; Shao et al. 2016). We chose this conservative approach due to relatively 235

poorly defined sequence composition and structure of especially the CC domains. 236

Clade 1 was highly enriched in TNLs (708/806), CNLs dominated clade 2 (307/510) and clade 4 237

(326/385), clade 5 was enriched for RNLs (62/87), and clade 3 contained mainly XNLs (211/245) 238

(Figure 2B and Supplemental table 7). The clear correlation between domain structure and the 239

NBD-based phylogeny indicated that the NBD sequences contained sufficient information for 240

inferring the evolutionary history of the plant NLR family, as previously suggested (Pan et al. 241

2000). 242

In accordance with previous studies, we did not observe any sequences from monocots in the TNL-243

enriched clade 1, but among all sequences analysed we recovered 7 monocot NLRs that had an 244

identifiable TIR-like domain, which has previously been observed to be juxtaposed irregularly 245

compared to the normal TIR domain (Meyers et al. 2002; Caplan et al. 2013). We did not identify 246

any monocot RNLs using our stringent filtering criteria, although at least one RNL has previously 247

been found in both rice and maize (Shao et al. 2016). Nor did we recover any TIR or TIR-related 248

domain containing NLR sequences from U. gibba, despite it being a dicot (Pan et al. 2000; Fluhr 249

2001; Tarr et al. 2009; Ibarra-Laclette et al. 2013). In fact, U. gibba sequences were only found in 250

clades 2 and 4 (Figure 2B and Supplemental table 7). 251

Examining the expression characteristics of NLRs grouped by their protein domain composition, we 252

did not observe expression bias towards either organ for TNLs and XNLs (Supplemental figure 253

4A and Supplemental table 8). In contrast, CNLs and RNLs displayed highly significant root 254

skews (Supplemental figure 4A and Supplemental table 8). Legume and monocot TNLs and 255



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CNLs showed significant root skews, but Brassicaceae CNLs and XNLs showed significant shoot 256

skews (Supplemental figure 4B and Supplemental table 8). Reflecting the contrasting 257

Brassicaceae and legume expression skews, XNLs, TNLs, and CNLs all showed significantly 258

different means in Brassicaceae vs. legume comparisons (Supplemental figure 4B and 259

Supplemental table 8). 260

We then studied NLR root/shoot ratios for the five NLR clades defined on the basis of the sequence 261

similarities of their NBDs. Across data from all species, we observed highly significant root skews 262

for the CNL-enriched clade 2 and for the RNL-enriched clade 5 (Figure 2C and Supplemental 263

table 9). When examining the Brassicaceae, legume and monocot species groups separately, we 264

found significant shoot skews for Brassicaceae clades 2, 3 and 4, and significant root skews for 265

monocot clades 2 and 4 and for all legume NLR clades. The mean Brassicaceae root/shoot 266

expression ratios deviated significantly from those of legumes for clades 1-4, and from monocots 267

for clades 3 and 4 (Figure 2D and Supplemental table 9). In contrast, we did not find significant 268

deviations between Brassicaceae and legumes for the RNL-enriched clade 5, where both species 269

groups showed root-skewed expression. Since we observed significant Brassicaceae deviations for 270

multiple NLR clades, a monophyletic group of NLRs was not responsible for the Brassicaceae 271

expression shift. However, there were differences between the NLR clades in the severity of the 272

shift, with the smallest effect seen for the TNL-enriched clade 1. 273

274

275

Comparing the species tree (Figure 2A) to the NBD-based NLR tree (Figure 2B), we noted that 276

clade 1 and 5 in the NBD tree contained mainly dicot members, whereas clades 3 and 4 comprised 277

monocot and dicot members from all species, in line with the species tree. In contrast, clade 2 from 278

the NBD-tree was depleted in dicot Brassicaceae members, while both legume and monocot 279



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members were well-represented, suggesting a possible family-specific depletion of a major NLR 280

clade in the Brassicaceae (Figure 2B and Supplemental table 7). 281

To investigate if NLR clade 2 depletion was Brassicaceae specific, we examined NLR protein 282

sequences from 8 additional plant species, including Brassicaceae members and species from other 283

families without a functional common symbiosis signaling pathway (Figure 3A-B, Supplemental 284

table 10, and Supplemental file 3). We found that 120 out of the 415 new NLR sequences were 285

present in clade 2, indicating that clade 2 was not generally depleted in species without a common 286

symbiosis signaling pathway (Figure 3C and Supplemental table 10). After including three 287

additional Brassicaceae species, we still observed a pronounced family-specific Brassicaceae 288

depletion in clade 2, as we only found 20 out of 544 Brassicaceae NLRs belonging to this family 289

(Supplemental table 10), suggesting that NLR clade 2 depletion is characteristic of the 290

Brassicaceae family. 291

292

Cytoplasmic NLRs make up the last line of defence against potentially pathogenic microbes that 293

have evaded physical barriers and membrane-localized PRRs to successfully deliver effectors into 294

plant cells. The stable root/shoot NLR expression ratios observed here are consistent with a defence 295

system in which NLR expression patterns are hardwired in anticipation of organ-specific effector 296

challenges (Ingle 2011; Wang et al. 2011). Indeed, we also found that rhizobium inoculation of the 297

nodulating legume Lotus did not alter the overall pattern of NLR expression, further underlining the 298

stability of NLR root/shoot expression ratios within species. It was striking that we found an overall 299

root-skew in NLR expression in the majority of plant species. This suggests that roots generally 300

experience a higher level of effector pressure than shoots, despite the fact that NLR function has 301

mainly been characterized in the context of shoot-pathogen interactions (Erb et al. 2009; Nishimura 302



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and Dangl 2010). It might not be surprising given the complexity of soil microbial communities, but 303

our data does underline the need for establishing new root pathosystems and for understanding the 304

role of NLRs in root-microbe interactions. 305

It is conceivable that a specialized set of phylogenetically related NLRs could have evolved 306

specifically to guard the root defense machinery or other root specific pathways, and that the 307

Brassicaceae NLR expression shift might be caused by the loss of such a group of NLRs. Here, we 308

tested this hypothesis by grouping NLRs according to the sequence homology of their NBD 309

domains, identifying five major clades. While the CNL-enriched NLR clade 2 was strongly 310

depleted in the Brassicaceae, it was well-represented in all other plant species examined. In 311

addition, we observed a Brassicaceae shoot skew for all NLR clades, with the smallest shift 312

observed for TNLs, which are absent in the monocots rice and maize, and therefore cannot be 313

generally required for protecting root components. The shift in Brassicaceae NLR expression could 314

thus not be attributed to the loss of a single NLR clade, and our data did not support the existence of 315

a specific group of phylogenetically distinct NLRs guarding the root. 316

Brassicaceae and monocot species have previously been identified as outliers with respect to NLR 317

regulation in the context of small RNAs. Whereas large numbers of NLR transcripts are targeted by 318

small RNAs in legumes and other dicots (Zhai et al., 2011; Zhang et al., 2016), Brassicaceae and 319

monocot species appear only to regulate a handful of NLRs by small RNA targeting (Zhang et al., 320

2016). Small RNA NLR regulation is often initiated by 22 nucleotide miRNA targeting followed by 321

NLR transcript degradation, which leads to the production of secondary phased and trans-acting 322

small interfering RNAs (Arikit et al., 2014; Axtell, 2013; Fei et al., 2015; Zhai et al., 2011). In most 323

species, the majority of small RNA-regulated NLRs are part of large gene families targeted by the 324

miR482/2118 superfamily of microRNAs (Li et al., 2012; Shivaprasad et al., 2012; Zhai et al., 325

2011; Zhang et al., 2016). It has been suggested that the limited miRNA targeting of NLRs in 326

Brassicaceae and monocots could be due to absence of the large NLR gene families targeted by 327



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miR482 (Zhang et al., 2016). Although the Brassicaceae and monocots show opposite trends with 328

respect to root/shoot NLR expression ratios, it is possible that small RNA regulation of NLR 329

transcript levels could play a role in establishing organ-specific NLR expression patterns in legumes 330

and other species with large numbers of NLR targeted by small RNAs. 331

In the Brassicaceae, the general expression shift towards the shoot across four major NLR clades 332

suggests a reduced anticipation of effector challenge to root cells relative to shoot cells. We 333

envisage two scenarios, which are not mutually exclusive, that could account for the shift. First, our 334

data is consistent with a model where NLRs were randomly recruited from an expanding NLR 335

complement, regardless of phylogenetic origin, for guarding root specific components. When the 336

guarded pathways became defunct in the Brassicaceae family, it gradually lost the associated root-337

expressed NLRs across the different NLR clades, leading to the overall shoot skew in NLR 338

expression. Second, rather than passively reducing the effector challenge level to roots by loss of a 339

signaling pathway prone to microbial effector targeting, the Brassicaceae could have minimised 340

their requirement for root NLR protection by developing family-specific active measures that 341

efficiently deter putative soil pathogens before they have a chance to deploy their effectors. One 342

possibility is that the Brassicaceae maintain high levels of antimicrobial glucosinolates in the root 343

apoplasm, and there are indications that roots have higher constitutive glucosinolate levels than 344

shoots (Van Dam, Tytgat, and Kirkegaard 2009). Another is that the Brassicaceae have evolved a 345

unique set of highly efficient pattern recognition receptors that quickly eliminate putative root 346

pathogens. For instance, the Ef-Tu and lipopolysaccharide PRRs are thought to be Brassicaceae-347

specific (Kunze et al. 2004; Ranf et al. 2015). 348

The Brassicaceae family made up a very conspicuous group of outliers that displayed shoot- rather 349

than root-skewed NLR expression. The Brassicaceae are also outliers in the sense that they have lost 350

the common symbiosis signalling pathway, which remains functional in 80-90% of land plants 351



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(Parniske 2008; Delaux et al. 2014). It is tempting speculate if the two events are related, since the 352

loss of the common symbiosis signalling pathway would both have removed a potentially heavily 353

NLR-guarded pathway and eliminated constraints impeding development of more effective general 354

root defence systems. In any case, the NLR expression shift described here suggests that the 355

Brassicaceae may have evolved rich repertoires of unique PRRs and antimicrobial root metabolites 356

to substitute for NLR protection. Such fundamental differences in root protection strategies could 357

potentially be exploited in crop rotation schemes or for enhancing root defence systems of non-358

Brassicaceae crops. 359

360

361

362

To allow identification of putative NLR genes, protein sequences were downloaded as indicated 363

(Supplemental table 1). Annotation versions were chosen for compatibility with the available 364

microarray or RNA-seq data to allow subsequent expression analysis. This is why the latest 365

versions were not used in all cases. NLR genes were then identified in a three-step procedure. First, 366

candidate genes were selected using HMMER 3.1b1 (Eddy 2011) based on the NB-ARC PFAM 367

protein domain PF00931. Second, the candidate list was filtered by performing a search for 368

conserved protein domains using CDD (Marchler-Bauer et al. 2011), requiring that the selected 369

putative NLR proteins contain, in addition to the NB-ARC domain, either LRR, TIR, PLN00113, 370

PLN03194, or PLN03210 domains. Third, all NLR protein sequences were manually curated to 371

identify and remove false positives. The total number of identified NLR proteins in each of the 18 372

species is shown in Supplemental table 5, with sequences available in Supplemental file 4. 373



Page 17 of 31

374

Lotus ecotype Gifu (Handberg and Stougaard 1992) seeds were surface sterilized, germinated and 375

grown in conditions as described previously (Kawaharada et al. 2015). Three biological replicates 376

per sample were analysed with each consisting of 10 seedlings grown on 1/4 B&D plates for 10 377

days before inoculation of the roots with 750 μL of an M. loti R7A suspension (OD600 = 0.02) or 378

water. Three days post-inoculation roots and shoots were separated and total RNA was isolated 379

using a NucleoSpin® RNA Plant kit (Machery-Nagel) according to the manufacturer’s instructions. 380

RNA quality was assessed with on an Agilent 2100 Bioanalyser and samples were sent to GATC 381

Biotech (http://gatc-biotech.com/) for library preparation and sequencing. Sequencing data have 382

been deposited at the NCBI Short Read Archive with BioProject ID PRJNA384655 and are 383

available for analysis on Lotus Base (Mun et al. 2016). Read counts were generated by mapping the 384

reads to the L. japonicus v. 3.0 genome using CLC Genomics Workbench 9.5.3. 385

386

For tissues-specific gene expression enrichment analysis (Figure 1 A-D), we classified genes as 387

being enriched in a specific tissue group if the average expression level in a that group was higher 388

than the average of all other tissue groups, and at least two times higher than that of at least one 389

other tissue group. 390

In order to evaluate root/shoot expression ratios, available expression data was downloaded as 391

indicated in Supplemental table 2. Sample IDs along with normalized expression values are 392

available in Supplemental file 1. For Lotus and B. rapa, probes were reassigned to the updated 393

annotation using BLAST to match probe and cDNA sequences (e-value cut-off 0.001), assigning 394

only the best matching probe to a gene. For Lotus, Medicago and soybean, samples representing 395

identical or closely related plant accessions were used in the analysis. For rice and maize, data from 396

a number of different accessions were used, but only data where both root and shoot samples had 397


http://gatc-biotech.com/)


Page 18 of 31

been assayed within the same experiment were used to ensure the comparability of samples from 398

the two tissues. For B. napus, the analysis was based on raw RNA-seq reads. RNA-seq data files 399

were downloaded from the NCBI short read archive (https://www.ncbi.nlm.nih.gov/sra) and reads 400

from each library were assembled using Trinity (--full_cleanup) (Haas et al. 2013) followed by 401

clustering using cd-hit-est v.4.6.6 (-M 16000 -T 8) (Fu et al. 2012). Next, the longest open reading 402

frames were identified for each transcript and the corresponding protein sequences were used for 403

identification of NLRs as described. Reads were mapped back to the gene set output from cd-hit-est 404

using STAR (--runMode genomeGenerate --genomeChrBinNbits 14) parameters for index 405

generation and standard options for mapping (Dobin et al. 2013). Finally reads mapping to multiple 406

locations were filtered out followed by summarizing read counts per gene for each sample. 407

Microarray data was analysed directly, maintaining the original inter-sample normalization. For 408

RNA-seq data, we simulated compositional bias by randomly selecting 100 genes and increasing 409

their expression level 10,000-fold in either root or shoot samples followed by downscaling 410

expression levels of all genes to match the original library size. RNA-seq data normalization was 411

carried out using TMM implemented in edgeR (Robinson et al., 2010), PoissonSeq (Li et al., 2012), 412

voom from the limma R package (Ritchie et al., 2015), and normalization factors calculated based 413

on total library read count. 414

For all species, expression data from the genes with the 15% lowest expression levels were filtered 415

out, and the log2 NLR root/shoot expression ratios were normalized by subtracting the mean value 416

for all genes. Expression ratios were plotted using ggplot2 in R version 3.1.2. Where multiple data 417

sets were available for each species, RNA-seq data was used in the analysis of root/shoot 418

expression ratios to include as many genes as possible. For Arabidopsis, average expression ratios 419

based on the two available RNA-seq data sets were used. 420

The significance of differences in mean expression ratios between all genes and NLR genes were 421

evaluated using Student’s t-test (t.test) and the Kolmogorov-Smirnov test (ks.test) as implemented 422


https://www.ncbi.nlm.nih.gov/sra


Page 19 of 31

in R (Supplemental table 4). Density plots were generated using the geom_density function of 423

ggplot2 in R with standard options, and experimental cumulative distribution plots were generated 424

using the R ecdf function with standard options. The significance levels of interspecies differences 425

in root/shoot expression ratios (Supplemental table 6) and differences in the average root/shoot 426

expression by NLR gene clade or domain based on the phylogenetic tree shown in Figure 2B 427

(Supplemental tables 8 and 9) were evaluated by fitting a generalized linear model, e.g. model <- 428

glm(log(root/shoot) ~ Species), and subsequently using the glht function from the multcomp R 429

package to calculate p-values, e.g. glht(model, linfct= mcp(Species="Tukey")). 430

431

Sequences of the NB-ARC domains of identified R genes were extracted using a python script, 432

based on domains as identified by the CCD search, and aligned using Clustal Omega v1.2.3 433

(Sievers et al. 2011). Sequences were then filtered for low coverage positions (50% cut-off) and 434

sequences lacking more than 50% of the aligned NB-ARC domain were removed. Phylogenetic 435

trees were constructed in IQ-Tree v.1.5.2 and evaluated using the ultrafast bootstrap approximation 436

approach (UFBoot) (Minh et al. 2013; L.-T. Nguyen et al. 2015). The resulting tree was coloured by 437

species using colorTree v1.1 and visualized using Dendroscope v3.5.7 (Chen et al. 2009; Huson et 438

al. 2012). See Supplemental files 2 and 3 for NB-ARC domain alignments of the trees described in 439

Figures 2B and 3B respectively, along with bootstrap analysis. See Supplemental file 4 for 440

sequences for all NLRs used to construct the phylogenetic trees, and Supplemental file 5 for a 441

general overview of all NLRs used in the study. All python scripts and commands for the above 442

analyses are available in Supplemental file 6. 443

444



Page 20 of 31

445

DM, VG, AB, TM, WB, and SUA analysed data. SK carried out the Lotus RNA-seq experiment. 446

SUA designed and supervised the study. DM and SUA wrote the manuscript. 447

448

This work was supported by the Danish National Research Foundation grant no. DNRF79. The 449

authors wish to acknowledge all research groups contributing expression data used in our meta-450

analysis. 451

Supplemental Data 452

Supplemental figures 453

Supplemental figure 1. Effect of rhizobium inoculation on root/shoot expression ratios. 454

Supplemental figure 2. Inter-species variation in root/shoot expression ratios – density plots. 455

Supplemental figure 3. Inter-species variation in root/shoot expression ratios – cumulative 456

distribution function plots. 457

Supplemental figure 4. Log root/shoot expression ratios by NLR domain type. 458

Supplemental files 459

Supplemental file 1. Normalized expression data. 460

Supplemental file 2. NB-ARC alignment of sequences used to construct the phylogenetic tree in 461

Figure 2B, along with bootstrap analysis of the resulting phylogenetic tree. 462

Supplemental file 3. NB-ARC alignment of sequences used to construct the phylogenetic tree in 463

Supplemental Figure 3B, along with bootstrap analysis of the resulting phylogenetic tree. 464

Supplemental file 4. Full length sequences for all NLRs identified and used in this study. 465

Supplemental file 5. Full list of NLR genes identified, with domains, designations and normalized 466

log2 root/shoot expression ratios. 467

Supplemental file 6. Python scripts and commands used for extraction, alignment, bootstrapping 468

and creation of phylogenetic trees of NBD sequences. 469

Supplemental tables 470

Supplemental table 1. Sources of the protein sequences used in the NLR analysis. 471

Supplemental table 2. Expression data sources used in the NLR analysis. 472



Page 21 of 31

Supplemental table 3. Effects of RNA-seq data normalization methods. 473 474

Supplemental table 4. Mean log (root/shoot) gene expression ratios for NLR and all genes. 475

Supplemental table 5. Summary of NLR genes and expression data availability. 476

Supplemental table 6. Cross-species comparison of normalized log2 root/shoot NLR 477

expression ratios supporting Figure 1I. 478

Supplemental table 7. Clade distribution of NLR genes for the phylogenetic tree used in 479

Figure 2B. 480

Supplemental table 8. Cross-species domain comparison of normalized log2 root/shoot 481

NLR gene expression ratios for Supplemental figure 4. 482

Supplemental table 9. Cross-species clade comparison of normalized log2 root/shoot 483

NLR gene expression ratios for Figure 2C-D. 484

Supplemental table 10. Clade distribution of NLR genes for the phylogenetic tree shown 485

in Figure 3B. 486

487

488

489 490 Figure 1. NLR gene expression patterns across species. 491

A) Expression patterns of 198 putative Lotus NLR genes. B) Enrichment of Lotus NLR genes by 492

tissue type. The fraction of all genes and NLR genes with enriched expression in the given tissue 493

are shown. C) Expression patterns of 160 putative Arabidopsis NLR genes. D) Enrichment of 494

Arabidopsis NLR genes by tissue type. The fraction of all genes and NLR genes with enriched 495

expression in the given tissue are shown. P-values indicate the probability that the fraction of NLR 496

genes showing enriched expression in a specific tissue is identical to that of all genes. E) Density 497

plots displaying the distribution of the logarithm of the root/shoot expression ratios of all genes and 498



Page 22 of 31

NLR genes for each Arabidopsis expression data set indicated. See main text for sources. F) 499

Root/shoot expression correlations for Arabidopsis NLR genes from the three data sets shown in 500

Figure 1E. Each circle represents one NLR gene for which expression data is available in both of 501

the datasets compared. G) Density plots displaying the distribution of the logarithm of the 502

root/shoot expression ratios of all genes and NLR genes for each Lotus expression data set 503

indicated. H) Root/shoot expression correlations for Lotus NLR genes between two datasets. Each 504

circle represents one NLR gene for which expression data is available in both datasets. I) 505

Phylogenetic tree of species for which both shoot and root expression data is available, along with 506

their average NLR gene root/shoot expression values (black dots). Error bars indicate SEM. The 507

symbiotic status of each species is indicated on the right; M: Mycorrhiza. R: Rhizobia. +: engages 508

in endosymbiosis. -: does not engage in endosymbiosis. Significance of each species group is 509

indicated on the far right. ***: Significant difference with p ≤ 0.001. n.s.: Not significant. 510

Generalized linear model ANOVA was used for calculation of p-values. See Supplemental table 6 511

for p-values for inter-species differences. 512

513

Figure 2. NLR expression patterns by phylogenic clade. 514

Colors indicate the plant species from which the NLR originates with reference to Figure 2A. A) 515

Species-level phylogenetic tree. The symbiotic status of each species is indicated on the right; M: 516

Mycorrhiza. R: Rhizobia. +: engages in endosymbiosis. -: does not engage in endosymbiosis. B) 517

Phylogenetic tree based on the NBD protein sequence of identified NLR genes in the species 518

indicated in Figure 2A. Numbers at branches indicate bootstrap values for the branching of the 5 519

major clades. Peripheral numbers indicate clade designation, and NLR designation indicate 520

enrichment of the corresponding NLR type in the given clade. Scale bar indicate 1.0 average amino 521

acid substitutions per site. See Supplemental File 2 for full bootstrap analysis of the tree. See 522

Supplemental table 7 for NLR distribution at the clade and species level. C) Per clade log2 523



Page 23 of 31

root/shoot expression ratios of the NLR genes shown in B) for which expression data is available. 524

Each colored dot represents one NLR gene. Box plot bars show median with boxes indicating 25th

525

and 75th

percentiles and whiskers indicating 1.5 times the interquartile range. D) Same as C) but 526

with expression data separated into groups depending on the species evolutionary descent colored 527

according to Figure 2A. ****: Significant difference with p ≤ 0.0001. ***: Significant difference 528

with p ≤ 0.001. **: Significant difference with p ≤ 0.01. *: Significant difference with p ≤ 0.05. n.s.: 529

Not significant. Student’s t-test was used for calculation of p-values. See Supplemental table 9 for 530

p-values for inter-clade and inter-species differences. 531

532

Figure 3. NBD phylogeny including additional non-mycorrhizal species. 533

A) Species-level phylogenetic tree. The symbiotic status of each species is indicated on the right. 534

M: Mycorrhiza. R: Rhizobia. +: engages in endosymbiosis. -: does not engage in endosymbiosis. B) 535

Phylogenetic tree based on the NBD protein sequence of identified NLR genes in the species 536

indicated in Figure 3A. Numbers at branches indicate bootstrap values for the branching of the 5 537

major clades. Peripheral numbers indicate clade designation. Scale bar indicates 1.0 average amino 538

acid substitutions per site. Colors indicate the plant species from which the NBD originates with 539

reference to Figure 3A. See Supplemental File 3 for full bootstrap analysis of the tree. See 540

Supplemental table 10 for NLR distribution at the clade and species level. C) Table showing the 541

percentage of NLRs in each species, with respect to each clade shown in Figure 3B. 542

543

544

545 546

547



Page 24 of 31

Aarts, N, M Metz, E Holub, Brian J Staskawicz, M J Daniels, and Jane E Parker. 1998. “Different 548

Requirements for EDS1 and NDR1 by Disease Resistance Genes Define at Least Two R 549

Gene-Mediated Signaling Pathways in Arabidopsis.” Proceedings of the National Academy 550

of Sciences of the United States of America 95 (17): 10306–11. 551

Arikit, S., Xia, R., Kakrana, A., Huang, K., Zhai, J., Yan, Z., et al. (2014). An atlas of soybean 552

small RNAs identifies phased siRNAs from hundreds of coding genes. The Plant Cell, 553

26(12), 4584–4601. http://doi.org/10.1105/tpc.114.131847 554

Axtell, M. J. (2013). Classification and comparison of small RNAs from plants. Annual Review of 555

Plant Biology, 64, 137–159. http://doi.org/10.1146/annurev-arplant-050312-120043 556

Banba, Mari, Caroline Gutjahr, Akio Miyao, Hirohiko Hirochika, Uta Paszkowski, Hiroshi Kouchi, 557

and Haruko Imaizumi-Anraku. 2008. “Divergence of Evolutionary Ways Among Common 558

