• Home

  • Documents

  • An expanded phylogeny for the genus Phytophthora
44
ARTICLE 355 © 2017 International Mycological Association You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. VOLUME 8 · NO. 2 INTRODUCTION The genus Phytophthora has had profound impacts on human history by causing agriculturally and ecologically important plant diseases (Erwin & Ribeiro 1996). Among the most notorious Phytophthora species is P. infestans, cause of the late blight disease, which was the primary cause of the Irish potato famine from 1845 to 1852 in which approximately one million people died and 1.5 million emigrated from Ireland (Turner 2005). Another example is the sudden oak death pathogen, P. ramorum, that has killed millions of coast live oak, tanoak and Japanese larch trees, and has permanently altered the forest ecosystems in California and Oregon, USA (Goheen et al. 2002, Rizzo et al. 2002, Rizzo et al. 2005). Other species, such as P. cinnamomi, P. nicotianae, and P. sojae, can also cause highly destructive plant diseases (Erwin & Ribeiro 1996). The impact caused by Phytophthora species has continued to increase with the emergence of new pathogens and diseases. The number of species known in the genus has doubled during the past decade due to extensive surveys in previously unexplored ecosystems such as natural forests (Jung et al. 2011, 2017, Rea et al. 2010, Reeser et al. 2013, Vettraino et al. 2011), streams (Bezuidenhout et al. 2010, Brazee et al. 2017, Reeser et al. 2007, Yang et al. 2016), riparian ecosystems (Brasier et al. 2003a, 2004, Hansen et al. 2012), and irrigation systems (Hong et al. 2010, 2012, Yang et al. 2014a, b). The total number of formally named species in the genus was about 58 in 1996 (Erwin & Ribeiro 1996), but now is more than 150. In addition, some provisionally or informally named species are also expected to be formally described in the near future. A sound taxonomic system is foundational for correctly identifying Phytophthora species and safeguarding agriculture, forestry, and natural ecosystems. Traditionally, taxonomy of the genus was based on morphological characters. A fundamental morphology-based classification of Phytophthora species was established by Waterhouse (1963) who classified the species into six groups based on the morphology of sporangia, homothallism, and configuration of antheridia. However, plasticity in morphological characters amongst isolates of individual species is significant, so is homology or homoplasy among different species. For example, isolates of P. constricta (Rea et al. 2011), P. gibbosa (Jung et al. 2011), P. lateralis (Kroon et al. 2012), P. mississippiae (Yang et al. 2013), and P. multivesiculata (Ilieva et al. 1998) all produce a mixture of semi-papillate and non-papillate sporangia. Many non-papillate species recovered from irrigation water such as Phytophthora hydropathica (Hong et al. 2010) and P. irrigata (Hong et al. 2008) were morphologically inseparable from P. drechsleri, while sequence analyses demonstrated that they are distinct species. Also, production of many morphological structures and physiological features needs specific environmental conditions, while observation of these features requires substantial training and expertise. Difficulty in obtaining important morphological data can impair accurate species identification. With the advent of DNA sequencing, the taxonomic concept for the genus has evolved from morphology to molecular phylogeny-based (Blair et al. 2008, Cooke et al. 2000, Kroon et al. 2004, Lara & Belbahri 2011, Martin et al. 2014, Martin & Tooley 2003, Robideau et al. 2011, Villa et al. 2006). In particular, the availability of whole genome doi:10.5598/imafungus.2017.08.02.09 IMA FUNGUS · 8(2): 355–384 (2017) An expanded phylogeny for the genus Phytophthora Xiao Yang 1 , Brett M. Tyler 2 , and Chuanxue Hong 1 1 Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA; corresponding author e-mail: [email protected] 2 Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA Abstract: A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species. Article info: Submitted: 8 June 2017; Accepted: 31 October 2017; Published: 21 November 2017. Key words: oomycetes systematics taxonomy evolution plant pathology

