Phylogenomic Analysis Demonstrates a Pattern of Rare and Ancient
Horizontal Gene Transfer between Plants and Fungi
(Richards et al. 2009 Plant Cell)
8/27/2010
Bioinformatics & Genomics, Ph.D. Candidacy Exam
Bongsoo Park
OutlineOutlineIntroductionResults MethodsDiscussion
What is What is HHorizontal orizontal GGene ene TTransfer?ransfer?
vs Vertical Gene Transfer (reproduction)
HGT provides opportunities for rapid genome innovation.
Abundant in prokaryotes (e.g. transfer of antibiotic resistance genes among bacteria, metabolic capability of certain substrates as nutrient sources, etc.)
http://tolweb.org/tree/
Examples of HGTs in Examples of HGTs in EukaryotesEukaryotes
Plant Pathogen, Fusarium oxysporum (Li-Jun et al. Nature, 2010)
Pea Aphid, Acyrthosiphon pisum (Nancy A.M. Science, 2010)
‘Carotenoids’ biosynthesis genestransferred from fungi to an ancestor of aphids
Entire Lineage-specific Chromosomes transferred to another strain of F. oxysporum, making the recipient pathogenic to Tomato.
Fungi > Fungi Fungi > Insect
HGT Putative Functional Protein Annotation Direction of Transfer
1a L-Fucose permease, sugar transporter Fungi > Plant
1b Zinc binding alcohol dehydrogenase Plant > Fungi
1c Major facilitator superfamily, membrane transporter Fungi > Plant
2 Phospholipase/carboxylesterase family protein Fungi > Plant
3a iucA/iucC family protein, siderophore biosynthesis Fungi > Plant
3b Unknown/conserved hypothetical protein Fungi > Plant
4a DUF239 domain protein Plant > Fungi
4b Phosphate-responsive 1 family protein Plant > Fungi
4c Unknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) protein
Plant > Fungi
Table 2. Nine putative HGT candidate genes
Results
Arabidopsis thaliana (Arabidopsis)
Populus trichocarpa (Western poplar)
Oryza sativa (Rice)
Sorghum bicolor(Sorghum, edible grain)
Selaginella moellendorffii (spikemosses)
Physomitrella patens (Moss)
Total number of proteins
31,913 45,555 26,777 35,899 22,285 35,938
Top hit versus fungi 1,206 1,426 1,045 1,043 802 776
Top hit versus fungi excluding TEs
1,160 1,331 852 965 794 764
Table 1. Identification of Putative HGTs between Plants and Fungi for Phylogenetic Analyses
Fungi > PlantFungi > Plant
Plant > FungiPlant > Fungi
BLAST, OrthoMCL pipeline Phylogenomic analyses
Plants(Query)Plants
(Query)Fungi, Algae,
Protists, Animals, Prokaryotes
(Target)
Fungi, Algae, Protists, Animals,
Prokaryotes(Target)
BLASTp (e-value 10-20)(Plant-Fungi, the highest similarity)
BLASTp (e-value 10-20)(Plant-Fungi, the highest similarity)
6,298 protein
sequences
6,298 protein
sequences
5,586 protein sequences
5,586 protein sequences
Excluding TEs(Putative functional proteome)
Excluding TEs(Putative functional proteome)
1,689 groups Initial Screening
1,689 groups Initial Screening
RiceDB
RiceDB
3,177 Orthology
Groups
3,177 Orthology
Groups
4,866 sequence groups, Ready
4,866 sequence groups, Ready
4,866 sequence groups
4,866 sequence groups
Four evidencesFour evidences
Putative 9 HGT candidatesPutative 9 HGT candidates
3838GenBank NR
GenBank EST, TBestDB(Improve sampling)
GenBank NRGenBank EST, TBestDB
(Improve sampling)
3535
221
OrthoMCL(e-value 1e-20; inflation value 1.5)
OrthoMCL(e-value 1e-20; inflation value 1.5)
1414
Methods
PHYML, HGT like taxaPHYML, HGT like taxa
MrBayes, PHYML, RAxML, SH Test
MrBayes, PHYML, RAxML, SH Test
Target DBTarget DB
BLASTp (e-value 10-20)
BLASTp (e-value 10-20)
Fungi
Plants
Strong bootstrapvalues
Ascomycete fungi
Selaginella
Weak bootstrapvalues
11
22
Evidences
Alternative Topology Test(CONSEL)
Alternative Topology Test(CONSEL) SH (Shimodaria-Hasegawa)SH (Shimodaria-Hasegawa)
P-valueP-value
1
Bayesian PHYML RAxML SH test
L-Fucose permease, sugar transporterL-Fucose permease, sugar transporter
Fungi
Plants
Strong bootstrap values
A single fungal species
Plants specific Gene family
33
44
Evidences
Strong bootstrap values
Prokaryotes
HGT Based on a Prokaryote Tagged-Chain Transfer HypothesisHGT Based on a Prokaryote Tagged-Chain Transfer Hypothesis
Weak bootstrap values
3
Bayesian PHYML RAxML SH test
DUF(Domain of Unknown Function)DUF(Domain of Unknown Function)iucA/iucC family protein, siderophore biosynthesisiucA/iucC family protein, siderophore biosynthesis