Sym Genes: CASTOR and CCaMK Show Functional Conservation Between Two 559

Symbiosis Systems and Constitute the Root of a Common Signaling Pathway..” Plant and 560

Cell Physiology 49 (11): 1659–71. doi:10.1093/pcp/pcn153. 561

Barker, David G, Sylvie Bianchi, François Blondon, Yvette Dattée, Gérard Duc, Sadi Essad, Pascal 562

Flament, Philippe Gallusci, Gérard Génier, and Pierre Guy. 1990. “Medicago Truncatula, a 563

Model Plant for Studying the Molecular Genetics of the Rhizobium-Legume Symbiosis.” 564

Plant Molecular Biology Reporter 8 (1). Springer: 40–49. doi:10.1007/BF02668879. 565

Bartsev, Alexander V, William J Deakin, Nawal M Boukli, Crystal B McAlvin, Gary Stacey, Pia 566

Malnoë, William J Broughton, and Christian Staehelin. 2004. “NopL, an Effector Protein of 567

Rhizobium Sp. NGR234, Thwarts Activation of Plant Defense Reactions..” Plant 568

Physiology 134 (2): 871–79. doi:10.1104/pp.103.031740. 569

Bellato, C, H B Krishnan, T Cubo, F Temprano, and S G Pueppke. 1997. “The Soybean Cultivar 570

Specificity Gene nolX Is Present, Expressed in a nodD-Dependent Manner, and of 571

Symbiotic Significance in Cultivar-Nonspecific Strains of Rhizobium (Sinorhizobium) 572

Fredii..” Microbiology (Reading, England) 143 ( Pt 4) (April): 1381–88. 573

doi:10.1099/00221287-143-4-1381. 574

Bonardi, Vera, Karen Cherkis, Marc T Nishimura, and Jeffery L Dangl. 2012. “A New Eye on NLR 575

Proteins: Focused on Clarity or Diffused by Complexity?.” Current Opinion in Immunology 576

24 (1): 41–50. doi:10.1016/j.coi.2011.12.006. 577

Bonardi, Vera, Saijun Tang, Anna Stallmann, Melinda Roberts, Karen Cherkis, and Jeffery L 578

Dangl. 2011. “Expanded Functions for a Family of Plant Intracellular Immune Receptors 579

Beyond Specific Recognition of Pathogen Effectors..” Proceedings of the National Academy 580

of Sciences of the United States of America 108 (39): 16463–68. 581

doi:10.1073/pnas.1113726108. 582

Bulgarelli, Davide, Klaus Schlaeppi, Stijn Spaepen, Emiel ver Loren van Themaat, and Paul 583

Schulze-Lefert. 2013. “Structure and Functions of the Bacterial Microbiota of Plants..” 584

Annual Review of Plant Biology 64: 807–38. doi:10.1146/annurev-arplant-050312-120106. 585

Caplan, Jeffery L, Tadeusz Wroblewski, Richard W Michelmore, and Blake C Meyers. 2013. “The 586

Role of TIR-NBS and TIR-X Proteins in Plant Basal Defense Responses..” Plant Physiology 587

162 (3): 1459–72. doi:10.1104/pp.113.219162. 588

Chen, H.-M., Chen, L.-T., Patel, K., Li, Y.-H., Baulcombe, D. C., & Wu, S.-H. (2010). 22-589

Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proceedings of the 590

National Academy of Sciences of the United States of America, 107(34), 15269–15274. 591

http://doi.org/10.1073/pnas.1001738107 592

Chen, Wei-Hua, and Martin J Lercher. 2009. “ColorTree: a Batch Customization Tool for 593

Phylogenic Trees..” BMC Research Notes 2 (July): 155. doi:10.1186/1756-0500-2-155. 594

Deguchi, Yuichi, Mari Banba, Yoshikazu Shimoda, Svetlana A Chechetka, Ryota Suzuri, Yasuhiro 595

Okusako, Yasuhiro Ooki, et al. 2007. “Transcriptome Profiling of Lotus Japonicus Roots 596

During Arbuscular Mycorrhiza Development and Comparison with That of Nodulation..” 597



Page 25 of 31

DNA Research : an International Journal for Rapid Publication of Reports on Genes and 598

Genomes 14 (3): 117–33. doi:10.1093/dnares/dsm014. 599

Delaux, Pierre-Marc, Kranthi Varala, Patrick P Edger, Gloria M Coruzzi, J Chris Pires, and Jean-600

Michel Ané. 2014. “Comparative Phylogenomics Uncovers the Impact of Symbiotic 601

Associations on Host Genome Evolution..” PLoS Genetics 10 (7): e1004487. 602

doi:10.1371/journal.pgen.1004487. 603

Dobin, Alexander, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, 604

Philippe Batut, Mark Chaisson, and Thomas R Gingeras. 2013. “STAR: Ultrafast Universal 605

RNA-Seq Aligner..” Bioinformatics (Oxford, England) 29 (1): 15–21. 606

doi:10.1093/bioinformatics/bts635. 607

Doyle, J J. 1998. “Phylogenetic Perspectives on Nodulation: Evolving Views of Plants and 608

Symbiotic Bacteria.” Trends in Plant Science. doi:10.1094/MPMI-05-11-0114. 609

Eddy, Sean R. 2011. “Accelerated Profile HMM Searches..” PLoS Computational Biology 7 (10): 610

e1002195. doi:10.1371/journal.pcbi.1002195. 611

Erb, Matthias, Claudia Lenk, Jörg Degenhardt, and Ted C J Turlings. 2009. “The Underestimated 612

Role of Roots in Defense Against Leaf Attackers.” Trends in Plant Science 14 (12): 653–59. 613

doi:10.1016/j.tplants.2009.08.006. 614

Falk, A, Bart J Feys, L N Frost, Jonathan D G Jones, M J Daniels, and Jane E Parker. 1999. “EDS1, 615

an Essential Component of R Gene-Mediated Disease Resistance in Arabidopsis Has 616

Homology to Eukaryotic Lipases.” Proceedings of the National Academy of Sciences of the 617

United States of America 96 (6): 3292–97. 618

Fatima, Urooj, and Muthappa Senthil-Kumar. 2015. “Plant and Pathogen Nutrient Acquisition 619

Strategies..” Frontiers in Plant Science 6: 750. doi:10.3389/fpls.2015.00750. 620

Fei, Q., Li, P., Teng, C., & Meyers, B. C. (2015). Secondary siRNAs from Medicago NB-LRRs 621

modulated via miRNA-target interactions and their abundances. The Plant Journal : for Cell 622

and Molecular Biology, 83(3), 451–465. http://doi.org/10.1111/tpj.12900 623

Fei, Q., Zhang, Y., Xia, R., & Meyers, B. C. (2016). Small RNAs Add Zing to the Zig-Zag-Zig 624

Model of Plant Defenses. Molecular Plant-Microbe Interactions : MPMI, 29(3), 165–169. 625

http://doi.org/10.1094/MPMI-09-15-0212-FI 626

Fluhr, R. 2001. “Sentinels of Disease. Plant Resistance Genes..” Plant Physiology 127 (4): 1367–627

74. 628

Fu, Limin, Beifang Niu, Zhengwei Zhu, Sitao Wu, and Weizhong Li. 2012. “CD-HIT: Accelerated 629

for Clustering the Next-Generation Sequencing Data..” Bioinformatics (Oxford, England) 28 630

(23): 3150–52. doi:10.1093/bioinformatics/bts565. 631

Gualtieri, G, and T Bisseling. 2000. “The Evolution of Nodulation..” Plant Molecular Biology 42 632

(1): 181–94. 633

Guillotin, Bruno, Jean-Malo Couzigou, and Jean-Philippe Combier. 2016. “NIN Is Involved in the 634

Regulation of Arbuscular Mycorrhizal Symbiosis..” Frontiers in Plant Science 7: 1704. 635

doi:10.3389/fpls.2016.01704. 636

Haas, Brian J, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua 637

Bowden, Matthew Brian Couger, et al. 2013. “De Novo Transcript Sequence Reconstruction 638

From RNA-Seq Using the Trinity Platform for Reference Generation and Analysis..” Nature 639

Protocols 8 (8): 1494–1512. doi:10.1038/nprot.2013.084. 640

Handberg, Kurt, and Jens Stougaard. 1992. “Lotus Japonicus, an Autogamous, Diploid Legume 641

Species for Classical and Molecular Genetics.” The Plant Journal : for Cell and Molecular 642

Biology 2 (4). Wiley Online Library: 487–96. 643

Hofius, Daniel, Dimitrios I Tsitsigiannis, Jonathan D G Jones, and John Mundy. 2007. “Inducible 644

Cell Death in Plant Immunity.” Seminars in Cancer Biology 17 (2): 166–87. 645

doi:10.1016/j.semcancer.2006.12.001. 646



Page 26 of 31

Hofius, Daniel, Torsten Schultz-Larsen, Jan Joensen, Dimitrios I Tsitsigiannis, Nikolaj H T 647

Petersen, Ole Mattsson, Lise Bolt Jørgensen, Jonathan D G Jones, John Mundy, and Morten 648

Petersen. 2009. “Autophagic Components Contribute to Hypersensitive Cell Death in 649

Arabidopsis..” Cell 137 (4): 773–83. doi:10.1016/j.cell.2009.02.036. 650

Howell, M. D., Fahlgren, N., Chapman, E. J., Cumbie, J. S., Sullivan, C. M., Givan, S. A., et al. 651

(2007). Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-652

LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed 653

targeting. The Plant Cell, 19(3), 926–942. http://doi.org/10.1105/tpc.107.050062 654

Huson, Daniel H, and Celine Scornavacca. 2012. “Dendroscope 3: an Interactive Tool for Rooted 655

Phylogenetic Trees and Networks..” Systematic Biology 61 (6): 1061–67. 656

doi:10.1093/sysbio/sys062. 657

Høgslund, Niels, Simona Radutoiu, Lene Krusell, Vera Voroshilova, Matthew A Hannah, Nicolas 658

Goffard, Diego H Sanchez, et al. 2009. “Dissection of Symbiosis and Organ Development 659

by Integrated Transcriptome Analysis of Lotus Japonicus Mutant and Wild-Type Plants..” 660

PloS One 4 (8): e6556. doi:10.1371/journal.pone.0006556. 661

Ibarra-Laclette, Enrique, Eric Lyons, Gustavo Hernandez-Guzman, Claudia Anahí Pérez-Torres, 662

Lorenzo Carretero-Paulet, Tien-Hao Chang, Tianying Lan, et al. 2013. “Architecture and 663

Evolution of a Minute Plant Genome..” Nature 498 (7452): 94–98. 664

doi:10.1038/nature12132. 665

Ingle, Robert A. 2011. “Defence Responses of Arabidopsis Thaliana to Infection by Pseudomonas 666

Syringae Are Regulated by the Circadian Clock..” PloS One 6 (10): e26968. 667

doi:10.1371/journal.pone.0026968. 668

Jacob, Florence, Saskia Vernaldi, and Takaki Maekawa. 2013. “Evolution and Conservation of 669

Plant NLR Functions..” Frontiers in Immunology 4: 297. doi:10.3389/fimmu.2013.00297. 670

Jiménez-Guerrero, Irene, Francisco Pérez-Montaño, José Antonio Monreal, Gail M Preston, Helen 671

Fones, Blanca Vioque, Francisco Javier Ollero, and Francisco Javier López-Baena. 2015. 672

“The Sinorhizobium (Ensifer) Fredii HH103 Type 3 Secretion System Suppresses Early 673

Defense Responses to Effectively Nodulate Soybean..” Molecular Plant-Microbe 674

Interactions : MPMI 28 (7): 790–99. doi:10.1094/MPMI-01-15-0020-R. 675

Jones, D A, and JDG Jones. 1997. “The Role of Leucine-Rich Repeat Proteins in Plant Defences.” 676

Advances in Botanical Research. 677

Jones, Jonathan D G, and Jeffery L Dangl. 2006. “The Plant Immune System.” Nature 444 (7117). 678

Nature Publishing Group: 323–29. doi:doi:10.1038/nature05286. 679

Kalo, Peter, Cynthia Gleason, Anne Edwards, John Marsh, Raka M Mitra, Sibylle Hirsch, Júlia 680

Jakab, et al. 2005. “Nodulation Signaling in Legumes Requires NSP2, a Member of the 681

GRAS Family of Transcriptional Regulators..” Science (New York, NY) 308 (5729): 1786–682

89. doi:10.1126/science.1110951. 683

Kambara, Kumiko, Silvia Ardissone, Hajime Kobayashi, Maged M Saad, Olivier Schumpp, 684

William J Broughton, and William J Deakin. 2009. “Rhizobia Utilize Pathogen-Like 685

Effector Proteins During Symbiosis..” Molecular Microbiology 71 (1): 92–106. 686

doi:10.1111/j.1365-2958.2008.06507.x. 687

Kawaharada, Y, S KELLY, M Wibroe Nielsen, C T Hjuler, K Gysel, A Muszyński, R W Carlson, 688

et al. 2015. “Receptor-Mediated Exopolysaccharide Perception Controls Bacterial 689

Infection..” Nature 523 (7560): 308–12. doi:10.1038/nature14611. 690

Khan, Madiha, Rajagopal Subramaniam, and Darrell Desveaux. 2015. “Of Guards, Decoys, Baits 691

and Traps: Pathogen Perception in Plants by Type III Effector Sensors..” Current Opinion in 692

Microbiology 29 (November): 49–55. doi:10.1016/j.mib.2015.10.006. 693

Kim, Won-Seok, and Hari B Krishnan. 2014. “A nopA Deletion Mutant of Sinorhizobium Fredii 694

USDA257, a Soybean Symbiont, Is Impaired in Nodulation..” Current Microbiology 68 (2): 695

239–46. doi:10.1007/s00284-013-0469-4. 696


http://doi.org/10.1105/tpc.107.050062


Page 27 of 31

Kouchi, Hiroshi, Haruko Imaizumi-Anraku, Makoto Hayashi, Tsuneo Hakoyama, Tomomi 697

Nakagawa, Yosuke Umehara, Norio Suganuma, and Masayoshi Kawaguchi. 2010. “How 698

Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground..” 699

Plant and Cell Physiology 51 (9): 1381–97. doi:10.1093/pcp/pcq107. 700

Kroj, Thomas, Emilie Chanclud, Corinne Michel Romiti, Xavier Grand, and Jean-Benoit Morel. 701

2016. “Integration of Decoy Domains Derived From Protein Targets of Pathogen Effectors 702

Into Plant Immune Receptors Is Widespread..” The New Phytologist, February. 703

doi:10.1111/nph.13869. 704

Kunze, Gernot, Cyril Zipfel, Silke Robatzek, Karsten Niehaus, Thomas Boller, and Georg Felix. 705

2004. “The N Terminus of Bacterial Elongation Factor Tu Elicits Innate Immunity in 706

Arabidopsis Plants..” The Plant Cell 16 (12): 3496–3507. doi:10.1105/tpc.104.026765. 707

Le Fevre, Ruth, Edouard Evangelisti, Thomas Rey, and Sebastian Schornack. 2015. “Modulation of 708

Host Cell Biology by Plant Pathogenic Microbes..” Annual Review of Cell and 709

Developmental Biology, September. doi:10.1146/annurev-cellbio-102314-112502. 710

Lévy, Julien, Cécile Bres, Rene Geurts, Boulos Chalhoub, Olga Kulikova, Gérard Duc, Etienne-711

Pascal Journet, et al. 2004. “A Putative Ca2+ and Calmodulin-Dependent Protein Kinase 712

Required for Bacterial and Fungal Symbioses..” Science (New York, NY) 303 (5662): 1361–713

64. doi:10.1126/science.1093038. 714

Li, F., Pignatta, D., Bendix, C., Brunkard, J. O., Cohn, M. M., Tung, J., et al. (2012). MicroRNA 715

regulation of plant innate immune receptors. Proceedings of the National Academy of 716

Sciences of the United States of America, 109(5), 1790–1795. 717

http://doi.org/10.1073/pnas.1118282109 718

Li, Jun, Daniela M Witten, Iain M Johnstone, and Robert Tibshirani. 2012. “Normalization, 719

Testing, and False Discovery Rate Estimation for RNA-Sequencing Data..” Biostatistics 720

(Oxford, England) 13 (3): 523–38. doi:10.1093/biostatistics/kxr031. 721

Limpens, Erik, Carolien Franken, Patrick Smit, Joost Willemse, Ton Bisseling, and Rene Geurts. 722

2003. “LysM Domain Receptor Kinases Regulating Rhizobial Nod Factor-Induced 723

Infection..” Science (New York, NY) 302 (5645): 630–33. doi:10.1126/science.1090074. 724

Liu, Tzu-Yin, Teng-Kuei Huang, Shu-Yi Yang, Yu-Ting Hong, Sheng-Min Huang, Fu-Nien Wang, 725

Su-Fen Chiang, Shang-Yueh Tsai, Wen-Chien Lu, and Tzyy-Jen Chiou. 2016. 726

“Identification of Plant Vacuolar Transporters Mediating Phosphate Storage..” Nature 727

Communications 7 (March): 11095. doi:10.1038/ncomms11095. 728

Long, S R. 1989. “Rhizobium-Legume Nodulation: Life Together in the Underground..” Cell 56 729

(2): 203–14. 730

Lukasik, Ewa, and Frank L W Takken. 2009. “STANDing Strong, Resistance Proteins Instigators 731

of Plant Defence..” Current Opinion in Plant Biology 12 (4): 427–36. 732

doi:10.1016/j.pbi.2009.03.001. 733

Madsen, Esben Bjørn, Lene Heegaard Madsen, Simona Radutoiu, Magdalena Olbryt, Magdalena 734

Rakwalska, Krzysztof Szczyglowski, Shusei Sato, et al. 2003. “A Receptor Kinase Gene of 735

the LysM Type Is Involved in Legume Perception of Rhizobial Signals..” Nature 425 736

(6958): 637–40. doi:10.1038/nature02045. 737

Madsen, Lene H, Leïla Tirichine, Anna Jurkiewicz, John T Sullivan, Anne B Heckmann, Anita S 738

Bek, Clive W Ronson, Euan K James, and Jens Stougaard. 2010. “The Molecular Network 739

Governing Nodule Organogenesis and Infection in the Model Legume Lotus Japonicus..” 740

Nature Communications 1: 10. doi:10.1038/ncomms1009. 741

Marchler-Bauer, Aron, Shennan Lu, John B Anderson, Farideh Chitsaz, Myra K Derbyshire, Carol 742

DeWeese-Scott, Jessica H Fong, et al. 2011. “CDD: a Conserved Domain Database for the 743

Functional Annotation of Proteins..” Nucleic Acids Research 39 (Database issue): D225–29. 744

doi:10.1093/nar/gkq1189. 745


http://doi.org/10.1073/pnas.1118282109


Page 28 of 31

Marquenet, Emélie, and Evelyne Richet. 2007. “How Integration of Positive and Negative 746

Regulatory Signals by a STAND Signaling Protein Depends on ATP Hydrolysis..” 747

Molecular Cell 28 (2): 187–99. doi:10.1016/j.molcel.2007.08.014. 748

Meinhardt, L W, H B Krishnan, P A Balatti, and S G Pueppke. 1993. “Molecular Cloning and 749

Characterization of a Sym Plasmid Locus That Regulates Cultivar-Specific Nodulation of 750

Soybean by Rhizobium Fredii USDA257..” Molecular Microbiology 9 (1): 17–29. 751

Meyers, B C, A W Dickerman, R W Michelmore, S Sivaramakrishnan, B W Sobral, and N D 752

Young. 1999. “Plant Disease Resistance Genes Encode Members of an Ancient and Diverse 753

Protein Family Within the Nucleotide-Binding Superfamily..” The Plant Journal : for Cell 754

and Molecular Biology 20 (3): 317–32. 755

Meyers, Blake C, Alexander Kozik, Alyssa Griego, Hanhui Kuang, and Richard W Michelmore. 756

2003. “Genome-Wide Analysis of NBS-LRR-Encoding Genes in Arabidopsis..” The Plant 757

Cell 15 (4): 809–34. 758

Meyers, Blake C, Michele Morgante, and Richard W Michelmore. 2002. “TIR-X and TIR-NBS 759

Proteins: Two New Families Related to Disease Resistance TIR-NBS-LRR Proteins 760

Encoded in Arabidopsis and Other Plant Genomes..” The Plant Journal : for Cell and 761

Molecular Biology 32 (1): 77–92. 762

Millet, Yves A, Cristian H Danna, Nicole K Clay, Wisuwat Songnuan, Matthew D Simon, Danièle 763

Werck-Reichhart, and Frederick M Ausubel. 2010. “Innate Immune Responses Activated in 764

Arabidopsis Roots by Microbe-Associated Molecular Patterns..” The Plant Cell 22 (3): 973–765

90. doi:10.1105/tpc.109.069658. 766

Minh, Bui Quang, Minh Anh Thi Nguyen, and Arndt von Haeseler. 2013. “Ultrafast Approximation 767

for Phylogenetic Bootstrap..” Molecular Biology and Evolution 30 (5): 1188–95. 768

doi:10.1093/molbev/mst024. 769

Mun, Terry, Asger Bachmann, Vikas Gupta, Jens Stougaard, and Stig U Andersen. 2016. “Lotus 770

Base: an Integrated Information Portal for the Model Legume Lotus Japonicus..” Scientific 771

Reports 6 (December): 39447. doi:10.1038/srep39447. 772

Muthamilarasan, Mehanathan, and Manoj Prasad. 2013. “Plant Innate Immunity: an Updated 773

Insight Into Defense Mechanism..” Journal of Biosciences 38 (2): 433–49. 774

Nguyen, Lam-Tung, Heiko A Schmidt, Arndt von Haeseler, and Bui Quang Minh. 2015. “IQ-775

TREE: a Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood 776

Phylogenies..” Molecular Biology and Evolution 32 (1): 268–74. 777

doi:10.1093/molbev/msu300. 778

Nishimura, Marc T, and Jeffery L Dangl. 2010. “Arabidopsis and the Plant Immune System..” The 779

Plant Journal : for Cell and Molecular Biology 61 (6): 1053–66. doi:10.1111/j.1365-780

313X.2010.04131.x. 781

Oldroyd, Giles E D. 2013. “Speak, Friend, and Enter: Signalling Systems That Promote Beneficial 782

Symbiotic Associations in Plants..” Nature Reviews Microbiology 11 (4): 252–63. 783

doi:10.1038/nrmicro2990. 784

Oldroyd, Giles E D, and J Allan Downie. 2006. “Nuclear Calcium Changes at the Core of 785

Symbiosis Signalling..” Current Opinion in Plant Biology 9 (4): 351–57. 786

doi:10.1016/j.pbi.2006.05.003. 787

Pan, Q, J Wendel, and R Fluhr. 2000. “Divergent Evolution of Plant NBS-LRR Resistance Gene 788

Homologues in Dicot and Cereal Genomes..” Journal of Molecular Evolution 50 (3): 203–789

13. doi:10.1007/s002399910023. 790

Parniske, M. 2000. “Intracellular Accommodation of Microbes by Plants: a Common 791

Developmental Program for Symbiosis and Disease?.” Current Opinion in Plant Biology 3 792

(4): 320–28. doi:10.1016/S1369-5266(00)00088-1. 793

Parniske, Martin. 2008. “Arbuscular Mycorrhiza: the Mother of Plant Root Endosymbioses..” 794

Nature Reviews Microbiology 6 (10): 763–75. doi:10.1038/nrmicro1987. 795



Page 29 of 31

Pel, Michiel J C, and Corné M J Pieterse. 2012. “Microbial Recognition and Evasion of Host 796

Immunity..” Journal of Experimental Botany, October. doi:10.1093/jxb/ers262. 797

Radutoiu, Simona, Lene H Madsen, Esben B Madsen, Anna Jurkiewicz, Eigo Fukai, Esben M H 798

Quistgaard, Anita S Albrektsen, Euan K James, Søren Thirup, and Jens Stougaard. 2007. 799

“LysM Domains Mediate Lipochitin-Oligosaccharide Recognition and Nfr Genes Extend 800

the Symbiotic Host Range..” The EMBO Journal 26 (17): 3923–35. 801

doi:10.1038/sj.emboj.7601826. 802

Radutoiu, Simona, Lene Heegaard Madsen, Esben Bjørn Madsen, Hubert H Felle, Yosuke 803

Umehara, Mette Grønlund, Shusei Sato, et al. 2003. “Plant Recognition of Symbiotic 804

Bacteria Requires Two LysM Receptor-Like Kinases..” Nature 425 (6958): 585–92. 805

doi:10.1038/nature02039. 806

Ranf, Stefanie, Nicolas Gisch, Milena Schäffer, Tina Illig, Lore Westphal, Yuriy A Knirel, Patricia 807

M Sánchez-Carballo, et al. 2015. “A Lectin S-Domain Receptor Kinase Mediates 808

Lipopolysaccharide Sensing in Arabidopsis Thaliana..” Nature Immunology, March. 809

doi:10.1038/ni.3124. 810

Ritchie, Matthew E, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, and Gordon K 811