An expanded phylogeny for the genus Phytophthora

  • Upload
    others

  • View
    2

  • Download
    0

Embed Size (px)

Citation preview

Page 1: An expanded phylogeny for the genus Phytophthora

ARTIC

LE

355

© 2017 International Mycological Association

You are free to share - to copy, distribute and transmit the work, under the following conditions:Attribution: Youmustattributetheworkinthemannerspecifiedbytheauthororlicensor(butnotinanywaythatsuggeststhattheyendorseyouoryouruseofthework). Non-commercial: Youmaynotusethisworkforcommercialpurposes.No derivative works: Youmaynotalter,transform,orbuilduponthiswork.For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights.

V O L U M E 8 · N O . 2

INTRODUCTION

The genus Phytophthora has had profound impacts on human history by causing agriculturally and ecologically important plant diseases (Erwin & Ribeiro 1996). Among the most notorious Phytophthora species is P. infestans, cause of the late blight disease, which was the primary cause of the Irish potato famine from 1845 to 1852 in which approximately one million people died and 1.5 million emigrated from Ireland (Turner 2005). Another example is the sudden oak death pathogen, P. ramorum, that has killed millions of coast live oak, tanoak and Japanese larch trees, and has permanently altered the forest ecosystems in California and Oregon, USA (Goheen et al. 2002, Rizzo et al. 2002, Rizzo et al. 2005). Other species, such as P. cinnamomi, P. nicotianae, and P. sojae, can also cause highly destructive plant diseases (Erwin & Ribeiro 1996). The impact caused by Phytophthora species has continued to increase with the emergence of new pathogens and diseases. The number of species known in the genus has doubled during the past decade due to extensive surveys in previously unexplored ecosystems such as natural forests (Jung et al. 2011, 2017, Rea et al. 2010, Reeser et al. 2013, Vettraino et al. 2011), streams (Bezuidenhout et al. 2010, Brazee et al. 2017, Reeser et al. 2007, Yang et al. 2016), riparian ecosystems (Brasier et al. 2003a, 2004, Hansen et al. 2012), and irrigation systems (Hong et al. 2010, 2012, Yang et al. 2014a, b). The total number of formally named species in the genus was about 58 in 1996 (Erwin & Ribeiro 1996), but now is more than 150. In addition, some provisionally or informally named species are also expected to be formally described in the near future.

A sound taxonomic system is foundational for correctly identifying Phytophthora species and safeguarding agriculture, forestry, and natural ecosystems. Traditionally, taxonomy of the genus was based on morphological characters. A fundamental morphology-based classification of Phytophthora species was established by Waterhouse (1963) who classified the species into six groups based on the morphology of sporangia, homothallism, and configuration of antheridia. However, plasticity in morphological characters amongst isolates of individual species is significant, so is homology or homoplasy among different species. For example, isolates of P. constricta (Rea et al. 2011), P. gibbosa (Jung et al. 2011), P. lateralis (Kroon et al. 2012), P. mississippiae (Yang et al. 2013), and P. multivesiculata (Ilieva et al. 1998) all produce a mixture of semi-papillate and non-papillate sporangia. Many non-papillate species recovered from irrigation water such as Phytophthora hydropathica (Hong et al. 2010) and P. irrigata (Hong et al. 2008) were morphologically inseparable from P. drechsleri, while sequence analyses demonstrated that they are distinct species. Also, production of many morphological structures and physiological features needs specific environmental conditions, while observation of these features requires substantial training and expertise. Difficulty in obtaining important morphological data can impair accurate species identification.