3A : iucA/iucC family protein, 3A : iucA/iucC family protein, siderophore biosynthesissiderophore biosynthesisSiderophores are small, high-affinity
iron chelating compounds
Non-pathogenic Bacteria, iron-poor environment Fungi, obtaining siderophore biosynthesis
survival in iron-poor environment
Lycophyte (Selaginella moellendorffii)
4
4
Bayesian PHYML RAxML SH test
DUF(Domain of Unknown Function)
Phosphate-responsive 1 family protein
HGT Putative Functional Protein Annotation Direction of Transfer
1a L-Fucose permease, sugar transporter Fungi > Plant
1b Zinc binding alcohol dehydrogenase Plant > Fungi
1c Major facilitator superfamily, membrane transporter Fungi > Plant
2 Phospholipase/carboxylesterase family protein Fungi > Plant
3a iucA/iucC family protein, siderophore biosynthesis Fungi > Plant
3b Unknown/conserved hypothetical protein Fungi > Plant
4a DUF239 domain protein (Domain of Unknown function) Plant > Fungi
4b Phosphate-responsive 1 family protein Plant > Fungi
4c Unknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) protein
Plant > Fungi
Putative functional assignments
Discussion
AngiospermAngiosperm
LycophyteLycophyteBryophyteBryophyte
Chytridiomycota
ZygomyceteBasidiomycet
e
Ascomycete
Fig 8.
Taphrinomycotina
My perspectivesMy perspectives
Genome SamplingTransposable ElementsApplying this methods to detect HGTs
in Fungal and Oomycete pathogens
This research, however, is a pioneer project to invest the eukaryote HGT by using currently available resources and methods.
Thank You
Bioinformatics and Genomics, Ph.D. Candidacy Exam
Bongsoo Park
Supplementary Slides
Bioinformatics and Genomics, Ph.D. Candidacy Exam
Bongsoo Park
History of HGTHistory of HGT
First described in Japan in 1959, 1960◦ Transfer of antibiotic resistance between different
species of bacteria; bacillary dysenteryTsutomu Watanabe, Bacteriology Review (1963)
Known mechanisms of Known mechanisms of HGTHGTTransformation, introduction, uptake
and expression of foreign genetic material
Transduction, transmission by virusBacterial conjugation, cell-to-cell
contact
http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens http://en.wikipedia.org/wiki/Transduction_(genetics) http://en.wikipedia.org/wiki/Bacterial_conjugation
1
Bayesian
PHYML RAxML SH test
1
1
2 2
3
3
4
4
4
Gene appears unique to genome
Could not confirm vertical inheritance
Phylogeny suggests vertical inheritance
Taxon distribution of gene family suggests vertical inheritance
Transposable element
1A
L-fucose permease, sugar transporterPhpa(173818)
1B
Zinc binding alcohol dehydrogenaseBDEG_06896
Fig 7. Strong vertical inheritance
HGT Putative Functional Protein Annotation Direction of Transfer
GenBank Accession No.
Phylogeny construction
1a L-Fucose permease, sugar transporter Fungi > Plant EDQ83581 98 sequences and 341 length62 sequences and 349 length
1b Zinc binding alcohol dehydrogenase Plant > Fungi EDQ61140*
95 sequences and 207 length
1c Major facilitator superfamily, membrane transporter
Fungi > Plant EAU93280*
40 sequences and 354 length
2 Phospholipase/carboxylesterase family protein
Fungi > Plant XP_389330*
122 sequences and 158 length62 sequences and 349 length
3a iucA/iucC family protein, siderophore biosynthesis
Fungi > Plant EDR08700*
44 sequences and 218 length15 sequences and 262 length
3b Unknown/conserved hypothetical protein Fungi > Plant EDQ68642 55 sequences and 174 length34 sequences and 247 length
4a DUF239 domain protein Plant > Fungi EDR02747 87 sequences and 210 length
4b Phosphate-responsive 1 family protein Plant > Fungi ABK92591*
93 sequences and 198 length
4c Unknown/conserved hypothetical protein with similarity to zinc finger (C2H2-type) protein
Plant > Fungi EDN23584 13 sequences and 222 length
GenBank accession numbers of transferred genes are given, and the asterisks indicate accession numbers of the closest BLAST hit in GenBank to the HGT, rather than that of the recipient gene
Table 1. Nine putative HGT candidate genes
Challenging QuestionsChallenging Questions
How long ago HGT processes occurred?DNA move back and forth between
donors and recipients?How environmental factors (light,
water, temperature, pH) affect the gene transfers?
Any new mechanisms of transfer?How transferred genes can be fixed in a
population successfully?
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