Smyth. 2015. “Limma Powers Differential Expression Analyses for RNA-Sequencing and 812

Microarray Studies..” Nucleic Acids Research 43 (7): e47. doi:10.1093/nar/gkv007. 813

Robinson, Mark D, Davis J McCarthy, and Gordon K Smyth. 2010. “edgeR: a Bioconductor 814

Package for Differential Expression Analysis of Digital Gene Expression Data..” 815

Bioinformatics (Oxford, England) 26 (1): 139–40. doi:10.1093/bioinformatics/btp616. 816

Saraste, M, P R Sibbald, and A Wittinghofer. 1990. “The P-Loop--a Common Motif in ATP- and 817

GTP-Binding Proteins..” Trends in Biochemical Sciences 15 (11): 430–34. 818

Schauser, L, A Roussis, J Stiller, and J Stougaard. 1999. “A Plant Regulator Controlling 819

Development of Symbiotic Root Nodules..” Nature 402 (6758): 191–95. doi:10.1038/46058. 820

Schmid, Markus, Timothy S Davison, Stefan R Henz, Utz J Pape, Monika Demar, Martin Vingron, 821

Bernhard Schölkopf, Detlef Weigel, and Jan U Lohmann. 2005. “A Gene Expression Map 822

of Arabidopsis Thaliana Development..” Nature Genetics 37 (5): 501–6. 823

doi:10.1038/ng1543. 824

Shao, Zhu-Qing, Jia-Yu Xue, Ping Wu, Yan-Mei Zhang, Yue Wu, Yue-Yu Hang, Bin Wang, and 825

Jian-Qun Chen. 2016. “Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-826

Leucine-Rich Repeat (NBS-LRR) Genes Reveal Three Anciently Diverged Classes with 827

Distinct Evolutionary Patterns..” Plant Physiology, February. doi:10.1104/pp.15.01487. 828

Shivaprasad, P. V., Chen, H.-M., Patel, K., Bond, D. M., Santos, B. A. C. M., & Baulcombe, D. C. 829

(2012). A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and 830

other mRNAs. The Plant Cell, 24(3), 859–874. http://doi.org/10.1105/tpc.111.095380 831

Sievers, Fabian, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, 832

Rodrigo Lopez, et al. 2011. “Fast, Scalable Generation of High-Quality Protein Multiple 833

Sequence Alignments Using Clustal Omega..” Molecular Systems Biology 7 (October): 539. 834

doi:10.1038/msb.2011.75. 835

Singh, Sylvia, and Martin Parniske. 2012. “Activation of Calcium- and Calmodulin-Dependent 836

Protein Kinase (CCaMK), the Central Regulator of Plant Root Endosymbiosis..” Current 837

Opinion in Plant Biology 15 (4): 444–53. doi:10.1016/j.pbi.2012.04.002. 838

Skorpil, Peter, Maged M Saad, Nawal M Boukli, Hajime Kobayashi, Florencia Ares-Orpel, William 839

J Broughton, and William J Deakin. 2005. “NopP, a Phosphorylated Effector of Rhizobium 840

Sp. Strain NGR234, Is a Major Determinant of Nodulation of the Tropical Legumes 841

Flemingia Congesta and Tephrosia Vogelii..” Molecular Microbiology 57 (5): 1304–17. 842

doi:10.1111/j.1365-2958.2005.04768.x. 843



Page 30 of 31

Smit, Patrick, John Raedts, Vladimir Portyanko, Frédéric Debellé, Clare Gough, Ton Bisseling, and 844

Rene Geurts. 2005. “NSP1 of the GRAS Protein Family Is Essential for Rhizobial Nod 845

Factor-Induced Transcription..” Science (New York, NY) 308 (5729): 1789–91. 846

doi:10.1126/science.1111025. 847

Smith, Sally E, and David J Read. 2010. Mycorrhizal Symbiosis. Academic Press. 848

Takken, Frank L W, and Aska Goverse. 2012. “How to Build a Pathogen Detector: Structural Basis 849

of NB-LRR Function..” Current Opinion in Plant Biology 15 (4): 375–84. 850

doi:10.1016/j.pbi.2012.05.001. 851

Takken, Frank Lw, Mario Albrecht, and Wladimir Il Tameling. 2006. “Resistance Proteins: 852

Molecular Switches of Plant Defence..” Current Opinion in Plant Biology 9 (4): 383–90. 853

doi:10.1016/j.pbi.2006.05.009. 854

Tang, Fang, Shengming Yang, Jinge Liu, and Hongyan Zhu. 2016. “Rj4, a Gene Controlling 855

Nodulation Specificity in Soybeans, Encodes a Thaumatin-Like Protein but Not the One 856

Previously Reported..” Plant Physiology 170 (1): 26–32. doi:10.1104/pp.15.01661. 857

Tanigaki, Yusuke, Kenji Ito, Yoshiyuki Obuchi, Akiko Kosaka, Katsuyuki T Yamato, Masahiro 858

Okanami, Mikko T Lehtonen, Jari P T Valkonen, and Motomu Akita. 2014. “Physcomitrella 859

Patens Has Kinase-LRR R Gene Homologs and Interacting Proteins..” PloS One 9 (4): 860

e95118. doi:10.1371/journal.pone.0095118. 861

Tarr, D Ellen K, and Helen M Alexander. 2009. “TIR-NBS-LRR Genes Are Rare in Monocots: 862

Evidence From Diverse Monocot Orders..” BMC Research Notes 2: 197. doi:10.1186/1756-863

0500-2-197. 864

Thordal-Christensen, Hans. 2003. “Fresh Insights Into Processes of Nonhost Resistance.” Current 865

Opinion in Plant Biology 6 (4): 351–57. 866

Tirichine, Leïla, Haruko Imaizumi-Anraku, Satoko Yoshida, Yasuhiro Murakami, Lene H Madsen, 867

Hiroki Miwa, Tomomi Nakagawa, et al. 2006. “Deregulation of a Ca2+/Calmodulin-868

Dependent Kinase Leads to Spontaneous Nodule Development..” Nature 441 (7097): 1153–869

56. doi:10.1038/nature04862. 870

Tsukui, Takahiro, Shima Eda, Takakazu Kaneko, Shusei Sato, Shin Okazaki, Kaori Kakizaki-871

Chiba, Manabu Itakura, et al. 2013. “The Type III Secretion System of Bradyrhizobium 872

Japonicum USDA122 Mediates Symbiotic Incompatibility with Rj2 Soybean Plants..” 873

Applied and Environmental Microbiology 79 (3): 1048–51. doi:10.1128/AEM.03297-12. 874

Tsurumaru, H, T Yamakawa, and M Tanaka. 2008. “Tn 5 Mutants of Bradyrhizobium Japonicum 875

Is-1 with Altered Compatibility with Rj 2-Soybean Cultivars.” Soil Science & Plant …. 876

doi:10.1111/j.1747-0765.2007.00225.x. 877

Van Dam, N M, TOG Tytgat, and J A Kirkegaard. 2009. “Root and Shoot Glucosinolates: a 878

Comparison of Their Diversity, Function and Interactions in Natural and Managed 879

Ecosystems.” Phytochemistry Reviews. doi:10.1007/s11101-008-9101-9. 880

van der Biezen, E A, and J D Jones. 1998. “The NB-ARC Domain: a Novel Signalling Motif 881

Shared by Plant Resistance Gene Products and Regulators of Cell Death in Animals..” 882

Current Biology : CB 8 (7): R226–27. 883

van Veen, Hans, Divya Vashisht, Melis Akman, Thomas Girke, Angelika Mustroph, Emilie Reinen, 884

Sjon Hartman, et al. 2016. “Transcriptomes of Eight Arabidopsis Thaliana Accessions 885

Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress..” 886

Plant Physiology 172 (2): 668–89. doi:10.1104/pp.16.00472. 887

Vandenkoornhuyse, Philippe, Achim Quaiser, Marie Duhamel, Amandine Le Van, and Alexis 888

Dufresne. 2015. “The Importance of the Microbiome of the Plant Holobiont..” The New 889

Phytologist 206 (4): 1196–1206. doi:10.1111/nph.13312. 890

Verdier, Jérôme, Ivone Torres-Jerez, Mingyi Wang, Andry Andriankaja, Stacy N Allen, Ji He, 891

Yuhong Tang, Jeremy D Murray, and Michael K Udvardi. 2013. “Establishment of the 892

Lotus Japonicus Gene Expression Atlas (LjGEA) and Its Use to Explore Legume Seed 893



Page 31 of 31

Maturation..” The Plant Journal : for Cell and Molecular Biology 74 (2): 351–62. 894

doi:10.1111/tpj.12119. 895

Viprey, V, A Del Greco, W Golinowski, W J Broughton, and X Perret. 1998. “Symbiotic 896

Implications of Type III Protein Secretion Machinery in Rhizobium..” Molecular 897

Microbiology 28 (6): 1381–89. 898

Wang, Wei, Jinyoung Yang Barnaby, Yasuomi Tada, Hairi Li, Mahmut Tör, Daniela Caldelari, 899

Dae-un Lee, Xiang-Dong Fu, and Xinnian Dong. 2011. “Timing of Plant Immune 900

Responses by a Central Circadian Regulator..” Nature 470 (7332): 110–14. 901

doi:10.1038/nature09766. 902

Xiao, S, S Ellwood, O Calis, E Patrick, T Li, M Coleman, and J G Turner. 2001. “Broad-Spectrum 903

Mildew Resistance in Arabidopsis Thaliana Mediated by RPW8..” Science (New York, NY) 904

291 (5501): 118–20. doi:10.1126/science.291.5501.118. 905

Xin, Da-Wei, Sha Liao, Zhi-Ping Xie, Dagmar R Hann, Lea Steinle, Thomas Boller, and Christian 906

Staehelin. 2012. “Functional Analysis of NopM, a Novel E3 Ubiquitin Ligase (NEL) 907

Domain Effector of Rhizobium Sp. Strain NGR234..” PLoS Pathogens 8 (5): e1002707. 908

doi:10.1371/journal.ppat.1002707. 909

Xin, Xiu-Fang, and Sheng Yang He. 2013. “Pseudomonas Syringae Pv. Tomato DC3000: a Model 910

Pathogen for Probing Disease Susceptibility and Hormone Signaling in Plants..” Annual 911

Review of Phytopathology 51: 473–98. doi:10.1146/annurev-phyto-082712-102321. 912

Xue, Jia-Yu, Yue Wang, Ping Wu, Qiang Wang, Le-Tian Yang, Xiao-Han Pan, Bin Wang, and 913

Jian-Qun Chen. 2012. “A Primary Survey on Bryophyte Species Reveals Two Novel 914

Classes of Nucleotide-Binding Site (NBS) Genes..” PloS One 7 (5): e36700. 915

doi:10.1371/journal.pone.0036700. 916

Yue, Jia-Xing, Blake C Meyers, Jian-Qun Chen, Dacheng Tian, and Sihai Yang. 2012. “Tracing the 917

Origin and Evolutionary History of Plant Nucleotide-Binding Site-Leucine-Rich Repeat 918

(NBS-LRR) Genes..” The New Phytologist 193 (4): 1049–63. doi:10.1111/j.1469-919

8137.2011.04006.x. 920

Zgadzaj, Rafal, Ruben Garrido-Oter, Dorthe Bodker Jensen, Anna Koprivova, Paul Schulze-Lefert, 921

and Simona Radutoiu. 2016. “Root Nodule Symbiosis in Lotus Japonicus Drives the 922

Establishment of Distinctive Rhizosphere, Root, and Nodule Bacterial Communities..” 923

Proceedings of the National Academy of Sciences of the United States of America 113 (49): 924

E7996–E8005. doi:10.1073/pnas.1616564113 925

Zhai, J., Jeong, D.-H., De Paoli, E., Park, S., Rosen, B. D., Li, Y., et al. (2011). MicroRNAs as 926

master regulators of the plant NB-LRR defense gene family via the production of phased, 927

trans-acting siRNAs. Genes & Development, 25(23), 2540–2553. 928

http://doi.org/10.1101/gad.177527.111 929

Zhang, Ling, Xue-Jiao Chen, Huang-Bin Lu, Zhi-Ping Xie, and Christian Staehelin. 2011. 930

“Functional Analysis of the Type 3 Effector Nodulation Outer Protein L (NopL) From 931

Rhizobium Sp. NGR234: Symbiotic Effects, Phosphorylation, and Interference with 932

Mitogen-Activated Protein Kinase Signaling..” Journal of Biological Chemistry 286 (37): 933

32178–87. doi:10.1074/jbc.M111.265942. 934

Zhang, Y., Xia, R., Kuang, H., & Meyers, B. C. (2016). The Diversification of Plant NBS-LRR 935

Defense Genes Directs the Evolution of MicroRNAs That Target Them. Molecular Biology 936

and Evolution, 33(10), 2692–2705. http://doi.org/10.1093/molbev/msw154 937

938

939

940


http://doi.org/10.1093/molbev/msw154


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Alismatales

Brassica napus

Arabidopsis lyrataCapsella rubellaEutrema salsugineumTarenaya hassleriana

Clade 1 Clade 2 Clade 3 Clade 4 Clade 5 TotalZea mays 0.00% 37.68% 4.35% 55.07% 2.90% 69Oryza sativa 0.00% 42.55% 5.28% 51.86% 0.31% 322Spirodela polyrhiza 0.00% 34.92% 36.51% 28.57% 0.00% 63Utricularia gibba 0.00% 23.53% 0.00% 76.47% 0.00% 17Dianthus caryophyllus 1.85% 57.41% 18.52% 22.22% 0.00% 54Beta vulgaris 2.04% 44.90% 38.78% 14.29% 0.00% 49Nelumbo nucifera 3.13% 53.13% 12.50% 31.25% 0.00% 64Tarenaya hassleriana 40.82% 6.12% 46.94% 6.12% 0.00% 49Eutrema salsugineum 37.50% 12.50% 29.17% 20.83% 0.00% 24Capsella rubella 34.04% 4.26% 42.55% 12.77% 6.38% 47Arabidopsis lyrata 54.41% 4.41% 29.41% 8.82% 2.94% 68Arabidopsis thaliana 66.01% 1.96% 15.69% 12.42% 3.92% 153Brassica rapa 66.85% 1.66% 17.68% 8.84% 4.97% 181Brassica napus 69.01% 8.45% 12.68% 1.41% 8.45% 71Glycine max 43.13% 22.80% 9.89% 18.41% 5.77% 364Medicago truncatula 43.98% 35.79% 9.53% 8.03% 2.68% 598Lotus japonicus 54.39% 14.04% 19.88% 9.36% 2.34% 171Lupinus albus 25.00% 13.10% 28.57% 5.95% 27.38% 84Total 891 631 366 467 93 2448TNL 782 1 26 11 0 744CNL 0 392 0 388 0 633RNL 0 1 0 0 68 63XNL 109 237 340 68 25 567Total 891 631 366 467 93 2448

Figure 3



Parsed CitationsAarts, N, M Metz, E Holub, Brian J Staskawicz, M J Daniels, and Jane E Parker. 1998. “Different Requirements for EDS1 and NDR1 byDisease Resistance Genes Define at Least Two R Gene-Mediated Signaling Pathways in Arabidopsis.” Proceedings of the NationalAcademy of Sciences of the United States of America 95 (17): 10306–11.

Arikit, S., Xia, R., Kakrana, A., Huang, K., Zhai, J., Yan, Z., et al. (2014). An atlas of soybean small RNAs identifies phased siRNAs fromhundreds of coding genes. The Plant Cell, 26(12), 4584–4601. http://doi.org/10.1105/tpc.114.131847

Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Axtell, M. J. (2013). Classification and comparison of small RNAs from plants. Annual Review of Plant Biology, 64, 137–159.http://doi.org/10.1146/annurev-arplant-050312-120043


Banba, Mari, Caroline Gutjahr, Akio Miyao, Hirohiko Hirochika, Uta Paszkowski, Hiroshi Kouchi, and Haruko Imaizumi-Anraku. 2008.“Divergence of Evolutionary Ways Among Common Sym Genes: CASTOR and CCaMK Show Functional Conservation Between TwoSymbiosis Systems and Constitute the Root of a Common Signaling Pathway..” Plant and Cell Physiology 49 (11): 1659–71.doi:10.1093/pcp/pcn153.


Barker, David G, Sylvie Bianchi, François Blondon, Yvette Dattée, Gérard Duc, Sadi Essad, Pascal Flament, Philippe Gallusci, GérardGénier, and Pierre Guy. 1990. “Medicago Truncatula, a Model Plant for Studying the Molecular Genetics of the Rhizobium-LegumeSymbiosis.” Plant Molecular Biology Reporter 8 (1). Springer: 40–49. doi:10.1007/BF02668879.


Bartsev, Alexander V, William J Deakin, Nawal M Boukli, Crystal B McAlvin, Gary Stacey, Pia Malnoë, William J Broughton, and ChristianStaehelin. 2004. “NopL, an Effector Protein of Rhizobium Sp. NGR234, Thwarts Activation of Plant Defense Reactions..” PlantPhysiology 134 (2): 871–79. doi:10.1104/pp.103.031740.


Bellato, C, H B Krishnan, T Cubo, F Temprano, and S G Pueppke. 1997. “The Soybean Cultivar Specificity Gene nolX Is Present,Expressed in a nodD-Dependent Manner, and of Symbiotic Significance in Cultivar-Nonspecific Strains of Rhizobium (Sinorhizobium)Fredii..” Microbiology (Reading, England) 143 ( Pt 4) (April): 1381–88. doi:10.1099/00221287-143-4-1381.


Bonardi, Vera, Karen Cherkis, Marc T Nishimura, and Jeffery L Dangl. 2012. “A New Eye on NLR Proteins: Focused on Clarity orDiffused by Complexity?.” Current Opinion in Immunology 24 (1): 41–50. doi:10.1016/j.coi.2011.12.006.


Bonardi, Vera, Saijun Tang, Anna Stallmann, Melinda Roberts, Karen Cherkis, and Jeffery L Dangl. 2011. “Expanded Functions for aFamily of Plant Intracellular Immune Receptors Beyond Specific Recognition of Pathogen Effectors..” Proceedings of the NationalAcademy of Sciences of the United States of America 108 (39): 16463–68. doi:10.1073/pnas.1113726108.


Bulgarelli, Davide, Klaus Schlaeppi, Stijn Spaepen, Emiel ver Loren van Themaat, and Paul Schulze-Lefert. 2013. “Structure andFunctions of the Bacterial Microbiota of Plants..” Annual Review of Plant Biology 64: 807–38. doi:10.1146/annurev-arplant-050312-120106.


Caplan, Jeffery L, Tadeusz Wroblewski, Richard W Michelmore, and Blake C Meyers. 2013. “The Role of TIR-NBS and TIR-X Proteinsin Plant Basal Defense Responses..” Plant Physiology 162 (3): 1459–72. doi:10.1104/pp.113.219162.


Chen, H.-M., Chen, L.-T., Patel, K., Li, Y.-H., Baulcombe, D. C., & Wu, S.-H. (2010). 22-Nucleotide RNAs trigger secondary siRNA www.plantphysiol.orgon October 14, 2020 - Published by Downloaded from Copyright © 2017 American Society of Plant Biologists. All rights reserved.

http://www.ncbi.nlm.nih.gov/pubmed?term=Arikit%2C S%2E%2C Xia%2C R%2E%2C Kakrana%2C A%2E%2C Huang%2C K%2E%2C Zhai%2C J%2E%2C Yan%2C Z%2E%2C et al%2E %282014%29%2E An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes%2E The Plant Cell%2C 26%2812%29%2C 4584�??4601%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1105%2Ftpc%2E114%2E131847&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Arikit, S., Xia, R., Kakrana, A., Huang, K., Zhai, J., Yan, Z., et al. (2014). An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes. The Plant Cell, 26(12), 4584?4601. http://doi.org/10.1105/tpc.114.131847

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Arikit,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Arikit,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Axtell%2C M%2E J%2E %282013%29%2E Classification and comparison of small RNAs from plants%2E Annual Review of Plant Biology%2C 64%2C 137�??159%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1146%2Fannurev%2Darplant%2D050312%2D120043&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Axtell, M. J. (2013). Classification and comparison of small RNAs from plants. Annual Review of Plant Biology, 64, 137?159. http://doi.org/10.1146/annurev-arplant-050312-120043

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Axtell,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Classification and comparison of small RNAs from plants&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Classification and comparison of small RNAs from plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Axtell,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Banba%2C Mari%2C Caroline Gutjahr%2C Akio Miyao%2C Hirohiko Hirochika%2C Uta Paszkowski%2C Hiroshi Kouchi%2C and Haruko Imaizumi%2DAnraku%2E 2008%2E �??Divergence of Evolutionary Ways Among Common Sym Genes%3A CASTOR and CCaMK Show Functional Conservation Between Two Symbiosis Systems and Constitute the Root of a Common Signaling Pathway%2E%2E�?� Plant and Cell Physiology 49 %2811%29%3A 1659�??71%2E doi%3A10%2E1093%2Fpcp%2Fpcn153%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Banba, Mari, Caroline Gutjahr, Akio Miyao, Hirohiko Hirochika, Uta Paszkowski, Hiroshi Kouchi, and Haruko Imaizumi-Anraku. 2008. ?Divergence of Evolutionary Ways Among Common Sym Genes: CASTOR and CCaMK Show Functional Conservation Between Two Symbiosis Systems and Constitute the Root of a Common Signaling Pathway..? Plant and Cell Physiology 49 (11): 1659?71. doi:10.1093/pcp/pcn153.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Banba,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Divergence of Evolutionary Ways Among Common Sym Genes: CASTOR and CCaMK Show Functional Conservation Between Two Symbiosis Systems and Constitute the Root of a Common Signaling Pathway..â�?� Plant and Cell Physiology 49 (11): 1659â�?�?71.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Divergence of Evolutionary Ways Among Common Sym Genes: CASTOR and CCaMK Show Functional Conservation Between Two Symbiosis Systems and Constitute the Root of a Common Signaling Pathway..â�?� Plant and Cell Physiology 49 (11): 1659â�?�?71.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Banba,&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Barker%2C David G%2C Sylvie Bianchi%2C François Blondon%2C Yvette Dattée%2C Gérard Duc%2C Sadi Essad%2C Pascal Flament%2C Philippe Gallusci%2C Gérard Génier%2C and Pierre Guy%2E 1990%2E �??Medicago Truncatula%2C a Model Plant for Studying the Molecular Genetics of the Rhizobium%2DLegume Symbiosis%2E�?� Plant Molecular Biology Reporter 8 %281%29%2E Springer%3A 40�??49%2E doi%3A10%2E1007%2FBF02668879%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Barker, David G, Sylvie Bianchi, Fran�ois Blondon, Yvette Datt�e, G�rard Duc, Sadi Essad, Pascal Flament, Philippe Gallusci, G�rard G�nier, and Pierre Guy. 1990. ?Medicago Truncatula, a Model Plant for Studying the Molecular Genetics of the Rhizobium-Legume Symbiosis.? Plant Molecular Biology Reporter 8 (1). Springer: 40?49. doi:10.1007/BF02668879.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Barker,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Medicago Truncatula, a Model Plant for Studying the Molecular Genetics of the Rhizobium-Legume Symbiosis.â�?� Plant Molecular Biology Reporter 8 (1).&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Medicago Truncatula, a Model Plant for Studying the Molecular Genetics of the Rhizobium-Legume Symbiosis.â�?� Plant Molecular Biology Reporter 8 (1).&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Barker,&as_ylo=1990&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bartsev%2C Alexander V%2C William J Deakin%2C Nawal M Boukli%2C Crystal B McAlvin%2C Gary Stacey%2C Pia Malnoë%2C William J Broughton%2C and Christian Staehelin%2E 2004%2E �??NopL%2C an Effector Protein of Rhizobium Sp%2E NGR234%2C Thwarts Activation of Plant Defense Reactions%2E%2E�?� Plant Physiology 134 %282%29%3A 871�??79%2E doi%3A10%2E1104%2Fpp%2E103%2E031740%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bartsev, Alexander V, William J Deakin, Nawal M Boukli, Crystal B McAlvin, Gary Stacey, Pia Malno�, William J Broughton, and Christian Staehelin. 2004. ?NopL, an Effector Protein of Rhizobium Sp. NGR234, Thwarts Activation of Plant Defense Reactions..? Plant Physiology 134 (2): 871?79. doi:10.1104/pp.103.031740.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bartsev,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?NopL, an Effector Protein of Rhizobium Sp&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?NopL, an Effector Protein of Rhizobium Sp&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bartsev,&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bellato%2C C%2C H B Krishnan%2C T Cubo%2C F Temprano%2C and S G Pueppke%2E 1997%2E �??The Soybean Cultivar Specificity Gene nolX Is Present%2C Expressed in a nodD%2DDependent Manner%2C and of Symbiotic Significance in Cultivar%2DNonspecific Strains of Rhizobium %28Sinorhizobium%29 Fredii%2E%2E�?� Microbiology %28Reading%2C England%29 143 %28 Pt 4%29 %28April%29%3A 1381�??88%2E doi%3A10%2E1099%2F00221287%2D143%2D4%2D1381%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bellato, C, H B Krishnan, T Cubo, F Temprano, and S G Pueppke. 1997. ?The Soybean Cultivar Specificity Gene nolX Is Present, Expressed in a nodD-Dependent Manner, and of Symbiotic Significance in Cultivar-Nonspecific Strains of Rhizobium (Sinorhizobium) Fredii..? Microbiology (Reading, England) 143 ( Pt 4) (April): 1381?88. doi:10.1099/00221287-143-4-1381.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bellato,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bellato,&as_ylo=1997&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bonardi%2C Vera%2C Karen Cherkis%2C Marc T Nishimura%2C and Jeffery L Dangl%2E 2012%2E �??A New Eye on NLR Proteins%3A Focused on Clarity or Diffused by Complexity%3F%2E�?� Current Opinion in Immunology 24 %281%29%3A 41�??50%2E doi%3A10%2E1016%2Fj%2Ecoi%2E2011%2E12%2E006%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bonardi, Vera, Karen Cherkis, Marc T Nishimura, and Jeffery L Dangl. 2012. ?A New Eye on NLR Proteins: Focused on Clarity or Diffused by Complexity?.? Current Opinion in Immunology 24 (1): 41?50. doi:10.1016/j.coi.2011.12.006.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bonardi,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?A New Eye on NLR Proteins: Focused on Clarity or Diffused by Complexity?.â�?� Current Opinion in Immunology 24 (1): 41â�?�?50.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?A New Eye on NLR Proteins: Focused on Clarity or Diffused by Complexity?.â�?� Current Opinion in Immunology 24 (1): 41â�?�?50.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bonardi,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bonardi%2C Vera%2C Saijun Tang%2C Anna Stallmann%2C Melinda Roberts%2C Karen Cherkis%2C and Jeffery L Dangl%2E 2011%2E �??Expanded Functions for a Family of Plant Intracellular Immune Receptors Beyond Specific Recognition of Pathogen Effectors%2E%2E�?� Proceedings of the National Academy of Sciences of the United States of America 108 %2839%29%3A 16463�??68%2E doi%3A10%2E1073%2Fpnas%2E1113726108%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bonardi, Vera, Saijun Tang, Anna Stallmann, Melinda Roberts, Karen Cherkis, and Jeffery L Dangl. 2011. ?Expanded Functions for a Family of Plant Intracellular Immune Receptors Beyond Specific Recognition of Pathogen Effectors..? Proceedings of the National Academy of Sciences of the United States of America 108 (39): 16463?68. doi:10.1073/pnas.1113726108.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bonardi,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Expanded Functions for a Family of Plant Intracellular Immune Receptors Beyond Specific Recognition of Pathogen Effectors..â�?� Proceedings of the National Academy of Sciences of the United States of America 108 (39): 16463â�?�?68.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Expanded Functions for a Family of Plant Intracellular Immune Receptors Beyond Specific Recognition of Pathogen Effectors..â�?� Proceedings of the National Academy of Sciences of the United States of America 108 (39): 16463â�?�?68.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bonardi,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bulgarelli%2C Davide%2C Klaus Schlaeppi%2C Stijn Spaepen%2C Emiel ver Loren van Themaat%2C and Paul Schulze%2DLefert%2E 2013%2E �??Structure and Functions of the Bacterial Microbiota of Plants%2E%2E�?� Annual Review of Plant Biology 64%3A 807�??38%2E doi%3A10%2E1146%2Fannurev%2Darplant%2D050312%2D120106%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bulgarelli, Davide, Klaus Schlaeppi, Stijn Spaepen, Emiel ver Loren van Themaat, and Paul Schulze-Lefert. 2013. ?Structure and Functions of the Bacterial Microbiota of Plants..? Annual Review of Plant Biology 64: 807?38. doi:10.1146/annurev-arplant-050312-120106.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bulgarelli,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Structure and Functions of the Bacterial Microbiota of Plants&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Structure and Functions of the Bacterial Microbiota of Plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bulgarelli,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Caplan%2C Jeffery L%2C Tadeusz Wroblewski%2C Richard W Michelmore%2C and Blake C Meyers%2E 2013%2E �??The Role of TIR%2DNBS and TIR%2DX Proteins in Plant Basal Defense Responses%2E%2E�?� Plant Physiology 162 %283%29%3A 1459�??72%2E doi%3A10%2E1104%2Fpp%2E113%2E219162%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Caplan, Jeffery L, Tadeusz Wroblewski, Richard W Michelmore, and Blake C Meyers. 2013. ?The Role of TIR-NBS and TIR-X Proteins in Plant Basal Defense Responses..? Plant Physiology 162 (3): 1459?72. doi:10.1104/pp.113.219162.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Caplan,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The Role of TIR-NBS and TIR-X Proteins in Plant Basal Defense Responses..â�?� Plant Physiology 162 (3): 1459â�?�?72.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The Role of TIR-NBS and TIR-X Proteins in Plant Basal Defense Responses..â�?� Plant Physiology 162 (3): 1459â�?�?72.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Caplan,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1