With the advent of DNA sequencing, the taxonomic concept for the genus has evolved from morphology to molecular phylogeny-based (Blair et al. 2008, Cooke et al. 2000, Kroon et al. 2004, Lara & Belbahri 2011, Martin et al. 2014, Martin & Tooley 2003, Robideau et al. 2011, Villa et al. 2006). In particular, the availability of whole genome

doi:10.5598/imafungus.2017.08.02.09IMA FUNGUS · 8(2): 355–384 (2017)

An expanded phylogeny for the genus PhytophthoraXiao Yang1, Brett M. Tyler2, and Chuanxue Hong1

1Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA 23455, USA; corresponding author e-mail: [email protected] 2Center for Genome Research and Biocomputing, and Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA

Abstract: A comprehensive phylogeny representing 142 described and 43 provisionally named Phytophthora species is reported here for this rapidly expanding genus. This phylogeny features signature sequences of 114 ex-types and numerous authentic isolates that were designated as representative isolates by the originators of the respective species. Multiple new subclades were assigned in clades 2, 6, 7, and 9. A single species P. lilii was placed basal to clades 1 to 5, and 7. Phytophthora stricta was placed basal to other clade 8 species, P. asparagi to clade 6 and P. intercalaris to clade 10. On the basis of this phylogeny and ancestral state reconstructions, new hypotheses were proposed for the evolutionary history of sporangial papillation of Phytophthora species. Non-papillate ancestral Phytophthora species were inferred to evolve through separate evolutionary paths to either papillate or semi-papillate species.

Article info: Submitted: 8 June 2017; Accepted: 31 October 2017; Published: 21 November 2017.

Key words: oomycetessystematicstaxonomyevolutionplant pathology

Page 2: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

356 I M A F U N G U S

sequences from P. sojae, P. ramorum (Tyler et al. 2006) and P. infestans (Haas et al. 2009) enabled the identification of genetic markers useful for multi-locus phylogenies (Blair et al. 2008).

Cooke et al. (2000) developed the first molecular phylogeny for the genus by analyzing sequences of the internal transcribed spacer region (ITS) of 51 species. Kroon et al. (2004) constructed a phylogeny based on sequences of four nuclear and mitochondrial genes of 48 species, and Blair et al. (2008) produced a sophisticated phylogeny based on sequences of seven nuclear genetic markers. That multi-locus phylogeny divided 82 Phytophthora species into 10 phylogenetically well-supported clades. Martin et al. (2014) analyzed sequences of seven nuclear and four mitochondrial genes of 90 formally named and 17 provisional species and provided phylogenies including 10 clades, almost identical to that of Blair et al. (2008), except that P. quercina and P. sp. ohioensis were excluded from clade 4 and grouped into a potentially new clade.

A comprehensive molecular phylogeny is required to understanding the evolution of Phytophthora species. Although discordance has been found between the molecular phylogeny and the morphology-based taxonomy (Cooke et al. 2000, Ersek & Ribeiro 2010), correlations have been observed between molecular phylogenies and individual morphological and physiological traits. Recent studies indicated that species in individual clades or subclades are mostly identical in sporangial papillation, and optimum and maximum growth temperatures (Cooke et al. 2000, Kroon et al. 2012, Martin et al. 2012, Yang 2014). However, there was limited to no correlation between phylogeny and the morphology of sexual organs, such as antheridial configuration (Cooke et al. 2000, Kroon et al. 2012, Martin et al. 2012, Yang 2014). These studies have implied that divergence in sporangial morphology and variation in environmental specialization may be the keys in the evolutionary history of Phytophthora species. Nevertheless, these hypotheses need to be further tested and the exact evolutionary history of the genus Phytophthora warranted more investigation.

In this study, an expanded phylogeny, including more than 180 Phytophthora taxa, many not included in any previous phylogeny, was constructed. Sequences of seven nuclear genetic markers were used for construction of the phylogeny. In light of this phylogeny, ancestral state reconstructions were conducted on the sporangial papillation of Phytophthora species. Important evolutionary divergence events and associated changes in the sporangial morphology of Phytophthora species are discussed.