biogenesis in plants. Proceedings of the National Academy of Sciences of the United States of America, 107(34), 15269–15274.http://doi.org/10.1073/pnas.1001738107


Chen, Wei-Hua, and Martin J Lercher. 2009. “ColorTree: a Batch Customization Tool for Phylogenic Trees..” BMC Research Notes 2(July): 155. doi:10.1186/1756-0500-2-155.


Deguchi, Yuichi, Mari Banba, Yoshikazu Shimoda, Svetlana A Chechetka, Ryota Suzuri, Yasuhiro Okusako, Yasuhiro Ooki, et al. 2007.“Transcriptome Profiling of Lotus Japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with That ofNodulation..” DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes 14 (3): 117–33.doi:10.1093/dnares/dsm014.


Delaux, Pierre-Marc, Kranthi Varala, Patrick P Edger, Gloria M Coruzzi, J Chris Pires, and Jean-Michel Ané. 2014. “ComparativePhylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution..” PLoS Genetics 10 (7): e1004487.doi:10.1371/journal.pgen.1004487.


Dobin, Alexander, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, andThomas R Gingeras. 2013. “STAR: Ultrafast Universal RNA-Seq Aligner..” Bioinformatics (Oxford, England) 29 (1): 15–21.doi:10.1093/bioinformatics/bts635.


Doyle, J J. 1998. “Phylogenetic Perspectives on Nodulation: Evolving Views of Plants and Symbiotic Bacteria.” Trends in PlantScience. doi:10.1094/MPMI-05-11-0114.


Eddy, Sean R. 2011. “Accelerated Profile HMM Searches..” PLoS Computational Biology 7 (10): e1002195.doi:10.1371/journal.pcbi.1002195.


Erb, Matthias, Claudia Lenk, Jörg Degenhardt, and Ted C J Turlings. 2009. “The Underestimated Role of Roots in Defense AgainstLeaf Attackers.” Trends in Plant Science 14 (12): 653–59. doi:10.1016/j.tplants.2009.08.006.


Falk, A, Bart J Feys, L N Frost, Jonathan D G Jones, M J Daniels, and Jane E Parker. 1999. “EDS1, an Essential Component of R Gene-Mediated Disease Resistance in Arabidopsis Has Homology to Eukaryotic Lipases.” Proceedings of the National Academy of Sciencesof the United States of America 96 (6): 3292–97.


Fatima, Urooj, and Muthappa Senthil-Kumar. 2015. “Plant and Pathogen Nutrient Acquisition Strategies..” Frontiers in Plant Science 6:750. doi:10.3389/fpls.2015.00750.


Fei, Q., Li, P., Teng, C., & Meyers, B. C. (2015). Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactionsand their abundances. The Plant Journal : for Cell and Molecular Biology, 83(3), 451–465. http://doi.org/10.1111/tpj.12900


Fei, Q., Zhang, Y., Xia, R., & Meyers, B. C. (2016). Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses. Molecular Plant-Microbe Interactions : MPMI, 29(3), 165–169. http://doi.org/10.1094/MPMI-09-15-0212-FI

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http://www.ncbi.nlm.nih.gov/pubmed?term=Chen%2C H%2E%2DM%2E%2C Chen%2C L%2E%2DT%2E%2C Patel%2C K%2E%2C Li%2C Y%2E%2DH%2E%2C Baulcombe%2C D%2E C%2E%2C %26 Wu%2C S%2E%2DH%2E %282010%29%2E 22%2DNucleotide RNAs trigger secondary siRNA biogenesis in plants%2E Proceedings of the National Academy of Sciences of the United States of America%2C 107%2834%29%2C 15269�??15274%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1073%2Fpnas%2E1001738107&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Chen, H.-M., Chen, L.-T., Patel, K., Li, Y.-H., Baulcombe, D. C., & Wu, S.-H. (2010). 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proceedings of the National Academy of Sciences of the United States of America, 107(34), 15269?15274. http://doi.org/10.1073/pnas.1001738107

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Chen,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Chen,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Chen%2C Wei%2DHua%2C and Martin J Lercher%2E 2009%2E �??ColorTree%3A a Batch Customization Tool for Phylogenic Trees%2E%2E�?� BMC Research Notes 2 %28July%29%3A 155%2E doi%3A10%2E1186%2F1756%2D0500%2D2%2D155%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Chen, Wei-Hua, and Martin J Lercher. 2009. ?ColorTree: a Batch Customization Tool for Phylogenic Trees..? BMC Research Notes 2 (July): 155. doi:10.1186/1756-0500-2-155.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Chen,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Chen,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Deguchi%2C Yuichi%2C Mari Banba%2C Yoshikazu Shimoda%2C Svetlana A Chechetka%2C Ryota Suzuri%2C Yasuhiro Okusako%2C Yasuhiro Ooki%2C et al%2E 2007%2E �??Transcriptome Profiling of Lotus Japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with That of Nodulation%2E%2E�?� DNA Research %3A an International Journal for Rapid Publication of Reports on Genes and Genomes 14 %283%29%3A 117�??33%2E doi%3A10%2E1093%2Fdnares%2Fdsm014%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Deguchi, Yuichi, Mari Banba, Yoshikazu Shimoda, Svetlana A Chechetka, Ryota Suzuri, Yasuhiro Okusako, Yasuhiro Ooki, et al. 2007. ?Transcriptome Profiling of Lotus Japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with That of Nodulation..? DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes 14 (3): 117?33. doi:10.1093/dnares/dsm014.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Deguchi,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Transcriptome Profiling of Lotus Japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with That of Nodulation..â�?� DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes 14 (3): 117â�?�?33.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Transcriptome Profiling of Lotus Japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with That of Nodulation..â�?� DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes 14 (3): 117â�?�?33.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Deguchi,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Delaux%2C Pierre%2DMarc%2C Kranthi Varala%2C Patrick P Edger%2C Gloria M Coruzzi%2C J Chris Pires%2C and Jean%2DMichel Ané%2E 2014%2E �??Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution%2E%2E�?� PLoS Genetics 10 %287%29%3A e1004487%2E doi%3A10%2E1371%2Fjournal%2Epgen%2E1004487%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Delaux, Pierre-Marc, Kranthi Varala, Patrick P Edger, Gloria M Coruzzi, J Chris Pires, and Jean-Michel An�. 2014. ?Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution..? PLoS Genetics 10 (7): e1004487. doi:10.1371/journal.pgen.1004487.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Delaux,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution..â�?� PLoS Genetics 10 (7): e1004487.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution..â�?� PLoS Genetics 10 (7): e1004487.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Delaux,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Dobin%2C Alexander%2C Carrie A Davis%2C Felix Schlesinger%2C Jorg Drenkow%2C Chris Zaleski%2C Sonali Jha%2C Philippe Batut%2C Mark Chaisson%2C and Thomas R Gingeras%2E 2013%2E �??STAR%3A Ultrafast Universal RNA%2DSeq Aligner%2E%2E�?� Bioinformatics %28Oxford%2C England%29 29 %281%29%3A 15�??21%2E doi%3A10%2E1093%2Fbioinformatics%2Fbts635%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Dobin, Alexander, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R Gingeras. 2013. ?STAR: Ultrafast Universal RNA-Seq Aligner..? Bioinformatics (Oxford, England) 29 (1): 15?21. doi:10.1093/bioinformatics/bts635.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Dobin,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?STAR: Ultrafast Universal RNA-Seq Aligner..â�?� Bioinformatics (Oxford, England) 29 (1): 15â�?�?21.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?STAR: Ultrafast Universal RNA-Seq Aligner..â�?� Bioinformatics (Oxford, England) 29 (1): 15â�?�?21.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Dobin,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Doyle%2C J J%2E 1998%2E �??Phylogenetic Perspectives on Nodulation%3A Evolving Views of Plants and Symbiotic Bacteria%2E�?� Trends in Plant Science%2E doi%3A10%2E1094%2FMPMI%2D05%2D11%2D0114%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Doyle, J J. 1998. ?Phylogenetic Perspectives on Nodulation: Evolving Views of Plants and Symbiotic Bacteria.? Trends in Plant Science. doi:10.1094/MPMI-05-11-0114.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Doyle,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Doyle,&as_ylo=1998&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Eddy%2C Sean R%2E 2011%2E �??Accelerated Profile HMM Searches%2E%2E�?� PLoS Computational Biology 7 %2810%29%3A e1002195%2E doi%3A10%2E1371%2Fjournal%2Epcbi%2E1002195%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Eddy, Sean R. 2011. ?Accelerated Profile HMM Searches..? PLoS Computational Biology 7 (10): e1002195. doi:10.1371/journal.pcbi.1002195.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Eddy,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Accelerated Profile HMM Searches..â�?� PLoS Computational Biology 7 (10): e1002195.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Accelerated Profile HMM Searches..â�?� PLoS Computational Biology 7 (10): e1002195.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Eddy,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Erb%2C Matthias%2C Claudia Lenk%2C Jörg Degenhardt%2C and Ted C J Turlings%2E 2009%2E �??The Underestimated Role of Roots in Defense Against Leaf Attackers%2E�?� Trends in Plant Science 14 %2812%29%3A 653�??59%2E doi%3A10%2E1016%2Fj%2Etplants%2E2009%2E08%2E006%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Erb, Matthias, Claudia Lenk, J�rg Degenhardt, and Ted C J Turlings. 2009. ?The Underestimated Role of Roots in Defense Against Leaf Attackers.? Trends in Plant Science 14 (12): 653?59. doi:10.1016/j.tplants.2009.08.006.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Erb,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The Underestimated Role of Roots in Defense Against Leaf Attackers.â�?� Trends in Plant Science 14 (12): 653â�?�?59.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The Underestimated Role of Roots in Defense Against Leaf Attackers.â�?� Trends in Plant Science 14 (12): 653â�?�?59.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Erb,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Falk%2C A%2C Bart J Feys%2C L N Frost%2C Jonathan D G Jones%2C M J Daniels%2C and Jane E Parker%2E 1999%2E �??EDS1%2C an Essential Component of R Gene%2DMediated Disease Resistance in Arabidopsis Has Homology to Eukaryotic Lipases%2E�?� Proceedings of the National Academy of Sciences of the United States of America 96 %286%29%3A 3292�??97%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Falk, A, Bart J Feys, L N Frost, Jonathan D G Jones, M J Daniels, and Jane E Parker. 1999. ?EDS1, an Essential Component of R Gene-Mediated Disease Resistance in Arabidopsis Has Homology to Eukaryotic Lipases.? Proceedings of the National Academy of Sciences of the United States of America 96 (6): 3292?97.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Falk,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Falk,&as_ylo=1999&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Fatima%2C Urooj%2C and Muthappa Senthil%2DKumar%2E 2015%2E �??Plant and Pathogen Nutrient Acquisition Strategies%2E%2E�?� Frontiers in Plant Science 6%3A 750%2E doi%3A10%2E3389%2Ffpls%2E2015%2E00750%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Fatima, Urooj, and Muthappa Senthil-Kumar. 2015. ?Plant and Pathogen Nutrient Acquisition Strategies..? Frontiers in Plant Science 6: 750. doi:10.3389/fpls.2015.00750.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Fatima,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Plant and Pathogen Nutrient Acquisition Strategies&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Plant and Pathogen Nutrient Acquisition Strategies&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Fatima,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Fei%2C Q%2E%2C Li%2C P%2E%2C Teng%2C C%2E%2C %26 Meyers%2C B%2E C%2E %282015%29%2E Secondary siRNAs from Medicago NB%2DLRRs modulated via miRNA%2Dtarget interactions and their abundances%2E The Plant Journal %3A for Cell and Molecular Biology%2C 83%283%29%2C 451�??465%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1111%2Ftpj%2E12900&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Fei, Q., Li, P., Teng, C., & Meyers, B. C. (2015). Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances. The Plant Journal : for Cell and Molecular Biology, 83(3), 451?465. http://doi.org/10.1111/tpj.12900

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Fei,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Fei,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Fei%2C Q%2E%2C Zhang%2C Y%2E%2C Xia%2C R%2E%2C %26 Meyers%2C B%2E C%2E %282016%29%2E Small RNAs Add Zing to the Zig%2DZag%2DZig Model of Plant Defenses%2E Molecular Plant%2DMicrobe Interactions %3A MPMI%2C 29%283%29%2C 165�??169%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1094%2FMPMI%2D09%2D15%2D0212%2DFI&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Fei, Q., Zhang, Y., Xia, R., & Meyers, B. C. (2016). Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses. Molecular Plant-Microbe Interactions : MPMI, 29(3), 165?169. http://doi.org/10.1094/MPMI-09-15-0212-FI


Google Scholar: Author Only Title Only Author and Title

Fluhr, R. 2001. “Sentinels of Disease. Plant Resistance Genes..” Plant Physiology 127 (4): 1367–74.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Fu, Limin, Beifang Niu, Zhengwei Zhu, Sitao Wu, and Weizhong Li. 2012. “CD-HIT: Accelerated for Clustering the Next-GenerationSequencing Data..” Bioinformatics (Oxford, England) 28 (23): 3150–52. doi:10.1093/bioinformatics/bts565.


Gualtieri, G, and T Bisseling. 2000. “The Evolution of Nodulation..” Plant Molecular Biology 42 (1): 181–94.

Guillotin, Bruno, Jean-Malo Couzigou, and Jean-Philippe Combier. 2016. “NIN Is Involved in the Regulation of Arbuscular MycorrhizalSymbiosis..” Frontiers in Plant Science 7: 1704. doi:10.3389/fpls.2016.01704.


Haas, Brian J, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, et al.2013. “De Novo Transcript Sequence Reconstruction From RNA-Seq Using the Trinity Platform for Reference Generation andAnalysis..” Nature Protocols 8 (8): 1494–1512. doi:10.1038/nprot.2013.084.


Handberg, Kurt, and Jens Stougaard. 1992. “Lotus Japonicus, an Autogamous, Diploid Legume Species for Classical and MolecularGenetics.” The Plant Journal : for Cell and Molecular Biology 2 (4). Wiley Online Library: 487–96.


Hofius, Daniel, Dimitrios I Tsitsigiannis, Jonathan D G Jones, and John Mundy. 2007. “Inducible Cell Death in Plant Immunity.”Seminars in Cancer Biology 17 (2): 166–87. doi:10.1016/j.semcancer.2006.12.001.


Hofius, Daniel, Torsten Schultz-Larsen, Jan Joensen, Dimitrios I Tsitsigiannis, Nikolaj H T Petersen, Ole Mattsson, Lise BoltJørgensen, Jonathan D G Jones, John Mundy, and Morten Petersen. 2009. “Autophagic Components Contribute to HypersensitiveCell Death in Arabidopsis..” Cell 137 (4): 773–83. doi:10.1016/j.cell.2009.02.036.


Howell, M. D., Fahlgren, N., Chapman, E. J., Cumbie, J. S., Sullivan, C. M., Givan, S. A., et al. (2007). Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directedtargeting. The Plant Cell, 19(3), 926–942. http://doi.org/10.1105/tpc.107.050062


Huson, Daniel H, and Celine Scornavacca. 2012. “Dendroscope 3: an Interactive Tool for Rooted Phylogenetic Trees and Networks..”Systematic Biology 61 (6): 1061–67. doi:10.1093/sysbio/sys062.


Høgslund, Niels, Simona Radutoiu, Lene Krusell, Vera Voroshilova, Matthew A Hannah, Nicolas Goffard, Diego H Sanchez, et al. 2009.“Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus Japonicus Mutant and Wild-TypePlants..” PloS One 4 (8): e6556. doi:10.1371/journal.pone.0006556.


Ibarra-Laclette, Enrique, Eric Lyons, Gustavo Hernandez-Guzman, Claudia Anahí Pérez-Torres, Lorenzo Carretero-Paulet, Tien-HaoChang, Tianying Lan, et al. 2013. “Architecture and Evolution of a Minute Plant Genome..” Nature 498 (7452): 94–98.doi:10.1038/nature12132.


Ingle, Robert A. 2011. “Defence Responses of Arabidopsis Thaliana to Infection by Pseudomonas Syringae Are Regulated by the www.plantphysiol.orgon October 14, 2020 - Published by Downloaded from


http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Fei,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Fei,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Fluhr%2C R%2E 2001%2E �??Sentinels of Disease%2E Plant Resistance Genes%2E%2E�?� Plant Physiology 127 %284%29%3A 1367�??74%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Fluhr, R. 2001. ?Sentinels of Disease. Plant Resistance Genes..? Plant Physiology 127 (4): 1367?74.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Fluhr,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Sentinels of Disease.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Sentinels of Disease.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Fluhr,&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Fu%2C Limin%2C Beifang Niu%2C Zhengwei Zhu%2C Sitao Wu%2C and Weizhong Li%2E 2012%2E �??CD%2DHIT%3A Accelerated for Clustering the Next%2DGeneration Sequencing Data%2E%2E�?� Bioinformatics %28Oxford%2C England%29 28 %2823%29%3A 3150�??52%2E doi%3A10%2E1093%2Fbioinformatics%2Fbts565%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Fu, Limin, Beifang Niu, Zhengwei Zhu, Sitao Wu, and Weizhong Li. 2012. ?CD-HIT: Accelerated for Clustering the Next-Generation Sequencing Data..? Bioinformatics (Oxford, England) 28 (23): 3150?52. doi:10.1093/bioinformatics/bts565.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Fu,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?CD-HIT: Accelerated for Clustering the Next-Generation Sequencing Data..â�?� Bioinformatics (Oxford, England) 28 (23): 3150â�?�?52.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?CD-HIT: Accelerated for Clustering the Next-Generation Sequencing Data..â�?� Bioinformatics (Oxford, England) 28 (23): 3150â�?�?52.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Fu,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Guillotin%2C Bruno%2C Jean%2DMalo Couzigou%2C and Jean%2DPhilippe Combier%2E 2016%2E �??NIN Is Involved in the Regulation of Arbuscular Mycorrhizal Symbiosis%2E%2E�?� Frontiers in Plant Science 7%3A 1704%2E doi%3A10%2E3389%2Ffpls%2E2016%2E01704%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Guillotin, Bruno, Jean-Malo Couzigou, and Jean-Philippe Combier. 2016. ?NIN Is Involved in the Regulation of Arbuscular Mycorrhizal Symbiosis..? Frontiers in Plant Science 7: 1704. doi:10.3389/fpls.2016.01704.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Guillotin,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?NIN Is Involved in the Regulation of Arbuscular Mycorrhizal Symbiosis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?NIN Is Involved in the Regulation of Arbuscular Mycorrhizal Symbiosis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Guillotin,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Haas%2C Brian J%2C Alexie Papanicolaou%2C Moran Yassour%2C Manfred Grabherr%2C Philip D Blood%2C Joshua Bowden%2C Matthew Brian Couger%2C et al%2E 2013%2E �??De Novo Transcript Sequence Reconstruction From RNA%2DSeq Using the Trinity Platform for Reference Generation and Analysis%2E%2E�?� Nature Protocols 8 %288%29%3A 1494�??1512%2E doi%3A10%2E1038%2Fnprot%2E2013%2E084%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Haas, Brian J, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D Blood, Joshua Bowden, Matthew Brian Couger, et al. 2013. ?De Novo Transcript Sequence Reconstruction From RNA-Seq Using the Trinity Platform for Reference Generation and Analysis..? Nature Protocols 8 (8): 1494?1512. doi:10.1038/nprot.2013.084.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Haas,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?De Novo Transcript Sequence Reconstruction From RNA-Seq Using the Trinity Platform for Reference Generation and Analysis..â�?� Nature Protocols 8 (8): 1494â�?�?1512.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?De Novo Transcript Sequence Reconstruction From RNA-Seq Using the Trinity Platform for Reference Generation and Analysis..â�?� Nature Protocols 8 (8): 1494â�?�?1512.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Haas,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Handberg%2C Kurt%2C and Jens Stougaard%2E 1992%2E �??Lotus Japonicus%2C an Autogamous%2C Diploid Legume Species for Classical and Molecular Genetics%2E�?� The Plant Journal %3A for Cell and Molecular Biology 2 %284%29%2E Wiley Online Library%3A 487�??96%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Handberg, Kurt, and Jens Stougaard. 1992. ?Lotus Japonicus, an Autogamous, Diploid Legume Species for Classical and Molecular Genetics.? The Plant Journal : for Cell and Molecular Biology 2 (4). Wiley Online Library: 487?96.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Handberg,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Lotus Japonicus, an Autogamous, Diploid Legume Species for Classical and Molecular Genetics.â�?� The Plant Journal : for Cell and Molecular Biology 2 (4).&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Lotus Japonicus, an Autogamous, Diploid Legume Species for Classical and Molecular Genetics.â�?� The Plant Journal : for Cell and Molecular Biology 2 (4).&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Handberg,&as_ylo=1992&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Hofius%2C Daniel%2C Dimitrios I Tsitsigiannis%2C Jonathan D G Jones%2C and John Mundy%2E 2007%2E �??Inducible Cell Death in Plant Immunity%2E�?� Seminars in Cancer Biology 17 %282%29%3A 166�??87%2E doi%3A10%2E1016%2Fj%2Esemcancer%2E2006%2E12%2E001%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hofius, Daniel, Dimitrios I Tsitsigiannis, Jonathan D G Jones, and John Mundy. 2007. ?Inducible Cell Death in Plant Immunity.? Seminars in Cancer Biology 17 (2): 166?87. doi:10.1016/j.semcancer.2006.12.001.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hofius,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Inducible Cell Death in Plant Immunity.â�?� Seminars in Cancer Biology 17 (2): 166â�?�?87.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Inducible Cell Death in Plant Immunity.â�?� Seminars in Cancer Biology 17 (2): 166â�?�?87.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hofius,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Hofius%2C Daniel%2C Torsten Schultz%2DLarsen%2C Jan Joensen%2C Dimitrios I Tsitsigiannis%2C Nikolaj H T Petersen%2C Ole Mattsson%2C Lise Bolt Jørgensen%2C Jonathan D G Jones%2C John Mundy%2C and Morten Petersen%2E 2009%2E �??Autophagic Components Contribute to Hypersensitive Cell Death in Arabidopsis%2E%2E�?� Cell 137 %284%29%3A 773�??83%2E doi%3A10%2E1016%2Fj%2Ecell%2E2009%2E02%2E036%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hofius, Daniel, Torsten Schultz-Larsen, Jan Joensen, Dimitrios I Tsitsigiannis, Nikolaj H T Petersen, Ole Mattsson, Lise Bolt J�rgensen, Jonathan D G Jones, John Mundy, and Morten Petersen. 2009. ?Autophagic Components Contribute to Hypersensitive Cell Death in Arabidopsis..? Cell 137 (4): 773?83. doi:10.1016/j.cell.2009.02.036.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hofius,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Autophagic Components Contribute to Hypersensitive Cell Death in Arabidopsis..â�?� Cell 137 (4): 773â�?�?83.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Autophagic Components Contribute to Hypersensitive Cell Death in Arabidopsis..â�?� Cell 137 (4): 773â�?�?83.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hofius,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Howell%2C M%2E D%2E%2C Fahlgren%2C N%2E%2C Chapman%2C E%2E J%2E%2C Cumbie%2C J%2E S%2E%2C Sullivan%2C C%2E M%2E%2C Givan%2C S%2E A%2E%2C et al%2E %282007%29%2E Genome%2Dwide analysis of the RNA%2DDEPENDENT RNA POLYMERASE6%2FDICER%2DLIKE4 pathway in Arabidopsis reveals dependency on miRNA%2D and tasiRNA%2Ddirected targeting%2E The Plant Cell%2C 19%283%29%2C 926�??942%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1105%2Ftpc%2E107%2E050062&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Howell, M. D., Fahlgren, N., Chapman, E. J., Cumbie, J. S., Sullivan, C. M., Givan, S. A., et al. (2007). Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. The Plant Cell, 19(3), 926?942. http://doi.org/10.1105/tpc.107.050062

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Howell,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Howell,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Huson%2C Daniel H%2C and Celine Scornavacca%2E 2012%2E �??Dendroscope 3%3A an Interactive Tool for Rooted Phylogenetic Trees and Networks%2E%2E�?� Systematic Biology 61 %286%29%3A 1061�??67%2E doi%3A10%2E1093%2Fsysbio%2Fsys062%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Huson, Daniel H, and Celine Scornavacca. 2012. ?Dendroscope 3: an Interactive Tool for Rooted Phylogenetic Trees and Networks..? Systematic Biology 61 (6): 1061?67. doi:10.1093/sysbio/sys062.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Huson,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Huson,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Høgslund%2C Niels%2C Simona Radutoiu%2C Lene Krusell%2C Vera Voroshilova%2C Matthew A Hannah%2C Nicolas Goffard%2C Diego H Sanchez%2C et al%2E 2009%2E �??Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus Japonicus Mutant and Wild%2DType Plants%2E%2E�?� PloS One 4 %288%29%3A e6556%2E doi%3A10%2E1371%2Fjournal%2Epone%2E0006556%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=H�gslund, Niels, Simona Radutoiu, Lene Krusell, Vera Voroshilova, Matthew A Hannah, Nicolas Goffard, Diego H Sanchez, et al. 2009. ?Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus Japonicus Mutant and Wild-Type Plants..? PloS One 4 (8): e6556. doi:10.1371/journal.pone.0006556.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=H�?¸gslund,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus Japonicus Mutant and Wild-Type Plants..â�?� PloS One 4 (8): e6556.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus Japonicus Mutant and Wild-Type Plants..â�?� PloS One 4 (8): e6556.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=H�?¸gslund,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Ibarra%2DLaclette%2C Enrique%2C Eric Lyons%2C Gustavo Hernandez%2DGuzman%2C Claudia Anahí Pérez%2DTorres%2C Lorenzo Carretero%2DPaulet%2C Tien%2DHao Chang%2C Tianying Lan%2C et al%2E 2013%2E �??Architecture and Evolution of a Minute Plant Genome%2E%2E�?� Nature 498 %287452%29%3A 94�??98%2E doi%3A10%2E1038%2Fnature12132%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ibarra-Laclette, Enrique, Eric Lyons, Gustavo Hernandez-Guzman, Claudia Anah� P�rez-Torres, Lorenzo Carretero-Paulet, Tien-Hao Chang, Tianying Lan, et al. 2013. ?Architecture and Evolution of a Minute Plant Genome..? Nature 498 (7452): 94?98. doi:10.1038/nature12132.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ibarra-Laclette,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=: 94â�?�?98.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=: 94â�?�?98.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ibarra-Laclette,&as_ylo=7452&as_allsubj=all&hl=en&c2coff=1


Circadian Clock..” PloS One 6 (10): e26968. doi:10.1371/journal.pone.0026968.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Jacob, Florence, Saskia Vernaldi, and Takaki Maekawa. 2013. “Evolution and Conservation of Plant NLR Functions..” Frontiers inImmunology 4: 297. doi:10.3389/fimmu.2013.00297.


Jiménez-Guerrero, Irene, Francisco Pérez-Montaño, José Antonio Monreal, Gail M Preston, Helen Fones, Blanca Vioque, FranciscoJavier Ollero, and Francisco Javier López-Baena. 2015. “The Sinorhizobium (Ensifer) Fredii HH103 Type 3 Secretion SystemSuppresses Early Defense Responses to Effectively Nodulate Soybean..” Molecular Plant-Microbe Interactions : MPMI 28 (7): 790–99.doi:10.1094/MPMI-01-15-0020-R.


Jones, D A, and JDG Jones. 1997. “The Role of Leucine-Rich Repeat Proteins in Plant Defences.” Advances in Botanical Research.

Jones, Jonathan D G, and Jeffery L Dangl. 2006. “The Plant Immune System.” Nature 444 (7117). Nature Publishing Group: 323–29.doi:doi:10.1038/nature05286.


Kalo, Peter, Cynthia Gleason, Anne Edwards, John Marsh, Raka M Mitra, Sibylle Hirsch, Júlia Jakab, et al. 2005. “Nodulation Signalingin Legumes Requires NSP2, a Member of the GRAS Family of Transcriptional Regulators..” Science (New York, NY) 308 (5729): 1786–89. doi:10.1126/science.1110951.


Kambara, Kumiko, Silvia Ardissone, Hajime Kobayashi, Maged M Saad, Olivier Schumpp, William J Broughton, and William J Deakin.2009. “Rhizobia Utilize Pathogen-Like Effector Proteins During Symbiosis..” Molecular Microbiology 71 (1): 92–106. doi:10.1111/j.1365-2958.2008.06507.x.


Kawaharada, Y, S KELLY, M Wibroe Nielsen, C T Hjuler, K Gysel, A Muszyński, R W Carlson, et al. 2015. “Receptor-MediatedExopolysaccharide Perception Controls Bacterial Infection..” Nature 523 (7560): 308–12. doi:10.1038/nature14611.


Khan, Madiha, Rajagopal Subramaniam, and Darrell Desveaux. 2015. “Of Guards, Decoys, Baits and Traps: Pathogen Perception inPlants by Type III Effector Sensors..” Current Opinion in Microbiology 29 (November): 49–55. doi:10.1016/j.mib.2015.10.006.


Kim, Won-Seok, and Hari B Krishnan. 2014. “A nopA Deletion Mutant of Sinorhizobium Fredii USDA257, a Soybean Symbiont, IsImpaired in Nodulation..” Current Microbiology 68 (2): 239–46. doi:10.1007/s00284-013-0469-4.


Kouchi, Hiroshi, Haruko Imaizumi-Anraku, Makoto Hayashi, Tsuneo Hakoyama, Tomomi Nakagawa, Yosuke Umehara, Norio Suganuma,and Masayoshi Kawaguchi. 2010. “How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground..”Plant and Cell Physiology 51 (9): 1381–97. doi:10.1093/pcp/pcq107.


Kroj, Thomas, Emilie Chanclud, Corinne Michel Romiti, Xavier Grand, and Jean-Benoit Morel. 2016. “Integration of Decoy DomainsDerived From Protein Targets of Pathogen Effectors Into Plant Immune Receptors Is Widespread..” The New Phytologist, February.doi:10.1111/nph.13869.


Kunze, Gernot, Cyril Zipfel, Silke Robatzek, Karsten Niehaus, Thomas Boller, and Georg Felix. 2004. “The N Terminus of BacterialElongation Factor Tu Elicits Innate Immunity in Arabidopsis Plants..” The Plant Cell 16 (12): 3496–3507. doi:10.1105/tpc.104.026765. www.plantphysiol.orgon October 14, 2020 - Published by Downloaded from


http://www.ncbi.nlm.nih.gov/pubmed?term=Ingle%2C Robert A%2E 2011%2E �??Defence Responses of Arabidopsis Thaliana to Infection by Pseudomonas Syringae Are Regulated by the Circadian Clock%2E%2E�?� PloS One 6 %2810%29%3A e26968%2E doi%3A10%2E1371%2Fjournal%2Epone%2E0026968%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ingle, Robert A. 2011. ?Defence Responses of Arabidopsis Thaliana to Infection by Pseudomonas Syringae Are Regulated by the Circadian Clock..? PloS One 6 (10): e26968. doi:10.1371/journal.pone.0026968.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ingle,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Defence Responses of Arabidopsis Thaliana to Infection by Pseudomonas Syringae Are Regulated by the Circadian Clock..â�?� PloS One 6 (10): e26968.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Defence Responses of Arabidopsis Thaliana to Infection by Pseudomonas Syringae Are Regulated by the Circadian Clock..â�?� PloS One 6 (10): e26968.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ingle,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Jacob%2C Florence%2C Saskia Vernaldi%2C and Takaki Maekawa%2E 2013%2E �??Evolution and Conservation of Plant NLR Functions%2E%2E�?� Frontiers in Immunology 4%3A 297%2E doi%3A10%2E3389%2Ffimmu%2E2013%2E00297%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jacob, Florence, Saskia Vernaldi, and Takaki Maekawa. 2013. ?Evolution and Conservation of Plant NLR Functions..? Frontiers in Immunology 4: 297. doi:10.3389/fimmu.2013.00297.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jacob,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Evolution and Conservation of Plant NLR Functions&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Evolution and Conservation of Plant NLR Functions&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jacob,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Jiménez%2DGuerrero%2C Irene%2C Francisco Pérez%2DMontaño%2C José Antonio Monreal%2C Gail M Preston%2C Helen Fones%2C Blanca Vioque%2C Francisco Javier Ollero%2C and Francisco Javier López%2DBaena%2E 2015%2E �??The Sinorhizobium %28Ensifer%29 Fredii HH103 Type 3 Secretion System Suppresses Early Defense Responses to Effectively Nodulate Soybean%2E%2E�?� Molecular Plant%2DMicrobe Interactions %3A MPMI 28 %287%29%3A 790�??99%2E doi%3A10%2E1094%2FMPMI%2D01%2D15%2D0020%2DR%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jim�nez-Guerrero, Irene, Francisco P�rez-Monta�o, Jos� Antonio Monreal, Gail M Preston, Helen Fones, Blanca Vioque, Francisco Javier Ollero, and Francisco Javier L�pez-Baena. 2015. ?The Sinorhizobium (Ensifer) Fredii HH103 Type 3 Secretion System Suppresses Early Defense Responses to Effectively Nodulate Soybean..? Molecular Plant-Microbe Interactions : MPMI 28 (7): 790?99. doi:10.1094/MPMI-01-15-0020-R.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jim�?©nez-Guerrero,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jim�?©nez-Guerrero,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Jones%2C Jonathan D G%2C and Jeffery L Dangl%2E 2006%2E �??The Plant Immune System%2E�?� Nature 444 %287117%29%2E Nature Publishing Group%3A 323�??29%2E doi%3Adoi%3A10%2E1038%2Fnature05286%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jones, Jonathan D G, and Jeffery L Dangl. 2006. ?The Plant Immune System.? Nature 444 (7117). Nature Publishing Group: 323?29. doi:doi:10.1038/nature05286.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jones,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Nature Publishing Group: 323â�?�?29.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Nature Publishing Group: 323â�?�?29.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jones,&as_ylo=7117&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kalo%2C Peter%2C Cynthia Gleason%2C Anne Edwards%2C John Marsh%2C Raka M Mitra%2C Sibylle Hirsch%2C Júlia Jakab%2C et al%2E 2005%2E �??Nodulation Signaling in Legumes Requires NSP2%2C a Member of the GRAS Family of Transcriptional Regulators%2E%2E�?� Science %28New York%2C NY%29 308 %285729%29%3A 1786�??89%2E doi%3A10%2E1126%2Fscience%2E1110951%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kalo, Peter, Cynthia Gleason, Anne Edwards, John Marsh, Raka M Mitra, Sibylle Hirsch, J�lia Jakab, et al. 2005. ?Nodulation Signaling in Legumes Requires NSP2, a Member of the GRAS Family of Transcriptional Regulators..? Science (New York, NY) 308 (5729): 1786?89. doi:10.1126/science.1110951.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kalo,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 1786â�?�?89.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kalo,&as_ylo=5729&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kambara%2C Kumiko%2C Silvia Ardissone%2C Hajime Kobayashi%2C Maged M Saad%2C Olivier Schumpp%2C William J Broughton%2C and William J Deakin%2E 2009%2E �??Rhizobia Utilize Pathogen%2DLike Effector Proteins During Symbiosis%2E%2E�?� Molecular Microbiology 71 %281%29%3A 92�??106%2E doi%3A10%2E1111%2Fj%2E1365%2D2958%2E2008%2E06507%2Ex%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kambara, Kumiko, Silvia Ardissone, Hajime Kobayashi, Maged M Saad, Olivier Schumpp, William J Broughton, and William J Deakin. 2009. ?Rhizobia Utilize Pathogen-Like Effector Proteins During Symbiosis..? Molecular Microbiology 71 (1): 92?106. doi:10.1111/j.1365-2958.2008.06507.x.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kambara,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kambara,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kawaharada%2C Y%2C S KELLY%2C M Wibroe Nielsen%2C C T Hjuler%2C K Gysel%2C A Muszy�?ski%2C R W Carlson%2C et al%2E 2015%2E �??Receptor%2DMediated Exopolysaccharide Perception Controls Bacterial Infection%2E%2E�?� Nature 523 %287560%29%3A 308�??12%2E doi%3A10%2E1038%2Fnature14611%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kawaharada, Y, S KELLY, M Wibroe Nielsen, C T Hjuler, K Gysel, A Muszy?ski, R W Carlson, et al. 2015. ?Receptor-Mediated Exopolysaccharide Perception Controls Bacterial Infection..? Nature 523 (7560): 308?12. doi:10.1038/nature14611.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kawaharada,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 308â�?�?12.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kawaharada,&as_ylo=7560&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Khan%2C Madiha%2C Rajagopal Subramaniam%2C and Darrell Desveaux%2E 2015%2E �??Of Guards%2C Decoys%2C Baits and Traps%3A Pathogen Perception in Plants by Type III Effector Sensors%2E%2E�?� Current Opinion in Microbiology 29 %28November%29%3A 49�??55%2E doi%3A10%2E1016%2Fj%2Emib%2E2015%2E10%2E006%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Khan, Madiha, Rajagopal Subramaniam, and Darrell Desveaux. 2015. ?Of Guards, Decoys, Baits and Traps: Pathogen Perception in Plants by Type III Effector Sensors..? Current Opinion in Microbiology 29 (November): 49?55. doi:10.1016/j.mib.2015.10.006.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Khan,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Of Guards, Decoys, Baits and Traps: Pathogen Perception in Plants by Type III Effector Sensors..â�?� Current Opinion in Microbiology 29 (November): 49â�?�?55.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Of Guards, Decoys, Baits and Traps: Pathogen Perception in Plants by Type III Effector Sensors..â�?� Current Opinion in Microbiology 29 (November): 49â�?�?55.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Khan,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kim%2C Won%2DSeok%2C and Hari B Krishnan%2E 2014%2E �??A nopA Deletion Mutant of Sinorhizobium Fredii USDA257%2C a Soybean Symbiont%2C Is Impaired in Nodulation%2E%2E�?� Current Microbiology 68 %282%29%3A 239�??46%2E doi%3A10%2E1007%2Fs00284%2D013%2D0469%2D4%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kim, Won-Seok, and Hari B Krishnan. 2014. ?A nopA Deletion Mutant of Sinorhizobium Fredii USDA257, a Soybean Symbiont, Is Impaired in Nodulation..? Current Microbiology 68 (2): 239?46. doi:10.1007/s00284-013-0469-4.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kim,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kim,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kouchi%2C Hiroshi%2C Haruko Imaizumi%2DAnraku%2C Makoto Hayashi%2C Tsuneo Hakoyama%2C Tomomi Nakagawa%2C Yosuke Umehara%2C Norio Suganuma%2C and Masayoshi Kawaguchi%2E 2010%2E �??How Many Peas in a Pod%3F Legume Genes Responsible for Mutualistic Symbioses Underground%2E%2E�?� Plant and Cell Physiology 51 %289%29%3A 1381�??97%2E doi%3A10%2E1093%2Fpcp%2Fpcq107%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kouchi, Hiroshi, Haruko Imaizumi-Anraku, Makoto Hayashi, Tsuneo Hakoyama, Tomomi Nakagawa, Yosuke Umehara, Norio Suganuma, and Masayoshi Kawaguchi. 2010. ?How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground..? Plant and Cell Physiology 51 (9): 1381?97. doi:10.1093/pcp/pcq107.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kouchi,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground..â�?� Plant and Cell Physiology 51 (9): 1381â�?�?97.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground..â�?� Plant and Cell Physiology 51 (9): 1381â�?�?97.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kouchi,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kroj%2C Thomas%2C Emilie Chanclud%2C Corinne Michel Romiti%2C Xavier Grand%2C and Jean%2DBenoit Morel%2E 2016%2E �??Integration of Decoy Domains Derived From Protein Targets of Pathogen Effectors Into Plant Immune Receptors Is Widespread%2E%2E�?� The New Phytologist%2C February%2E doi%3A10%2E1111%2Fnph%2E13869%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kroj, Thomas, Emilie Chanclud, Corinne Michel Romiti, Xavier Grand, and Jean-Benoit Morel. 2016. ?Integration of Decoy Domains Derived From Protein Targets of Pathogen Effectors Into Plant Immune Receptors Is Widespread..? The New Phytologist, February. doi:10.1111/nph.13869.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kroj,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Integration of Decoy Domains Derived From Protein Targets of Pathogen Effectors Into Plant Immune Receptors Is Widespread..â�?� The New Phytologist, February.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Integration of Decoy Domains Derived From Protein Targets of Pathogen Effectors Into Plant Immune Receptors Is Widespread..â�?� The New Phytologist, February.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kroj,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1



Le Fevre, Ruth, Edouard Evangelisti, Thomas Rey, and Sebastian Schornack. 2015. “Modulation of Host Cell Biology by PlantPathogenic Microbes..” Annual Review of Cell and Developmental Biology, September. doi:10.1146/annurev-cellbio-102314-112502.


Lévy, Julien, Cécile Bres, Rene Geurts, Boulos Chalhoub, Olga Kulikova, Gérard Duc, Etienne-Pascal Journet, et al. 2004. “A PutativeCa2+ and Calmodulin-Dependent Protein Kinase Required for Bacterial and Fungal Symbioses..” Science (New York, NY) 303 (5662):1361–64. doi:10.1126/science.1093038.


Li, F., Pignatta, D., Bendix, C., Brunkard, J. O., Cohn, M. M., Tung, J., et al. (2012). MicroRNA regulation of plant innate immunereceptors. Proceedings of the National Academy of Sciences of the United States of America, 109(5), 1790–1795.http://doi.org/10.1073/pnas.1118282109


Li, Jun, Daniela M Witten, Iain M Johnstone, and Robert Tibshirani. 2012. “Normalization, Testing, and False Discovery Rate Estimationfor RNA-Sequencing Data..” Biostatistics (Oxford, England) 13 (3): 523–38. doi:10.1093/biostatistics/kxr031.


Limpens, Erik, Carolien Franken, Patrick Smit, Joost Willemse, Ton Bisseling, and Rene Geurts. 2003. “LysM Domain Receptor KinasesRegulating Rhizobial Nod Factor-Induced Infection..” Science (New York, NY) 302 (5645): 630–33. doi:10.1126/science.1090074.


Liu, Tzu-Yin, Teng-Kuei Huang, Shu-Yi Yang, Yu-Ting Hong, Sheng-Min Huang, Fu-Nien Wang, Su-Fen Chiang, Shang-Yueh Tsai, Wen-Chien Lu, and Tzyy-Jen Chiou. 2016. “Identification of Plant Vacuolar Transporters Mediating Phosphate Storage..” NatureCommunications 7 (March): 11095. doi:10.1038/ncomms11095.


Long, S R. 1989. “Rhizobium-Legume Nodulation: Life Together in the Underground..” Cell 56 (2): 203–14.

Lukasik, Ewa, and Frank L W Takken. 2009. “STANDing Strong, Resistance Proteins Instigators of Plant Defence..” Current Opinion inPlant Biology 12 (4): 427–36. doi:10.1016/j.pbi.2009.03.001.


Madsen, Esben Bjørn, Lene Heegaard Madsen, Simona Radutoiu, Magdalena Olbryt, Magdalena Rakwalska, Krzysztof Szczyglowski,Shusei Sato, et al. 2003. “A Receptor Kinase Gene of the LysM Type Is Involved in Legume Perception of Rhizobial Signals..” Nature425 (6958): 637–40. doi:10.1038/nature02045.


Madsen, Lene H, Leïla Tirichine, Anna Jurkiewicz, John T Sullivan, Anne B Heckmann, Anita S Bek, Clive W Ronson, Euan K James,and Jens Stougaard. 2010. “The Molecular Network Governing Nodule Organogenesis and Infection in the Model Legume LotusJaponicus..” Nature Communications 1: 10. doi:10.1038/ncomms1009.


Marchler-Bauer, Aron, Shennan Lu, John B Anderson, Farideh Chitsaz, Myra K Derbyshire, Carol DeWeese-Scott, Jessica H Fong, etal. 2011. “CDD: a Conserved Domain Database for the Functional Annotation of Proteins..” Nucleic Acids Research 39 (Databaseissue): D225–29. doi:10.1093/nar/gkq1189.


Marquenet, Emélie, and Evelyne Richet. 2007. “How Integration of Positive and Negative Regulatory Signals by a STAND SignalingProtein Depends on ATP Hydrolysis..” Molecular Cell 28 (2): 187–99. doi:10.1016/j.molcel.2007.08.014.