MATERIALS AND METHODS

Isolate selection A total of 376 Phytophthora isolates representing 142 described and 43 provisionally named species, plus one isolate of each Elongisporangium undulatum (basionym: Pythium undulatum), Halophytophthora fluviatilis, and Phytopythium vexans (basionym: Pythium vexans) as outgroup taxa were included (Table 1). These included 114 ex-types (Table 2). Also included were 164 authentic isolates

that were designated as representative isolates by the originators of the respective species names (Table 1). The majority of these isolates were provided by the originators of the respective species, while the rest were purchased from the Westerdijk Fungal Biodiversity Institute (CBS), Utrecht, The Netherlands.

DNA extraction To extract genomic DNA (gDNA), an approximately 5 × 5 mm culture plug of each isolate was taken from the actively growing area of a fresh culture. This was then grown in 20 % clarified V8 broth (lima bean broth for growing a P. infestans isolate 27A8) at room temperature (ca. 23 °C) for 7–14 d to produce a mycelial mass. The mass was then blot-dried using sterile tissue paper and then lysed in liquid nitrogen or using a FastPrep®-24 system (MP Biomedicals, Santa Ana, CA). gDNA was extracted using the DNeasy® Plant Mini kit (Qiagen, Valencia, CA) or the Maxwell® Plant DNA kit in combination with a Maxwell® Rapid Sample Concentrator (Promega, Madison, WI).

DNA amplification and sequencing A set of primers for seven genetic markers were used for DNA amplification including 60S Ribosomal protein L10 (60S), beta-tubulin (Btub), elongation factor 1 alpha (EF1α), enolase (Enl), heat shock protein 90 (HSP90), 28S ribosomal DNA (28S), and tigA gene fusion protein (TigA) as indicated in Blair et al. (2008). PCR reaction mixtures were prepared with the Takara Taq DNA polymerase (Takara Shuzo, Shiga, Japan) according to the manufacturer’s instructions. The PCR cycling protocol was the same as indicated by Blair et al. (2008), except that the Eppendorf® Mastercycler® Pro thermal cycler (Eppendorf, Hamburg) was used in this study. All PCR products were evaluated for successful amplification using agarose gel electrophoresis. Unsuccessful PCR amplifications were repeated using a modified protocol to attempt successful amplifications by optimizing annealing temperature using gradient PCR (typically with lower annealing temperatures) or using the GoTaq® Flexi DNA Polymerase (Promega, Madison, WI) PCR mixture system.

Prior to sequencing, excess primer and dNTPs were removed from successful PCR products with shrimp alkaline phosphatase and exonuclease I (USB Catalog # 70092Y and 70073Z). One unit of each enzyme was added to 15 µL PCR product, incubated at 37 °C for 30 min, followed by heat inactivation at 65 °C for 15 min. Sequencing was performed with both amplifying primers as well as internal primers, if any, for individual genetic markers at the University of Kentucky Advanced Genetic Technologies Center (Lexington, KY). Derived sequencing files were visualized with FinchTV version 1.4.0 (Geospiza, Seattle, WA). Sequences of each isolate with all primers for individual genetic markers were aligned with Clustal W (Larkin et al. 2007) and edited manually to correct obvious sequencing errors and code ambiguous sites according to the International Union of Pure and Applied Chemistry (IUPAC) nucleotide ambiguity codes to produce a consensus sequence. All sequences produced in this study have been deposited in GenBank (Supplementary Table 1).

Among 379 isolates (including three isolates of the outgroup taxa) in the following phylogenetic analyses,

Page 3: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

357V O L U M E 8 · N O . 2

Tabl

e 1.

Info

rmat

ion

rega

rdin

g is

olat

es u

sed

in th

is s

tudy

. Gen

Ban

k ac

cess

ion

num

bers

are

list

ed in

Tab

le S

1.

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar1a

P. c

acto

rum

P22

E6

P10

194

p25

Rho

dode

ndro

n sp

.O

hio,

US

An.

a.f

(Sch

röte

r 188

6)22

E7

1669

321

168

P07

15p6

n.a.