Pubmed: Author and Title www.plantphysiol.orgon October 14, 2020 - Published by Downloaded from Copyright © 2017 American Society of Plant Biologists. All rights reserved.

http://www.ncbi.nlm.nih.gov/pubmed?term=Kunze%2C Gernot%2C Cyril Zipfel%2C Silke Robatzek%2C Karsten Niehaus%2C Thomas Boller%2C and Georg Felix%2E 2004%2E �??The N Terminus of Bacterial Elongation Factor Tu Elicits Innate Immunity in Arabidopsis Plants%2E%2E�?� The Plant Cell 16 %2812%29%3A 3496�??3507%2E doi%3A10%2E1105%2Ftpc%2E104%2E026765%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kunze, Gernot, Cyril Zipfel, Silke Robatzek, Karsten Niehaus, Thomas Boller, and Georg Felix. 2004. ?The N Terminus of Bacterial Elongation Factor Tu Elicits Innate Immunity in Arabidopsis Plants..? The Plant Cell 16 (12): 3496?3507. doi:10.1105/tpc.104.026765.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kunze,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The N Terminus of Bacterial Elongation Factor Tu Elicits Innate Immunity in Arabidopsis Plants..â�?� The Plant Cell 16 (12): 3496â�?�?3507.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The N Terminus of Bacterial Elongation Factor Tu Elicits Innate Immunity in Arabidopsis Plants..â�?� The Plant Cell 16 (12): 3496â�?�?3507.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kunze,&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Le Fevre%2C Ruth%2C Edouard Evangelisti%2C Thomas Rey%2C and Sebastian Schornack%2E 2015%2E �??Modulation of Host Cell Biology by Plant Pathogenic Microbes%2E%2E�?� Annual Review of Cell and Developmental Biology%2C September%2E doi%3A10%2E1146%2Fannurev%2Dcellbio%2D102314%2D112502%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Le Fevre, Ruth, Edouard Evangelisti, Thomas Rey, and Sebastian Schornack. 2015. ?Modulation of Host Cell Biology by Plant Pathogenic Microbes..? Annual Review of Cell and Developmental Biology, September. doi:10.1146/annurev-cellbio-102314-112502.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Le&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Le&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Lévy%2C Julien%2C Cécile Bres%2C Rene Geurts%2C Boulos Chalhoub%2C Olga Kulikova%2C Gérard Duc%2C Etienne%2DPascal Journet%2C et al%2E 2004%2E �??A Putative Ca2%2B and Calmodulin%2DDependent Protein Kinase Required for Bacterial and Fungal Symbioses%2E%2E�?� Science %28New York%2C NY%29 303 %285662%29%3A 1361�??64%2E doi%3A10%2E1126%2Fscience%2E1093038%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=L�vy, Julien, C�cile Bres, Rene Geurts, Boulos Chalhoub, Olga Kulikova, G�rard Duc, Etienne-Pascal Journet, et al. 2004. ?A Putative Ca2+ and Calmodulin-Dependent Protein Kinase Required for Bacterial and Fungal Symbioses..? Science (New York, NY) 303 (5662): 1361?64. doi:10.1126/science.1093038.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=L�?©vy,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 1361â�?�?64.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=L�?©vy,&as_ylo=5662&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Li%2C F%2E%2C Pignatta%2C D%2E%2C Bendix%2C C%2E%2C Brunkard%2C J%2E O%2E%2C Cohn%2C M%2E M%2E%2C Tung%2C J%2E%2C et al%2E %282012%29%2E MicroRNA regulation of plant innate immune receptors%2E Proceedings of the National Academy of Sciences of the United States of America%2C 109%285%29%2C 1790�??1795%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1073%2Fpnas%2E1118282109&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Li, F., Pignatta, D., Bendix, C., Brunkard, J. O., Cohn, M. M., Tung, J., et al. (2012). MicroRNA regulation of plant innate immune receptors. Proceedings of the National Academy of Sciences of the United States of America, 109(5), 1790?1795. http://doi.org/10.1073/pnas.1118282109

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Li,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=MicroRNA regulation of plant innate immune receptors.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=MicroRNA regulation of plant innate immune receptors.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Li,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Li%2C Jun%2C Daniela M Witten%2C Iain M Johnstone%2C and Robert Tibshirani%2E 2012%2E �??Normalization%2C Testing%2C and False Discovery Rate Estimation for RNA%2DSequencing Data%2E%2E�?� Biostatistics %28Oxford%2C England%29 13 %283%29%3A 523�??38%2E doi%3A10%2E1093%2Fbiostatistics%2Fkxr031%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Li, Jun, Daniela M Witten, Iain M Johnstone, and Robert Tibshirani. 2012. ?Normalization, Testing, and False Discovery Rate Estimation for RNA-Sequencing Data..? Biostatistics (Oxford, England) 13 (3): 523?38. doi:10.1093/biostatistics/kxr031.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Li,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Normalization, Testing, and False Discovery Rate Estimation for RNA-Sequencing Data..â�?� Biostatistics (Oxford, England) 13 (3): 523â�?�?38.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Normalization, Testing, and False Discovery Rate Estimation for RNA-Sequencing Data..â�?� Biostatistics (Oxford, England) 13 (3): 523â�?�?38.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Li,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Limpens%2C Erik%2C Carolien Franken%2C Patrick Smit%2C Joost Willemse%2C Ton Bisseling%2C and Rene Geurts%2E 2003%2E �??LysM Domain Receptor Kinases Regulating Rhizobial Nod Factor%2DInduced Infection%2E%2E�?� Science %28New York%2C NY%29 302 %285645%29%3A 630�??33%2E doi%3A10%2E1126%2Fscience%2E1090074%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Limpens, Erik, Carolien Franken, Patrick Smit, Joost Willemse, Ton Bisseling, and Rene Geurts. 2003. ?LysM Domain Receptor Kinases Regulating Rhizobial Nod Factor-Induced Infection..? Science (New York, NY) 302 (5645): 630?33. doi:10.1126/science.1090074.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Limpens,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 630â�?�?33.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Limpens,&as_ylo=5645&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Liu%2C Tzu%2DYin%2C Teng%2DKuei Huang%2C Shu%2DYi Yang%2C Yu%2DTing Hong%2C Sheng%2DMin Huang%2C Fu%2DNien Wang%2C Su%2DFen Chiang%2C Shang%2DYueh Tsai%2C Wen%2DChien Lu%2C and Tzyy%2DJen Chiou%2E 2016%2E �??Identification of Plant Vacuolar Transporters Mediating Phosphate Storage%2E%2E�?� Nature Communications 7 %28March%29%3A 11095%2E doi%3A10%2E1038%2Fncomms11095%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Liu, Tzu-Yin, Teng-Kuei Huang, Shu-Yi Yang, Yu-Ting Hong, Sheng-Min Huang, Fu-Nien Wang, Su-Fen Chiang, Shang-Yueh Tsai, Wen-Chien Lu, and Tzyy-Jen Chiou. 2016. ?Identification of Plant Vacuolar Transporters Mediating Phosphate Storage..? Nature Communications 7 (March): 11095. doi:10.1038/ncomms11095.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Liu,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Identification of Plant Vacuolar Transporters Mediating Phosphate Storage..â�?� Nature Communications 7 (March): 11095.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Identification of Plant Vacuolar Transporters Mediating Phosphate Storage..â�?� Nature Communications 7 (March): 11095.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Liu,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Lukasik%2C Ewa%2C and Frank L W Takken%2E 2009%2E �??STANDing Strong%2C Resistance Proteins Instigators of Plant Defence%2E%2E�?� Current Opinion in Plant Biology 12 %284%29%3A 427�??36%2E doi%3A10%2E1016%2Fj%2Epbi%2E2009%2E03%2E001%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Lukasik, Ewa, and Frank L W Takken. 2009. ?STANDing Strong, Resistance Proteins Instigators of Plant Defence..? Current Opinion in Plant Biology 12 (4): 427?36. doi:10.1016/j.pbi.2009.03.001.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Lukasik,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?STANDing Strong, Resistance Proteins Instigators of Plant Defence..â�?� Current Opinion in Plant Biology 12 (4): 427â�?�?36.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?STANDing Strong, Resistance Proteins Instigators of Plant Defence..â�?� Current Opinion in Plant Biology 12 (4): 427â�?�?36.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lukasik,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Madsen%2C Esben Bjørn%2C Lene Heegaard Madsen%2C Simona Radutoiu%2C Magdalena Olbryt%2C Magdalena Rakwalska%2C Krzysztof Szczyglowski%2C Shusei Sato%2C et al%2E 2003%2E �??A Receptor Kinase Gene of the LysM Type Is Involved in Legume Perception of Rhizobial Signals%2E%2E�?� Nature 425 %286958%29%3A 637�??40%2E doi%3A10%2E1038%2Fnature02045%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Madsen, Esben Bj�rn, Lene Heegaard Madsen, Simona Radutoiu, Magdalena Olbryt, Magdalena Rakwalska, Krzysztof Szczyglowski, Shusei Sato, et al. 2003. ?A Receptor Kinase Gene of the LysM Type Is Involved in Legume Perception of Rhizobial Signals..? Nature 425 (6958): 637?40. doi:10.1038/nature02045.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Madsen,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 637â�?�?40.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Madsen,&as_ylo=6958&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Madsen%2C Lene H%2C Leïla Tirichine%2C Anna Jurkiewicz%2C John T Sullivan%2C Anne B Heckmann%2C Anita S Bek%2C Clive W Ronson%2C Euan K James%2C and Jens Stougaard%2E 2010%2E �??The Molecular Network Governing Nodule Organogenesis and Infection in the Model Legume Lotus Japonicus%2E%2E�?� Nature Communications 1%3A 10%2E doi%3A10%2E1038%2Fncomms1009%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Madsen, Lene H, Le�la Tirichine, Anna Jurkiewicz, John T Sullivan, Anne B Heckmann, Anita S Bek, Clive W Ronson, Euan K James, and Jens Stougaard. 2010. ?The Molecular Network Governing Nodule Organogenesis and Infection in the Model Legume Lotus Japonicus..? Nature Communications 1: 10. doi:10.1038/ncomms1009.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Madsen,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The Molecular Network Governing Nodule Organogenesis and Infection in the Model Legume Lotus Japonicus&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The Molecular Network Governing Nodule Organogenesis and Infection in the Model Legume Lotus Japonicus&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Madsen,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Marchler%2DBauer%2C Aron%2C Shennan Lu%2C John B Anderson%2C Farideh Chitsaz%2C Myra K Derbyshire%2C Carol DeWeese%2DScott%2C Jessica H Fong%2C et al%2E 2011%2E �??CDD%3A a Conserved Domain Database for the Functional Annotation of Proteins%2E%2E�?� Nucleic Acids Research 39 %28Database issue%29%3A D225�??29%2E doi%3A10%2E1093%2Fnar%2Fgkq1189%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Marchler-Bauer, Aron, Shennan Lu, John B Anderson, Farideh Chitsaz, Myra K Derbyshire, Carol DeWeese-Scott, Jessica H Fong, et al. 2011. ?CDD: a Conserved Domain Database for the Functional Annotation of Proteins..? Nucleic Acids Research 39 (Database issue): D225?29. doi:10.1093/nar/gkq1189.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Marchler-Bauer,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?CDD: a Conserved Domain Database for the Functional Annotation of Proteins..â�?� Nucleic Acids Research 39 (Database issue): D225â�?�?29.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?CDD: a Conserved Domain Database for the Functional Annotation of Proteins..â�?� Nucleic Acids Research 39 (Database issue): D225â�?�?29.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Marchler-Bauer,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Marquenet%2C Emélie%2C and Evelyne Richet%2E 2007%2E �??How Integration of Positive and Negative Regulatory Signals by a STAND Signaling Protein Depends on ATP Hydrolysis%2E%2E�?� Molecular Cell 28 %282%29%3A 187�??99%2E doi%3A10%2E1016%2Fj%2Emolcel%2E2007%2E08%2E014%2E&dopt=abstract


CrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Meinhardt, L W, H B Krishnan, P A Balatti, and S G Pueppke. 1993. “Molecular Cloning and Characterization of a Sym Plasmid LocusThat Regulates Cultivar-Specific Nodulation of Soybean by Rhizobium Fredii USDA257..” Molecular Microbiology 9 (1): 17–29.

Meyers, B C, A W Dickerman, R W Michelmore, S Sivaramakrishnan, B W Sobral, and N D Young. 1999. “Plant Disease ResistanceGenes Encode Members of an Ancient and Diverse Protein Family Within the Nucleotide-Binding Superfamily..” The Plant Journal : forCell and Molecular Biology 20 (3): 317–32.

Meyers, Blake C, Alexander Kozik, Alyssa Griego, Hanhui Kuang, and Richard W Michelmore. 2003. “Genome-Wide Analysis of NBS-LRR-Encoding Genes in Arabidopsis..” The Plant Cell 15 (4): 809–34.

Meyers, Blake C, Michele Morgante, and Richard W Michelmore. 2002. “TIR-X and TIR-NBS Proteins: Two New Families Related toDisease Resistance TIR-NBS-LRR Proteins Encoded in Arabidopsis and Other Plant Genomes..” The Plant Journal : for Cell andMolecular Biology 32 (1): 77–92.

Millet, Yves A, Cristian H Danna, Nicole K Clay, Wisuwat Songnuan, Matthew D Simon, Danièle Werck-Reichhart, and Frederick MAusubel. 2010. “Innate Immune Responses Activated in Arabidopsis Roots by Microbe-Associated Molecular Patterns..” The Plant Cell22 (3): 973–90. doi:10.1105/tpc.109.069658.


Minh, Bui Quang, Minh Anh Thi Nguyen, and Arndt von Haeseler. 2013. “Ultrafast Approximation for Phylogenetic Bootstrap..”Molecular Biology and Evolution 30 (5): 1188–95. doi:10.1093/molbev/mst024.


Mun, Terry, Asger Bachmann, Vikas Gupta, Jens Stougaard, and Stig U Andersen. 2016. “Lotus Base: an Integrated Information Portalfor the Model Legume Lotus Japonicus..” Scientific Reports 6 (December): 39447. doi:10.1038/srep39447.


Muthamilarasan, Mehanathan, and Manoj Prasad. 2013. “Plant Innate Immunity: an Updated Insight Into Defense Mechanism..” Journalof Biosciences 38 (2): 433–49.

Nguyen, Lam-Tung, Heiko A Schmidt, Arndt von Haeseler, and Bui Quang Minh. 2015. “IQ-TREE: a Fast and Effective StochasticAlgorithm for Estimating Maximum-Likelihood Phylogenies..” Molecular Biology and Evolution 32 (1): 268–74.doi:10.1093/molbev/msu300.


Nishimura, Marc T, and Jeffery L Dangl. 2010. “Arabidopsis and the Plant Immune System..” The Plant Journal : for Cell and MolecularBiology 61 (6): 1053–66. doi:10.1111/j.1365-313X.2010.04131.x.


Oldroyd, Giles E D. 2013. “Speak, Friend, and Enter: Signalling Systems That Promote Beneficial Symbiotic Associations in Plants..”Nature Reviews Microbiology 11 (4): 252–63. doi:10.1038/nrmicro2990.


Oldroyd, Giles E D, and J Allan Downie. 2006. “Nuclear Calcium Changes at the Core of Symbiosis Signalling..” Current Opinion inPlant Biology 9 (4): 351–57. doi:10.1016/j.pbi.2006.05.003.


Pan, Q, J Wendel, and R Fluhr. 2000. “Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and CerealGenomes..” Journal of Molecular Evolution 50 (3): 203–13. doi:10.1007/s002399910023.


Parniske, M. 2000. “Intracellular Accommodation of Microbes by Plants: a Common Developmental Program for Symbiosis andDisease?.” Current Opinion in Plant Biology 3 (4): 320–28. doi:10.1016/S1369-5266(00)00088-1.

Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title www.plantphysiol.orgon October 14, 2020 - Published by Downloaded from


http://search.crossref.org/?page=1&rows=2&q=Marquenet, Em�lie, and Evelyne Richet. 2007. ?How Integration of Positive and Negative Regulatory Signals by a STAND Signaling Protein Depends on ATP Hydrolysis..? Molecular Cell 28 (2): 187?99. doi:10.1016/j.molcel.2007.08.014.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Marquenet,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?How Integration of Positive and Negative Regulatory Signals by a STAND Signaling Protein Depends on ATP Hydrolysis..â�?� Molecular Cell 28 (2): 187â�?�?99.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?How Integration of Positive and Negative Regulatory Signals by a STAND Signaling Protein Depends on ATP Hydrolysis..â�?� Molecular Cell 28 (2): 187â�?�?99.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Marquenet,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Millet%2C Yves A%2C Cristian H Danna%2C Nicole K Clay%2C Wisuwat Songnuan%2C Matthew D Simon%2C Danièle Werck%2DReichhart%2C and Frederick M Ausubel%2E 2010%2E �??Innate Immune Responses Activated in Arabidopsis Roots by Microbe%2DAssociated Molecular Patterns%2E%2E�?� The Plant Cell 22 %283%29%3A 973�??90%2E doi%3A10%2E1105%2Ftpc%2E109%2E069658%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Millet, Yves A, Cristian H Danna, Nicole K Clay, Wisuwat Songnuan, Matthew D Simon, Dani�le Werck-Reichhart, and Frederick M Ausubel. 2010. ?Innate Immune Responses Activated in Arabidopsis Roots by Microbe-Associated Molecular Patterns..? The Plant Cell 22 (3): 973?90. doi:10.1105/tpc.109.069658.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Millet,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Innate Immune Responses Activated in Arabidopsis Roots by Microbe-Associated Molecular Patterns..â�?� The Plant Cell 22 (3): 973â�?�?90.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Innate Immune Responses Activated in Arabidopsis Roots by Microbe-Associated Molecular Patterns..â�?� The Plant Cell 22 (3): 973â�?�?90.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Millet,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Minh%2C Bui Quang%2C Minh Anh Thi Nguyen%2C and Arndt von Haeseler%2E 2013%2E �??Ultrafast Approximation for Phylogenetic Bootstrap%2E%2E�?� Molecular Biology and Evolution 30 %285%29%3A 1188�??95%2E doi%3A10%2E1093%2Fmolbev%2Fmst024%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Minh, Bui Quang, Minh Anh Thi Nguyen, and Arndt von Haeseler. 2013. ?Ultrafast Approximation for Phylogenetic Bootstrap..? Molecular Biology and Evolution 30 (5): 1188?95. doi:10.1093/molbev/mst024.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Minh,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Ultrafast Approximation for Phylogenetic Bootstrap..â�?� Molecular Biology and Evolution 30 (5): 1188â�?�?95.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Ultrafast Approximation for Phylogenetic Bootstrap..â�?� Molecular Biology and Evolution 30 (5): 1188â�?�?95.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Minh,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Mun%2C Terry%2C Asger Bachmann%2C Vikas Gupta%2C Jens Stougaard%2C and Stig U Andersen%2E 2016%2E �??Lotus Base%3A an Integrated Information Portal for the Model Legume Lotus Japonicus%2E%2E�?� Scientific Reports 6 %28December%29%3A 39447%2E doi%3A10%2E1038%2Fsrep39447%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Mun, Terry, Asger Bachmann, Vikas Gupta, Jens Stougaard, and Stig U Andersen. 2016. ?Lotus Base: an Integrated Information Portal for the Model Legume Lotus Japonicus..? Scientific Reports 6 (December): 39447. doi:10.1038/srep39447.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mun,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Lotus Base: an Integrated Information Portal for the Model Legume Lotus Japonicus..â�?� Scientific Reports 6 (December): 39447.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Lotus Base: an Integrated Information Portal for the Model Legume Lotus Japonicus..â�?� Scientific Reports 6 (December): 39447.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mun,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Nguyen%2C Lam%2DTung%2C Heiko A Schmidt%2C Arndt von Haeseler%2C and Bui Quang Minh%2E 2015%2E �??IQ%2DTREE%3A a Fast and Effective Stochastic Algorithm for Estimating Maximum%2DLikelihood Phylogenies%2E%2E�?� Molecular Biology and Evolution 32 %281%29%3A 268�??74%2E doi%3A10%2E1093%2Fmolbev%2Fmsu300%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Nguyen, Lam-Tung, Heiko A Schmidt, Arndt von Haeseler, and Bui Quang Minh. 2015. ?IQ-TREE: a Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies..? Molecular Biology and Evolution 32 (1): 268?74. doi:10.1093/molbev/msu300.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Nguyen,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?IQ-TREE: a Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies..â�?� Molecular Biology and Evolution 32 (1): 268â�?�?74.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?IQ-TREE: a Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies..â�?� Molecular Biology and Evolution 32 (1): 268â�?�?74.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Nguyen,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Nishimura%2C Marc T%2C and Jeffery L Dangl%2E 2010%2E �??Arabidopsis and the Plant Immune System%2E%2E�?� The Plant Journal %3A for Cell and Molecular Biology 61 %286%29%3A 1053�??66%2E doi%3A10%2E1111%2Fj%2E1365%2D313X%2E2010%2E04131%2Ex%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Nishimura, Marc T, and Jeffery L Dangl. 2010. ?Arabidopsis and the Plant Immune System..? The Plant Journal : for Cell and Molecular Biology 61 (6): 1053?66. doi:10.1111/j.1365-313X.2010.04131.x.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Nishimura,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Nishimura,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Oldroyd%2C Giles E D%2E 2013%2E �??Speak%2C Friend%2C and Enter%3A Signalling Systems That Promote Beneficial Symbiotic Associations in Plants%2E%2E�?� Nature Reviews Microbiology 11 %284%29%3A 252�??63%2E doi%3A10%2E1038%2Fnrmicro2990%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Oldroyd, Giles E D. 2013. ?Speak, Friend, and Enter: Signalling Systems That Promote Beneficial Symbiotic Associations in Plants..? Nature Reviews Microbiology 11 (4): 252?63. doi:10.1038/nrmicro2990.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Oldroyd,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Speak, Friend, and Enter: Signalling Systems That Promote Beneficial Symbiotic Associations in Plants..â�?� Nature Reviews Microbiology 11 (4): 252â�?�?63.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Speak, Friend, and Enter: Signalling Systems That Promote Beneficial Symbiotic Associations in Plants..â�?� Nature Reviews Microbiology 11 (4): 252â�?�?63.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Oldroyd,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Oldroyd%2C Giles E D%2C and J Allan Downie%2E 2006%2E �??Nuclear Calcium Changes at the Core of Symbiosis Signalling%2E%2E�?� Current Opinion in Plant Biology 9 %284%29%3A 351�??57%2E doi%3A10%2E1016%2Fj%2Epbi%2E2006%2E05%2E003%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Oldroyd, Giles E D, and J Allan Downie. 2006. ?Nuclear Calcium Changes at the Core of Symbiosis Signalling..? Current Opinion in Plant Biology 9 (4): 351?57. doi:10.1016/j.pbi.2006.05.003.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Oldroyd,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Nuclear Calcium Changes at the Core of Symbiosis Signalling..â�?� Current Opinion in Plant Biology 9 (4): 351â�?�?57.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Nuclear Calcium Changes at the Core of Symbiosis Signalling..â�?� Current Opinion in Plant Biology 9 (4): 351â�?�?57.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Oldroyd,&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Pan%2C Q%2C J Wendel%2C and R Fluhr%2E 2000%2E �??Divergent Evolution of Plant NBS%2DLRR Resistance Gene Homologues in Dicot and Cereal Genomes%2E%2E�?� Journal of Molecular Evolution 50 %283%29%3A 203�??13%2E doi%3A10%2E1007%2Fs002399910023%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Pan, Q, J Wendel, and R Fluhr. 2000. ?Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and Cereal Genomes..? Journal of Molecular Evolution 50 (3): 203?13. doi:10.1007/s002399910023.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Pan,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and Cereal Genomes..â�?� Journal of Molecular Evolution 50 (3): 203â�?�?13.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and Cereal Genomes..â�?� Journal of Molecular Evolution 50 (3): 203â�?�?13.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Pan,&as_ylo=2000&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Parniske%2C M%2E 2000%2E �??Intracellular Accommodation of Microbes by Plants%3A a Common Developmental Program for Symbiosis and Disease%3F%2E�?� Current Opinion in Plant Biology 3 %284%29%3A 320�??28%2E doi%3A10%2E1016%2FS1369%2D5266%2800%2900088%2D1%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Parniske, M. 2000. ?Intracellular Accommodation of Microbes by Plants: a Common Developmental Program for Symbiosis and Disease?.? Current Opinion in Plant Biology 3 (4): 320?28. doi:10.1016/S1369-5266(00)00088-1.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Parniske,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Intracellular Accommodation of Microbes by Plants: a Common Developmental Program for Symbiosis and Disease&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Intracellular Accommodation of Microbes by Plants: a Common Developmental Program for Symbiosis and Disease&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Parniske,&as_ylo=2000&as_allsubj=all&hl=en&c2coff=1


Parniske, Martin. 2008. “Arbuscular Mycorrhiza: the Mother of Plant Root Endosymbioses..” Nature Reviews Microbiology 6 (10): 763–75. doi:10.1038/nrmicro1987.


Pel, Michiel J C, and Corné M J Pieterse. 2012. “Microbial Recognition and Evasion of Host Immunity..” Journal of ExperimentalBotany, October. doi:10.1093/jxb/ers262.


Radutoiu, Simona, Lene H Madsen, Esben B Madsen, Anna Jurkiewicz, Eigo Fukai, Esben M H Quistgaard, Anita S Albrektsen, Euan KJames, Søren Thirup, and Jens Stougaard. 2007. “LysM Domains Mediate Lipochitin-Oligosaccharide Recognition and Nfr GenesExtend the Symbiotic Host Range..” The EMBO Journal 26 (17): 3923–35. doi:10.1038/sj.emboj.7601826.


Radutoiu, Simona, Lene Heegaard Madsen, Esben Bjørn Madsen, Hubert H Felle, Yosuke Umehara, Mette Grønlund, Shusei Sato, etal. 2003. “Plant Recognition of Symbiotic Bacteria Requires Two LysM Receptor-Like Kinases..” Nature 425 (6958): 585–92.doi:10.1038/nature02039.


Ranf, Stefanie, Nicolas Gisch, Milena Schäffer, Tina Illig, Lore Westphal, Yuriy A Knirel, Patricia M Sánchez-Carballo, et al. 2015. “ALectin S-Domain Receptor Kinase Mediates Lipopolysaccharide Sensing in Arabidopsis Thaliana..” Nature Immunology, March.doi:10.1038/ni.3124.


Ritchie, Matthew E, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, and Gordon K Smyth. 2015. “Limma Powers DifferentialExpression Analyses for RNA-Sequencing and Microarray Studies..” Nucleic Acids Research 43 (7): e47. doi:10.1093/nar/gkv007.


Robinson, Mark D, Davis J McCarthy, and Gordon K Smyth. 2010. “edgeR: a Bioconductor Package for Differential Expression Analysisof Digital Gene Expression Data..” Bioinformatics (Oxford, England) 26 (1): 139–40. doi:10.1093/bioinformatics/btp616.


Saraste, M, P R Sibbald, and A Wittinghofer. 1990. “The P-Loop--a Common Motif in ATP- and GTP-Binding Proteins..” Trends inBiochemical Sciences 15 (11): 430–34.

Schauser, L, A Roussis, J Stiller, and J Stougaard. 1999. “A Plant Regulator Controlling Development of Symbiotic Root Nodules..”Nature 402 (6758): 191–95. doi:10.1038/46058.


Schmid, Markus, Timothy S Davison, Stefan R Henz, Utz J Pape, Monika Demar, Martin Vingron, Bernhard Schölkopf, Detlef Weigel,and Jan U Lohmann. 2005. “A Gene Expression Map of Arabidopsis Thaliana Development..” Nature Genetics 37 (5): 501–6.doi:10.1038/ng1543.


Shao, Zhu-Qing, Jia-Yu Xue, Ping Wu, Yan-Mei Zhang, Yue Wu, Yue-Yu Hang, Bin Wang, and Jian-Qun Chen. 2016. “Large-ScaleAnalyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) Genes Reveal Three Anciently Diverged Classeswith Distinct Evolutionary Patterns..” Plant Physiology, February. doi:10.1104/pp.15.01487.


Shivaprasad, P. V., Chen, H.-M., Patel, K., Bond, D. M., Santos, B. A. C. M., & Baulcombe, D. C. (2012). A microRNA superfamilyregulates nucleotide binding site-leucine-rich repeats and other mRNAs. The Plant Cell, 24(3), 859–874.http://doi.org/10.1105/tpc.111.095380



http://www.ncbi.nlm.nih.gov/pubmed?term=Parniske%2C Martin%2E 2008%2E �??Arbuscular Mycorrhiza%3A the Mother of Plant Root Endosymbioses%2E%2E�?� Nature Reviews Microbiology 6 %2810%29%3A 763�??75%2E doi%3A10%2E1038%2Fnrmicro1987%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Parniske, Martin. 2008. ?Arbuscular Mycorrhiza: the Mother of Plant Root Endosymbioses..? Nature Reviews Microbiology 6 (10): 763?75. doi:10.1038/nrmicro1987.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Parniske,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Arbuscular Mycorrhiza: the Mother of Plant Root Endosymbioses..â�?� Nature Reviews Microbiology 6 (10): 763â�?�?75.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Arbuscular Mycorrhiza: the Mother of Plant Root Endosymbioses..â�?� Nature Reviews Microbiology 6 (10): 763â�?�?75.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Parniske,&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Pel%2C Michiel J C%2C and Corné M J Pieterse%2E 2012%2E �??Microbial Recognition and Evasion of Host Immunity%2E%2E�?� Journal of Experimental Botany%2C October%2E doi%3A10%2E1093%2Fjxb%2Fers262%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Pel, Michiel J C, and Corn� M J Pieterse. 2012. ?Microbial Recognition and Evasion of Host Immunity..? Journal of Experimental Botany, October. doi:10.1093/jxb/ers262.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Pel,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Microbial Recognition and Evasion of Host Immunity..â�?� Journal of Experimental Botany, October.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Microbial Recognition and Evasion of Host Immunity..â�?� Journal of Experimental Botany, October.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Pel,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Radutoiu%2C Simona%2C Lene H Madsen%2C Esben B Madsen%2C Anna Jurkiewicz%2C Eigo Fukai%2C Esben M H Quistgaard%2C Anita S Albrektsen%2C Euan K James%2C Søren Thirup%2C and Jens Stougaard%2E 2007%2E �??LysM Domains Mediate Lipochitin%2DOligosaccharide Recognition and Nfr Genes Extend the Symbiotic Host Range%2E%2E�?� The EMBO Journal 26 %2817%29%3A 3923�??35%2E doi%3A10%2E1038%2Fsj%2Eemboj%2E7601826%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Radutoiu, Simona, Lene H Madsen, Esben B Madsen, Anna Jurkiewicz, Eigo Fukai, Esben M H Quistgaard, Anita S Albrektsen, Euan K James, S�ren Thirup, and Jens Stougaard. 2007. ?LysM Domains Mediate Lipochitin-Oligosaccharide Recognition and Nfr Genes Extend the Symbiotic Host Range..? The EMBO Journal 26 (17): 3923?35. doi:10.1038/sj.emboj.7601826.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Radutoiu,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?LysM Domains Mediate Lipochitin-Oligosaccharide Recognition and Nfr Genes Extend the Symbiotic Host Range..â�?� The EMBO Journal 26 (17): 3923â�?�?35.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?LysM Domains Mediate Lipochitin-Oligosaccharide Recognition and Nfr Genes Extend the Symbiotic Host Range..â�?� The EMBO Journal 26 (17): 3923â�?�?35.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Radutoiu,&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Radutoiu%2C Simona%2C Lene Heegaard Madsen%2C Esben Bjørn Madsen%2C Hubert H Felle%2C Yosuke Umehara%2C Mette Grønlund%2C Shusei Sato%2C et al%2E 2003%2E �??Plant Recognition of Symbiotic Bacteria Requires Two LysM Receptor%2DLike Kinases%2E%2E�?� Nature 425 %286958%29%3A 585�??92%2E doi%3A10%2E1038%2Fnature02039%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Radutoiu, Simona, Lene Heegaard Madsen, Esben Bj�rn Madsen, Hubert H Felle, Yosuke Umehara, Mette Gr�nlund, Shusei Sato, et al. 2003. ?Plant Recognition of Symbiotic Bacteria Requires Two LysM Receptor-Like Kinases..? Nature 425 (6958): 585?92. doi:10.1038/nature02039.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Radutoiu,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 585â�?�?92.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Radutoiu,&as_ylo=6958&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Ranf%2C Stefanie%2C Nicolas Gisch%2C Milena Schäffer%2C Tina Illig%2C Lore Westphal%2C Yuriy A Knirel%2C Patricia M Sánchez%2DCarballo%2C et al%2E 2015%2E �??A Lectin S%2DDomain Receptor Kinase Mediates Lipopolysaccharide Sensing in Arabidopsis Thaliana%2E%2E�?� Nature Immunology%2C March%2E doi%3A10%2E1038%2Fni%2E3124%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ranf, Stefanie, Nicolas Gisch, Milena Sch�ffer, Tina Illig, Lore Westphal, Yuriy A Knirel, Patricia M S�nchez-Carballo, et al. 2015. ?A Lectin S-Domain Receptor Kinase Mediates Lipopolysaccharide Sensing in Arabidopsis Thaliana..? Nature Immunology, March. doi:10.1038/ni.3124.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ranf,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?A Lectin S-Domain Receptor Kinase Mediates Lipopolysaccharide Sensing in Arabidopsis Thaliana..â�?� Nature Immunology, March.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?A Lectin S-Domain Receptor Kinase Mediates Lipopolysaccharide Sensing in Arabidopsis Thaliana..â�?� Nature Immunology, March.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ranf,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Ritchie%2C Matthew E%2C Belinda Phipson%2C Di Wu%2C Yifang Hu%2C Charity W Law%2C Wei Shi%2C and Gordon K Smyth%2E 2015%2E �??Limma Powers Differential Expression Analyses for RNA%2DSequencing and Microarray Studies%2E%2E�?� Nucleic Acids Research 43 %287%29%3A e47%2E doi%3A10%2E1093%2Fnar%2Fgkv007%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ritchie, Matthew E, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, and Gordon K Smyth. 2015. ?Limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies..? Nucleic Acids Research 43 (7): e47. doi:10.1093/nar/gkv007.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ritchie,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies..â�?� Nucleic Acids Research 43 (7): e47.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Limma Powers Differential Expression Analyses for RNA-Sequencing and Microarray Studies..â�?� Nucleic Acids Research 43 (7): e47.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ritchie,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Robinson%2C Mark D%2C Davis J McCarthy%2C and Gordon K Smyth%2E 2010%2E �??edgeR%3A a Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data%2E%2E�?� Bioinformatics %28Oxford%2C England%29 26 %281%29%3A 139�??40%2E doi%3A10%2E1093%2Fbioinformatics%2Fbtp616%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Robinson, Mark D, Davis J McCarthy, and Gordon K Smyth. 2010. ?edgeR: a Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data..? Bioinformatics (Oxford, England) 26 (1): 139?40. doi:10.1093/bioinformatics/btp616.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Robinson,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?edgeR: a Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data..â�?� Bioinformatics (Oxford, England) 26 (1): 139â�?�?40.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?edgeR: a Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data..â�?� Bioinformatics (Oxford, England) 26 (1): 139â�?�?40.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Robinson,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Schauser%2C L%2C A Roussis%2C J Stiller%2C and J Stougaard%2E 1999%2E �??A Plant Regulator Controlling Development of Symbiotic Root Nodules%2E%2E�?� Nature 402 %286758%29%3A 191�??95%2E doi%3A10%2E1038%2F46058%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Schauser, L, A Roussis, J Stiller, and J Stougaard. 1999. ?A Plant Regulator Controlling Development of Symbiotic Root Nodules..? Nature 402 (6758): 191?95. doi:10.1038/46058.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Schauser,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 191â�?�?95.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Schauser,&as_ylo=6758&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Schmid%2C Markus%2C Timothy S Davison%2C Stefan R Henz%2C Utz J Pape%2C Monika Demar%2C Martin Vingron%2C Bernhard Schölkopf%2C Detlef Weigel%2C and Jan U Lohmann%2E 2005%2E �??A Gene Expression Map of Arabidopsis Thaliana Development%2E%2E�?� Nature Genetics 37 %285%29%3A 501�??6%2E doi%3A10%2E1038%2Fng1543%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Schmid, Markus, Timothy S Davison, Stefan R Henz, Utz J Pape, Monika Demar, Martin Vingron, Bernhard Sch�lkopf, Detlef Weigel, and Jan U Lohmann. 2005. ?A Gene Expression Map of Arabidopsis Thaliana Development..? Nature Genetics 37 (5): 501?6. doi:10.1038/ng1543.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Schmid,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?A Gene Expression Map of Arabidopsis Thaliana Development..â�?� Nature Genetics 37 (5): 501â�?�?6.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?A Gene Expression Map of Arabidopsis Thaliana Development..â�?� Nature Genetics 37 (5): 501â�?�?6.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Schmid,&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Shao%2C Zhu%2DQing%2C Jia%2DYu Xue%2C Ping Wu%2C Yan%2DMei Zhang%2C Yue Wu%2C Yue%2DYu Hang%2C Bin Wang%2C and Jian%2DQun Chen%2E 2016%2E �??Large%2DScale Analyses of Angiosperm Nucleotide%2DBinding Site%2DLeucine%2DRich Repeat %28NBS%2DLRR%29 Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns%2E%2E�?� Plant Physiology%2C February%2E doi%3A10%2E1104%2Fpp%2E15%2E01487%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Shao, Zhu-Qing, Jia-Yu Xue, Ping Wu, Yan-Mei Zhang, Yue Wu, Yue-Yu Hang, Bin Wang, and Jian-Qun Chen. 2016. ?Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns..? Plant Physiology, February. doi:10.1104/pp.15.01487.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Shao,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns..â�?� Plant Physiology, February.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns..â�?� Plant Physiology, February.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Shao,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Shivaprasad%2C P%2E V%2E%2C Chen%2C H%2E%2DM%2E%2C Patel%2C K%2E%2C Bond%2C D%2E M%2E%2C Santos%2C B%2E A%2E C%2E M%2E%2C %26 Baulcombe%2C D%2E C%2E %282012%29%2E A microRNA superfamily regulates nucleotide binding site%2Dleucine%2Drich repeats and other mRNAs%2E The Plant Cell%2C 24%283%29%2C 859�??874%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1105%2Ftpc%2E111%2E095380&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Shivaprasad, P. V., Chen, H.-M., Patel, K., Bond, D. M., Santos, B. A. C. M., & Baulcombe, D. C. (2012). A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. The Plant Cell, 24(3), 859?874. http://doi.org/10.1105/tpc.111.095380

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Shivaprasad,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Shivaprasad,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1


Sievers, Fabian, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, et al. 2011. “Fast, ScalableGeneration of High-Quality Protein Multiple Sequence Alignments Using Clustal Omega..” Molecular Systems Biology 7 (October): 539.doi:10.1038/msb.2011.75.


Singh, Sylvia, and Martin Parniske. 2012. “Activation of Calcium- and Calmodulin-Dependent Protein Kinase (CCaMK), the CentralRegulator of Plant Root Endosymbiosis..” Current Opinion in Plant Biology 15 (4): 444–53. doi:10.1016/j.pbi.2012.04.002.


Skorpil, Peter, Maged M Saad, Nawal M Boukli, Hajime Kobayashi, Florencia Ares-Orpel, William J Broughton, and William J Deakin.2005. “NopP, a Phosphorylated Effector of Rhizobium Sp. Strain NGR234, Is a Major Determinant of Nodulation of the TropicalLegumes Flemingia Congesta and Tephrosia Vogelii..” Molecular Microbiology 57 (5): 1304–17. doi:10.1111/j.1365-2958.2005.04768.x.


Smit, Patrick, John Raedts, Vladimir Portyanko, Frédéric Debellé, Clare Gough, Ton Bisseling, and Rene Geurts. 2005. “NSP1 of theGRAS Protein Family Is Essential for Rhizobial Nod Factor-Induced Transcription..” Science (New York, NY) 308 (5729): 1789–91.doi:10.1126/science.1111025.


Smith, Sally E, and David J Read. 2010. Mycorrhizal Symbiosis. Academic Press.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Takken, Frank L W, and Aska Goverse. 2012. “How to Build a Pathogen Detector: Structural Basis of NB-LRR Function..” CurrentOpinion in Plant Biology 15 (4): 375–84. doi:10.1016/j.pbi.2012.05.001.


Takken, Frank Lw, Mario Albrecht, and Wladimir Il Tameling. 2006. “Resistance Proteins: Molecular Switches of Plant Defence..”Current Opinion in Plant Biology 9 (4): 383–90. doi:10.1016/j.pbi.2006.05.009.


Tang, Fang, Shengming Yang, Jinge Liu, and Hongyan Zhu. 2016. “Rj4, a Gene Controlling Nodulation Specificity in Soybeans,Encodes a Thaumatin-Like Protein but Not the One Previously Reported..” Plant Physiology 170 (1): 26–32. doi:10.1104/pp.15.01661.


Tanigaki, Yusuke, Kenji Ito, Yoshiyuki Obuchi, Akiko Kosaka, Katsuyuki T Yamato, Masahiro Okanami, Mikko T Lehtonen, Jari P TValkonen, and Motomu Akita. 2014. “Physcomitrella Patens Has Kinase-LRR R Gene Homologs and Interacting Proteins..” PloS One 9(4): e95118. doi:10.1371/journal.pone.0095118.


Tarr, D Ellen K, and Helen M Alexander. 2009. “TIR-NBS-LRR Genes Are Rare in Monocots: Evidence From Diverse MonocotOrders..” BMC Research Notes 2: 197. doi:10.1186/1756-0500-2-197.


Thordal-Christensen, Hans. 2003. “Fresh Insights Into Processes of Nonhost Resistance.” Current Opinion in Plant Biology 6 (4): 351–57.

Tirichine, Leïla, Haruko Imaizumi-Anraku, Satoko Yoshida, Yasuhiro Murakami, Lene H Madsen, Hiroki Miwa, Tomomi Nakagawa, et al.2006. “Deregulation of a Ca2+/Calmodulin-Dependent Kinase Leads to Spontaneous Nodule Development..” Nature 441 (7097): 1153–56. doi:10.1038/nature04862.


Tsukui, Takahiro, Shima Eda, Takakazu Kaneko, Shusei Sato, Shin Okazaki, Kaori Kakizaki-Chiba, Manabu Itakura, et al. 2013. “TheType III Secretion System of Bradyrhizobium Japonicum USDA122 Mediates Symbiotic Incompatibility with Rj2 Soybean Plants..” www.plantphysiol.orgon October 14, 2020 - Published by Downloaded from


http://www.ncbi.nlm.nih.gov/pubmed?term=Sievers%2C Fabian%2C Andreas Wilm%2C David Dineen%2C Toby J Gibson%2C Kevin Karplus%2C Weizhong Li%2C Rodrigo Lopez%2C et al%2E 2011%2E �??Fast%2C Scalable Generation of High%2DQuality Protein Multiple Sequence Alignments Using Clustal Omega%2E%2E�?� Molecular Systems Biology 7 %28October%29%3A 539%2E doi%3A10%2E1038%2Fmsb%2E2011%2E75%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Sievers, Fabian, Andreas Wilm, David Dineen, Toby J Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, et al. 2011. ?Fast, Scalable Generation of High-Quality Protein Multiple Sequence Alignments Using Clustal Omega..? Molecular Systems Biology 7 (October): 539. doi:10.1038/msb.2011.75.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Sievers,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Fast, Scalable Generation of High-Quality Protein Multiple Sequence Alignments Using Clustal Omega..â�?� Molecular Systems Biology 7 (October): 539.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Fast, Scalable Generation of High-Quality Protein Multiple Sequence Alignments Using Clustal Omega..â�?� Molecular Systems Biology 7 (October): 539.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Sievers,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Singh%2C Sylvia%2C and Martin Parniske%2E 2012%2E �??Activation of Calcium%2D and Calmodulin%2DDependent Protein Kinase %28CCaMK%29%2C the Central Regulator of Plant Root Endosymbiosis%2E%2E�?� Current Opinion in Plant Biology 15 %284%29%3A 444�??53%2E doi%3A10%2E1016%2Fj%2Epbi%2E2012%2E04%2E002%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Singh, Sylvia, and Martin Parniske. 2012. ?Activation of Calcium- and Calmodulin-Dependent Protein Kinase (CCaMK), the Central Regulator of Plant Root Endosymbiosis..? Current Opinion in Plant Biology 15 (4): 444?53. doi:10.1016/j.pbi.2012.04.002.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Singh,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Activation of Calcium- and Calmodulin-Dependent Protein Kinase (CCaMK), the Central Regulator of Plant Root Endosymbiosis..â�?� Current Opinion in Plant Biology 15 (4): 444â�?�?53.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Activation of Calcium- and Calmodulin-Dependent Protein Kinase (CCaMK), the Central Regulator of Plant Root Endosymbiosis..â�?� Current Opinion in Plant Biology 15 (4): 444â�?�?53.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Singh,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Skorpil%2C Peter%2C Maged M Saad%2C Nawal M Boukli%2C Hajime Kobayashi%2C Florencia Ares%2DOrpel%2C William J Broughton%2C and William J Deakin%2E 2005%2E �??NopP%2C a Phosphorylated Effector of Rhizobium Sp%2E Strain NGR234%2C Is a Major Determinant of Nodulation of the Tropical Legumes Flemingia Congesta and Tephrosia Vogelii%2E%2E�?� Molecular Microbiology 57 %285%29%3A 1304�??17%2E doi%3A10%2E1111%2Fj%2E1365%2D2958%2E2005%2E04768%2Ex%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Skorpil, Peter, Maged M Saad, Nawal M Boukli, Hajime Kobayashi, Florencia Ares-Orpel, William J Broughton, and William J Deakin. 2005. ?NopP, a Phosphorylated Effector of Rhizobium Sp. Strain NGR234, Is a Major Determinant of Nodulation of the Tropical Legumes Flemingia Congesta and Tephrosia Vogelii..? Molecular Microbiology 57 (5): 1304?17. doi:10.1111/j.1365-2958.2005.04768.x.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Skorpil,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?NopP, a Phosphorylated Effector of Rhizobium Sp&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?NopP, a Phosphorylated Effector of Rhizobium Sp&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Skorpil,&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Smit%2C Patrick%2C John Raedts%2C Vladimir Portyanko%2C Frédéric Debellé%2C Clare Gough%2C Ton Bisseling%2C and Rene Geurts%2E 2005%2E �??NSP1 of the GRAS Protein Family Is Essential for Rhizobial Nod Factor%2DInduced Transcription%2E%2E�?� Science %28New York%2C NY%29 308 %285729%29%3A 1789�??91%2E doi%3A10%2E1126%2Fscience%2E1111025%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Smit, Patrick, John Raedts, Vladimir Portyanko, Fr�d�ric Debell�, Clare Gough, Ton Bisseling, and Rene Geurts. 2005. ?NSP1 of the GRAS Protein Family Is Essential for Rhizobial Nod Factor-Induced Transcription..? Science (New York, NY) 308 (5729): 1789?91. doi:10.1126/science.1111025.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Smit,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 1789â�?�?91.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Smit,&as_ylo=5729&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Smith%2C Sally E%2C and David J Read%2E 2010%2E Mycorrhizal Symbiosis%2E Academic Press%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Smith, Sally E, and David J Read. 2010. Mycorrhizal Symbiosis. Academic Press.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Smith,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Mycorrhizal Symbiosis.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Mycorrhizal Symbiosis.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Smith,&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Takken%2C Frank L W%2C and Aska Goverse%2E 2012%2E �??How to Build a Pathogen Detector%3A Structural Basis of NB%2DLRR Function%2E%2E�?� Current Opinion in Plant Biology 15 %284%29%3A 375�??84%2E doi%3A10%2E1016%2Fj%2Epbi%2E2012%2E05%2E001%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Takken, Frank L W, and Aska Goverse. 2012. ?How to Build a Pathogen Detector: Structural Basis of NB-LRR Function..? Current Opinion in Plant Biology 15 (4): 375?84. doi:10.1016/j.pbi.2012.05.001.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Takken,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?How to Build a Pathogen Detector: Structural Basis of NB-LRR Function..â�?� Current Opinion in Plant Biology 15 (4): 375â�?�?84.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?How to Build a Pathogen Detector: Structural Basis of NB-LRR Function..â�?� Current Opinion in Plant Biology 15 (4): 375â�?�?84.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Takken,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Takken%2C Frank Lw%2C Mario Albrecht%2C and Wladimir Il Tameling%2E 2006%2E �??Resistance Proteins%3A Molecular Switches of Plant Defence%2E%2E�?� Current Opinion in Plant Biology 9 %284%29%3A 383�??90%2E doi%3A10%2E1016%2Fj%2Epbi%2E2006%2E05%2E009%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Takken, Frank Lw, Mario Albrecht, and Wladimir Il Tameling. 2006. ?Resistance Proteins: Molecular Switches of Plant Defence..? Current Opinion in Plant Biology 9 (4): 383?90. doi:10.1016/j.pbi.2006.05.009.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Takken,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Resistance Proteins: Molecular Switches of Plant Defence..â�?� Current Opinion in Plant Biology 9 (4): 383â�?�?90.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Resistance Proteins: Molecular Switches of Plant Defence..â�?� Current Opinion in Plant Biology 9 (4): 383â�?�?90.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Takken,&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Tang%2C Fang%2C Shengming Yang%2C Jinge Liu%2C and Hongyan Zhu%2E 2016%2E �??Rj4%2C a Gene Controlling Nodulation Specificity in Soybeans%2C Encodes a Thaumatin%2DLike Protein but Not the One Previously Reported%2E%2E�?� Plant Physiology 170 %281%29%3A 26�??32%2E doi%3A10%2E1104%2Fpp%2E15%2E01661%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tang, Fang, Shengming Yang, Jinge Liu, and Hongyan Zhu. 2016. ?Rj4, a Gene Controlling Nodulation Specificity in Soybeans, Encodes a Thaumatin-Like Protein but Not the One Previously Reported..? Plant Physiology 170 (1): 26?32. doi:10.1104/pp.15.01661.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tang,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tang,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Tanigaki%2C Yusuke%2C Kenji Ito%2C Yoshiyuki Obuchi%2C Akiko Kosaka%2C Katsuyuki T Yamato%2C Masahiro Okanami%2C Mikko T Lehtonen%2C Jari P T Valkonen%2C and Motomu Akita%2E 2014%2E �??Physcomitrella Patens Has Kinase%2DLRR R Gene Homologs and Interacting Proteins%2E%2E�?� PloS One 9 %284%29%3A e95118%2E doi%3A10%2E1371%2Fjournal%2Epone%2E0095118%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tanigaki, Yusuke, Kenji Ito, Yoshiyuki Obuchi, Akiko Kosaka, Katsuyuki T Yamato, Masahiro Okanami, Mikko T Lehtonen, Jari P T Valkonen, and Motomu Akita. 2014. ?Physcomitrella Patens Has Kinase-LRR R Gene Homologs and Interacting Proteins..? PloS One 9 (4): e95118. doi:10.1371/journal.pone.0095118.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tanigaki,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Physcomitrella Patens Has Kinase-LRR R Gene Homologs and Interacting Proteins..â�?� PloS One 9 (4): e95118.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Physcomitrella Patens Has Kinase-LRR R Gene Homologs and Interacting Proteins..â�?� PloS One 9 (4): e95118.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tanigaki,&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Tarr%2C D Ellen K%2C and Helen M Alexander%2E 2009%2E �??TIR%2DNBS%2DLRR Genes Are Rare in Monocots%3A Evidence From Diverse Monocot Orders%2E%2E�?� BMC Research Notes 2%3A 197%2E doi%3A10%2E1186%2F1756%2D0500%2D2%2D197%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tarr, D Ellen K, and Helen M Alexander. 2009. ?TIR-NBS-LRR Genes Are Rare in Monocots: Evidence From Diverse Monocot Orders..? BMC Research Notes 2: 197. doi:10.1186/1756-0500-2-197.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tarr,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?TIR-NBS-LRR Genes Are Rare in Monocots: Evidence From Diverse Monocot Orders&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?TIR-NBS-LRR Genes Are Rare in Monocots: Evidence From Diverse Monocot Orders&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tarr,&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Tirichine%2C Leïla%2C Haruko Imaizumi%2DAnraku%2C Satoko Yoshida%2C Yasuhiro Murakami%2C Lene H Madsen%2C Hiroki Miwa%2C Tomomi Nakagawa%2C et al%2E 2006%2E �??Deregulation of a Ca2%2B%2FCalmodulin%2DDependent Kinase Leads to Spontaneous Nodule Development%2E%2E�?� Nature 441 %287097%29%3A 1153�??56%2E doi%3A10%2E1038%2Fnature04862%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tirichine, Le�la, Haruko Imaizumi-Anraku, Satoko Yoshida, Yasuhiro Murakami, Lene H Madsen, Hiroki Miwa, Tomomi Nakagawa, et al. 2006. ?Deregulation of a Ca2+/Calmodulin-Dependent Kinase Leads to Spontaneous Nodule Development..? Nature 441 (7097): 1153?56. doi:10.1038/nature04862.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tirichine,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 1153â�?�?56.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tirichine,&as_ylo=7097&as_allsubj=all&hl=en&c2coff=1


Applied and Environmental Microbiology 79 (3): 1048–51. doi:10.1128/AEM.03297-12.Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Tsurumaru, H, T Yamakawa, and M Tanaka. 2008. “Tn 5 Mutants of Bradyrhizobium Japonicum Is-1 with Altered Compatibility with Rj 2-Soybean Cultivars.” Soil Science & Plant …. doi:10.1111/j.1747-0765.2007.00225.x.


Van Dam, N M, TOG Tytgat, and J A Kirkegaard. 2009. “Root and Shoot Glucosinolates: a Comparison of Their Diversity, Function andInteractions in Natural and Managed Ecosystems.” Phytochemistry Reviews. doi:10.1007/s11101-008-9101-9.


van der Biezen, E A, and J D Jones. 1998. “The NB-ARC Domain: a Novel Signalling Motif Shared by Plant Resistance Gene Productsand Regulators of Cell Death in Animals..” Current Biology : CB 8 (7): R226–27.

van Veen, Hans, Divya Vashisht, Melis Akman, Thomas Girke, Angelika Mustroph, Emilie Reinen, Sjon Hartman, et al. 2016.“Transcriptomes of Eight Arabidopsis Thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses toFlooding Stress..” Plant Physiology 172 (2): 668–89. doi:10.1104/pp.16.00472.


Vandenkoornhuyse, Philippe, Achim Quaiser, Marie Duhamel, Amandine Le Van, and Alexis Dufresne. 2015. “The Importance of theMicrobiome of the Plant Holobiont..” The New Phytologist 206 (4): 1196–1206. doi:10.1111/nph.13312.


Verdier, Jérôme, Ivone Torres-Jerez, Mingyi Wang, Andry Andriankaja, Stacy N Allen, Ji He, Yuhong Tang, Jeremy D Murray, andMichael K Udvardi. 2013. “Establishment of the Lotus Japonicus Gene Expression Atlas (LjGEA) and Its Use to Explore Legume SeedMaturation..” The Plant Journal : for Cell and Molecular Biology 74 (2): 351–62. doi:10.1111/tpj.12119.


Viprey, V, A Del Greco, W Golinowski, W J Broughton, and X Perret. 1998. “Symbiotic Implications of Type III Protein SecretionMachinery in Rhizobium..” Molecular Microbiology 28 (6): 1381–89.

Wang, Wei, Jinyoung Yang Barnaby, Yasuomi Tada, Hairi Li, Mahmut Tör, Daniela Caldelari, Dae-un Lee, Xiang-Dong Fu, and XinnianDong. 2011. “Timing of Plant Immune Responses by a Central Circadian Regulator..” Nature 470 (7332): 110–14.doi:10.1038/nature09766.


Xiao, S, S Ellwood, O Calis, E Patrick, T Li, M Coleman, and J G Turner. 2001. “Broad-Spectrum Mildew Resistance in ArabidopsisThaliana Mediated by RPW8..” Science (New York, NY) 291 (5501): 118–20. doi:10.1126/science.291.5501.118.


Xin, Da-Wei, Sha Liao, Zhi-Ping Xie, Dagmar R Hann, Lea Steinle, Thomas Boller, and Christian Staehelin. 2012. “Functional Analysis ofNopM, a Novel E3 Ubiquitin Ligase (NEL) Domain Effector of Rhizobium Sp. Strain NGR234..” PLoS Pathogens 8 (5): e1002707.doi:10.1371/journal.ppat.1002707.


Xin, Xiu-Fang, and Sheng Yang He. 2013. “Pseudomonas Syringae Pv. Tomato DC3000: a Model Pathogen for Probing DiseaseSusceptibility and Hormone Signaling in Plants..” Annual Review of Phytopathology 51: 473–98. doi:10.1146/annurev-phyto-082712-102321.


Xue, Jia-Yu, Yue Wang, Ping Wu, Qiang Wang, Le-Tian Yang, Xiao-Han Pan, Bin Wang, and Jian-Qun Chen. 2012. “A Primary Survey onBryophyte Species Reveals Two Novel Classes of Nucleotide-Binding Site (NBS) Genes..” PloS One 7 (5): e36700.doi:10.1371/journal.pone.0036700.

Pubmed: Author and TitleCrossRef: Author and Title www.plantphysiol.orgon October 14, 2020 - Published by Downloaded from


http://www.ncbi.nlm.nih.gov/pubmed?term=Tsukui%2C Takahiro%2C Shima Eda%2C Takakazu Kaneko%2C Shusei Sato%2C Shin Okazaki%2C Kaori Kakizaki%2DChiba%2C Manabu Itakura%2C et al%2E 2013%2E �??The Type III Secretion System of Bradyrhizobium Japonicum USDA122 Mediates Symbiotic Incompatibility with Rj2 Soybean Plants%2E%2E�?� Applied and Environmental Microbiology 79 %283%29%3A 1048�??51%2E doi%3A10%2E1128%2FAEM%2E03297%2D12%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tsukui, Takahiro, Shima Eda, Takakazu Kaneko, Shusei Sato, Shin Okazaki, Kaori Kakizaki-Chiba, Manabu Itakura, et al. 2013. ?The Type III Secretion System of Bradyrhizobium Japonicum USDA122 Mediates Symbiotic Incompatibility with Rj2 Soybean Plants..? Applied and Environmental Microbiology 79 (3): 1048?51. doi:10.1128/AEM.03297-12.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tsukui,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tsukui,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Tsurumaru%2C H%2C T Yamakawa%2C and M Tanaka%2E 2008%2E �??Tn 5 Mutants of Bradyrhizobium Japonicum Is%2D1 with Altered Compatibility with Rj 2%2DSoybean Cultivars%2E�?� Soil Science %26 Plant �?�%2E doi%3A10%2E1111%2Fj%2E1747%2D0765%2E2007%2E00225%2Ex%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tsurumaru, H, T Yamakawa, and M Tanaka. 2008. ?Tn 5 Mutants of Bradyrhizobium Japonicum Is-1 with Altered Compatibility with Rj 2-Soybean Cultivars.? Soil Science & Plant ?. doi:10.1111/j.1747-0765.2007.00225.x.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tsurumaru,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tsurumaru,&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Van Dam%2C N M%2C TOG Tytgat%2C and J A Kirkegaard%2E 2009%2E �??Root and Shoot Glucosinolates%3A a Comparison of Their Diversity%2C Function and Interactions in Natural and Managed Ecosystems%2E�?� Phytochemistry Reviews%2E doi%3A10%2E1007%2Fs11101%2D008%2D9101%2D9%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Van Dam, N M, TOG Tytgat, and J A Kirkegaard. 2009. ?Root and Shoot Glucosinolates: a Comparison of Their Diversity, Function and Interactions in Natural and Managed Ecosystems.? Phytochemistry Reviews. doi:10.1007/s11101-008-9101-9.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Van&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Van&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=van Veen%2C Hans%2C Divya Vashisht%2C Melis Akman%2C Thomas Girke%2C Angelika Mustroph%2C Emilie Reinen%2C Sjon Hartman%2C et al%2E 2016%2E �??Transcriptomes of Eight Arabidopsis Thaliana Accessions Reveal Core Conserved%2C Genotype%2D and Organ%2DSpecific Responses to Flooding Stress%2E%2E�?� Plant Physiology 172 %282%29%3A 668�??89%2E doi%3A10%2E1104%2Fpp%2E16%2E00472%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=van Veen, Hans, Divya Vashisht, Melis Akman, Thomas Girke, Angelika Mustroph, Emilie Reinen, Sjon Hartman, et al. 2016. ?Transcriptomes of Eight Arabidopsis Thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress..? Plant Physiology 172 (2): 668?89. doi:10.1104/pp.16.00472.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=van&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Transcriptomes of Eight Arabidopsis Thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress..â�?� Plant Physiology 172 (2): 668â�?�?89.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Transcriptomes of Eight Arabidopsis Thaliana Accessions Reveal Core Conserved, Genotype- and Organ-Specific Responses to Flooding Stress..â�?� Plant Physiology 172 (2): 668â�?�?89.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=van&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Vandenkoornhuyse%2C Philippe%2C Achim Quaiser%2C Marie Duhamel%2C Amandine Le Van%2C and Alexis Dufresne%2E 2015%2E �??The Importance of the Microbiome of the Plant Holobiont%2E%2E�?� The New Phytologist 206 %284%29%3A 1196�??1206%2E doi%3A10%2E1111%2Fnph%2E13312%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Vandenkoornhuyse, Philippe, Achim Quaiser, Marie Duhamel, Amandine Le Van, and Alexis Dufresne. 2015. ?The Importance of the Microbiome of the Plant Holobiont..? The New Phytologist 206 (4): 1196?1206. doi:10.1111/nph.13312.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Vandenkoornhuyse,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The Importance of the Microbiome of the Plant Holobiont..â�?� The New Phytologist 206 (4): 1196â�?�?1206.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?The Importance of the Microbiome of the Plant Holobiont..â�?� The New Phytologist 206 (4): 1196â�?�?1206.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Vandenkoornhuyse,&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Verdier%2C Jérôme%2C Ivone Torres%2DJerez%2C Mingyi Wang%2C Andry Andriankaja%2C Stacy N Allen%2C Ji He%2C Yuhong Tang%2C Jeremy D Murray%2C and Michael K Udvardi%2E 2013%2E �??Establishment of the Lotus Japonicus Gene Expression Atlas %28LjGEA%29 and Its Use to Explore Legume Seed Maturation%2E%2E�?� The Plant Journal %3A for Cell and Molecular Biology 74 %282%29%3A 351�??62%2E doi%3A10%2E1111%2Ftpj%2E12119%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Verdier, J�r�me, Ivone Torres-Jerez, Mingyi Wang, Andry Andriankaja, Stacy N Allen, Ji He, Yuhong Tang, Jeremy D Murray, and Michael K Udvardi. 2013. ?Establishment of the Lotus Japonicus Gene Expression Atlas (LjGEA) and Its Use to Explore Legume Seed Maturation..? The Plant Journal : for Cell and Molecular Biology 74 (2): 351?62. doi:10.1111/tpj.12119.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Verdier,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Establishment of the Lotus Japonicus Gene Expression Atlas (LjGEA) and Its Use to Explore Legume Seed Maturation..â�?� The Plant Journal : for Cell and Molecular Biology 74 (2): 351â�?�?62.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Establishment of the Lotus Japonicus Gene Expression Atlas (LjGEA) and Its Use to Explore Legume Seed Maturation..â�?� The Plant Journal : for Cell and Molecular Biology 74 (2): 351â�?�?62.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Verdier,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Wang%2C Wei%2C Jinyoung Yang Barnaby%2C Yasuomi Tada%2C Hairi Li%2C Mahmut Tör%2C Daniela Caldelari%2C Dae%2Dun Lee%2C Xiang%2DDong Fu%2C and Xinnian Dong%2E 2011%2E �??Timing of Plant Immune Responses by a Central Circadian Regulator%2E%2E�?� Nature 470 %287332%29%3A 110�??14%2E doi%3A10%2E1038%2Fnature09766%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Wang, Wei, Jinyoung Yang Barnaby, Yasuomi Tada, Hairi Li, Mahmut T�r, Daniela Caldelari, Dae-un Lee, Xiang-Dong Fu, and Xinnian Dong. 2011. ?Timing of Plant Immune Responses by a Central Circadian Regulator..? Nature 470 (7332): 110?14. doi:10.1038/nature09766.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wang,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 110â�?�?14.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang,&as_ylo=7332&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Xiao%2C S%2C S Ellwood%2C O Calis%2C E Patrick%2C T Li%2C M Coleman%2C and J G Turner%2E 2001%2E �??Broad%2DSpectrum Mildew Resistance in Arabidopsis Thaliana Mediated by RPW8%2E%2E�?� Science %28New York%2C NY%29 291 %285501%29%3A 118�??20%2E doi%3A10%2E1126%2Fscience%2E291%2E5501%2E118%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Xiao, S, S Ellwood, O Calis, E Patrick, T Li, M Coleman, and J G Turner. 2001. ?Broad-Spectrum Mildew Resistance in Arabidopsis Thaliana Mediated by RPW8..? Science (New York, NY) 291 (5501): 118?20. doi:10.1126/science.291.5501.118.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Xiao,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=: 118â�?�?20.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Xiao,&as_ylo=5501&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Xin%2C Da%2DWei%2C Sha Liao%2C Zhi%2DPing Xie%2C Dagmar R Hann%2C Lea Steinle%2C Thomas Boller%2C and Christian Staehelin%2E 2012%2E �??Functional Analysis of NopM%2C a Novel E3 Ubiquitin Ligase %28NEL%29 Domain Effector of Rhizobium Sp%2E Strain NGR234%2E%2E�?� PLoS Pathogens 8 %285%29%3A e1002707%2E doi%3A10%2E1371%2Fjournal%2Eppat%2E1002707%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Xin, Da-Wei, Sha Liao, Zhi-Ping Xie, Dagmar R Hann, Lea Steinle, Thomas Boller, and Christian Staehelin. 2012. ?Functional Analysis of NopM, a Novel E3 Ubiquitin Ligase (NEL) Domain Effector of Rhizobium Sp. Strain NGR234..? PLoS Pathogens 8 (5): e1002707. doi:10.1371/journal.ppat.1002707.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Xin,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Functional Analysis of NopM, a Novel E3 Ubiquitin Ligase (NEL) Domain Effector of Rhizobium Sp.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Functional Analysis of NopM, a Novel E3 Ubiquitin Ligase (NEL) Domain Effector of Rhizobium Sp.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Xin,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Xin%2C Xiu%2DFang%2C and Sheng Yang He%2E 2013%2E �??Pseudomonas Syringae Pv%2E Tomato DC3000%3A a Model Pathogen for Probing Disease Susceptibility and Hormone Signaling in Plants%2E%2E�?� Annual Review of Phytopathology 51%3A 473�??98%2E doi%3A10%2E1146%2Fannurev%2Dphyto%2D082712%2D102321%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Xin, Xiu-Fang, and Sheng Yang He. 2013. ?Pseudomonas Syringae Pv. Tomato DC3000: a Model Pathogen for Probing Disease Susceptibility and Hormone Signaling in Plants..? Annual Review of Phytopathology 51: 473?98. doi:10.1146/annurev-phyto-082712-102321.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Xin,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Pseudomonas Syringae Pv&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Pseudomonas Syringae Pv&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Xin,&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Xue%2C Jia%2DYu%2C Yue Wang%2C Ping Wu%2C Qiang Wang%2C Le%2DTian Yang%2C Xiao%2DHan Pan%2C Bin Wang%2C and Jian%2DQun Chen%2E 2012%2E �??A Primary Survey on Bryophyte Species Reveals Two Novel Classes of Nucleotide%2DBinding Site %28NBS%29 Genes%2E%2E�?� PloS One 7 %285%29%3A e36700%2E doi%3A10%2E1371%2Fjournal%2Epone%2E0036700%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Xue, Jia-Yu, Yue Wang, Ping Wu, Qiang Wang, Le-Tian Yang, Xiao-Han Pan, Bin Wang, and Jian-Qun Chen. 2012. ?A Primary Survey on Bryophyte Species Reveals Two Novel Classes of Nucleotide-Binding Site (NBS) Genes..? PloS One 7 (5): e36700. doi:10.1371/journal.pone.0036700.


Google Scholar: Author Only Title Only Author and Title

Yue, Jia-Xing, Blake C Meyers, Jian-Qun Chen, Dacheng Tian, and Sihai Yang. 2012. “Tracing the Origin and Evolutionary History ofPlant Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) Genes..” The New Phytologist 193 (4): 1049–63. doi:10.1111/j.1469-8137.2011.04006.x.


Zgadzaj, Rafal, Ruben Garrido-Oter, Dorthe Bodker Jensen, Anna Koprivova, Paul Schulze-Lefert, and Simona Radutoiu. 2016. “RootNodule Symbiosis in Lotus Japonicus Drives the Establishment of Distinctive Rhizosphere, Root, and Nodule Bacterial Communities..”Proceedings of the National Academy of Sciences of the United States of America 113 (49): E7996–E8005. doi:10.1073/pnas.1616564113


Zhai, J., Jeong, D.-H., De Paoli, E., Park, S., Rosen, B. D., Li, Y., et al. (2011). MicroRNAs as master regulators of the plant NB-LRRdefense gene family via the production of phased, trans-acting siRNAs. Genes & Development, 25(23), 2540–2553.http://doi.org/10.1101/gad.177527.111


Zhang, Ling, Xue-Jiao Chen, Huang-Bin Lu, Zhi-Ping Xie, and Christian Staehelin. 2011. “Functional Analysis of the Type 3 EffectorNodulation Outer Protein L (NopL) From Rhizobium Sp. NGR234: Symbiotic Effects, Phosphorylation, and Interference with Mitogen-Activated Protein Kinase Signaling..” Journal of Biological Chemistry 286 (37): 32178–87. doi:10.1074/jbc.M111.265942.


Zhang, Y., Xia, R., Kuang, H., & Meyers, B. C. (2016). The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution ofMicroRNAs That Target Them. Molecular Biology and Evolution, 33(10), 2692–2705. http://doi.org/10.1093/molbev/msw154



http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Xue,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?A Primary Survey on Bryophyte Species Reveals Two Novel Classes of Nucleotide-Binding Site (NBS) Genes..â�?� PloS One 7 (5): e36700.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?A Primary Survey on Bryophyte Species Reveals Two Novel Classes of Nucleotide-Binding Site (NBS) Genes..â�?� PloS One 7 (5): e36700.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Xue,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Yue%2C Jia%2DXing%2C Blake C Meyers%2C Jian%2DQun Chen%2C Dacheng Tian%2C and Sihai Yang%2E 2012%2E �??Tracing the Origin and Evolutionary History of Plant Nucleotide%2DBinding Site%2DLeucine%2DRich Repeat %28NBS%2DLRR%29 Genes%2E%2E�?� The New Phytologist 193 %284%29%3A 1049�??63%2E doi%3A10%2E1111%2Fj%2E1469%2D8137%2E2011%2E04006%2Ex%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Yue, Jia-Xing, Blake C Meyers, Jian-Qun Chen, Dacheng Tian, and Sihai Yang. 2012. ?Tracing the Origin and Evolutionary History of Plant Nucleotide-Binding Site-Leucine-Rich Repeat (NBS-LRR) Genes..? The New Phytologist 193 (4): 1049?63. doi:10.1111/j.1469-8137.2011.04006.x.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yue,&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yue,&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zgadzaj%2C Rafal%2C Ruben Garrido%2DOter%2C Dorthe Bodker Jensen%2C Anna Koprivova%2C Paul Schulze%2DLefert%2C and Simona Radutoiu%2E 2016%2E �??Root Nodule Symbiosis in Lotus Japonicus Drives the Establishment of Distinctive Rhizosphere%2C Root%2C and Nodule Bacterial Communities%2E%2E�?� Proceedings of the National Academy of Sciences of the United States of America 113 %2849%29%3A E7996�??E8005%2E doi%3A10%2E1073%2Fpnas%2E1616564113&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zgadzaj, Rafal, Ruben Garrido-Oter, Dorthe Bodker Jensen, Anna Koprivova, Paul Schulze-Lefert, and Simona Radutoiu. 2016. ?Root Nodule Symbiosis in Lotus Japonicus Drives the Establishment of Distinctive Rhizosphere, Root, and Nodule Bacterial Communities..? Proceedings of the National Academy of Sciences of the United States of America 113 (49): E7996?E8005. doi:10.1073/pnas.1616564113

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zgadzaj,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Root Nodule Symbiosis in Lotus Japonicus Drives the Establishment of Distinctive Rhizosphere, Root, and Nodule Bacterial Communities..â�?� Proceedings of the National Academy of Sciences of the United States of America 113 (49): E7996â�?�?E8005.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Root Nodule Symbiosis in Lotus Japonicus Drives the Establishment of Distinctive Rhizosphere, Root, and Nodule Bacterial Communities..â�?� Proceedings of the National Academy of Sciences of the United States of America 113 (49): E7996â�?�?E8005.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zgadzaj,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhai%2C J%2E%2C Jeong%2C D%2E%2DH%2E%2C De Paoli%2C E%2E%2C Park%2C S%2E%2C Rosen%2C B%2E D%2E%2C Li%2C Y%2E%2C et al%2E %282011%29%2E MicroRNAs as master regulators of the plant NB%2DLRR defense gene family via the production of phased%2C trans%2Dacting siRNAs%2E Genes %26 Development%2C 25%2823%29%2C 2540�??2553%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1101%2Fgad%2E177527%2E111&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhai, J., Jeong, D.-H., De Paoli, E., Park, S., Rosen, B. D., Li, Y., et al. (2011). MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes & Development, 25(23), 2540?2553. http://doi.org/10.1101/gad.177527.111

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhai,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhai,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhang%2C Ling%2C Xue%2DJiao Chen%2C Huang%2DBin Lu%2C Zhi%2DPing Xie%2C and Christian Staehelin%2E 2011%2E �??Functional Analysis of the Type 3 Effector Nodulation Outer Protein L %28NopL%29 From Rhizobium Sp%2E NGR234%3A Symbiotic Effects%2C Phosphorylation%2C and Interference with Mitogen%2DActivated Protein Kinase Signaling%2E%2E�?� Journal of Biological Chemistry 286 %2837%29%3A 32178�??87%2E doi%3A10%2E1074%2Fjbc%2EM111%2E265942%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhang, Ling, Xue-Jiao Chen, Huang-Bin Lu, Zhi-Ping Xie, and Christian Staehelin. 2011. ?Functional Analysis of the Type 3 Effector Nodulation Outer Protein L (NopL) From Rhizobium Sp. NGR234: Symbiotic Effects, Phosphorylation, and Interference with Mitogen-Activated Protein Kinase Signaling..? Journal of Biological Chemistry 286 (37): 32178?87. doi:10.1074/jbc.M111.265942.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhang,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Functional Analysis of the Type 3 Effector Nodulation Outer Protein L (NopL) From Rhizobium Sp&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=â�?�?Functional Analysis of the Type 3 Effector Nodulation Outer Protein L (NopL) From Rhizobium Sp&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang,&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zhang%2C Y%2E%2C Xia%2C R%2E%2C Kuang%2C H%2E%2C %26 Meyers%2C B%2E C%2E %282016%29%2E The Diversification of Plant NBS%2DLRR Defense Genes Directs the Evolution of MicroRNAs That Target Them%2E Molecular Biology and Evolution%2C 33%2810%29%2C 2692�??2705%2E http%3A%2F%2Fdoi%2Eorg%2F10%2E1093%2Fmolbev%2Fmsw154&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zhang, Y., Xia, R., Kuang, H., & Meyers, B. C. (2016). The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them. Molecular Biology and Evolution, 33(10), 2692?2705. http://doi.org/10.1093/molbev/msw154

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zhang,&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zhang,&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1


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