UK

n.a.

22E

816

694,

MYA

-365

350

470

P10

193

p7M

alus

sp.

Zim

babw

en.

a.P.

hed

raia

ndra

P33

F3M

YA-4

165

p225

Rho

dode

ndro

n sp

.M

inne

sota

, US

A20

02(d

e C

ock

&

Léve

sque

200

4)38

C2

Irrig

atio

n w

ater

Virg

inia

, US

A20

0662

A5

1117

25P

1952

3T

Vibu

rnum

sp.

The

Net

herla

nds

2001

P. id

aei

P34

D4

971.

95M

YA-4

065

3137

28P

6767

p220

TR

ubus

idae

us

Sco

tland

, UK

1987

(Ken

nedy

&

Dun

can

1995

)62

A1

968.

95A

Rub

us id

aeus

S

cotla

nd, U

K19

85P.

pse

udot

suga

eP

5293

833

1662

P10

339

TP

send

otsu

ga m

enzi

esii

Ore

gon,

US

A n.

a.(H

amm

& H

anse

n 19

83)

P. a

ff. h

edra

iand

raP

33F4

p226

Rho

dode

ndro

n sp

.M

inne

sota

, US

A20

03n.

a.P.

aff.

pse

udot

suga

eP

29B

3p1

85A

Pse

ndot

suga

men

zies

ii O

rego

n, U

SA

1975

n.a.

1bP.

cla

ndes

tina

P32

G1

347.

8658

713,

604

3827

8933

P39

43p2

00T

Trifo

lium

sub

terr

aneu

m

Aus

tralia

1985

(Tay

lor e

t al.

1985

)33

D8

MYA

-406

428

7317

p215

ATr

ifoliu

m s

ubte

rran

eaA

ustra

lia19

8538

D4

p304

n.a.

Aus

tralia

n.a.

P. ir

anic

aP

61J4

374.

7260

237

1589

64P

3882

p218

TS

olan

um m

elon

gena

Iran

1969

(Ers

had

1971

)P.

tent

acul

ata

P29

F255

2.96

P84

97A

Chr

ysan

them

um

leuc

anth

emum

Ger

man

yn.

a.(K

röbe

r & M

arw

itz

1993

)30

D5

Bac

opa

sp.

The

Net

herla

nds

2004

30G

8M

YA-3

655

Arg

yran

them

um

frute

scen

sG

erm

any

2004

1cP.

and

ina

SP

60A

2p4

60A

Sol

anum

bet

aceu

mE

cuad

orn.

a.(O

liva

et a

l. 20

10)

60A

3p4

61A

Sol

anum

bet

aceu

mE

cuad

orn.

a.P

1336

5T

Sol

anum

bre

vifo

lium

E

cuad

or20

01P.

infe

stan

sS

P27

A8

Sol

anum

tube

rosu

mM

exic

o19

92(D

e B

ary

1876

)P

1065

0S

olan

um tu

bero

sum

M

exic

on.

a.P.

ipom

oeae

SP

31B

4P

1022

6A

Ipom

oea

long

iped

uncu

lata

Mex

ico

n.a.

(Flie

r et a

l. 20

02)

31B

510

9229

P10

225

TIp

omoe

a lo

ngip

edun

cula

taM

exic

o19

99

31B

6P

1022

7A

Ipom

oea

long

iped

uncu

lata

Mex

ico

n.a.

P. m

irabi

lisS

P30

C1

6406

9, M

YA-4

062

P30

06p1

45A

Mira

bilis

jala

paM

exic

on.

a.(G

alin

do-A

& H

ohl

1985

)30

C2

6407

0, M

YA-4

063

P30

07p1

53A

Mira

bilis

jala

paM

exic

on.

a.P.

pha

seol

iS

P23

B4

p106

Pha

seol

us lu

natu

sD

elaw

are,

US

A20

00(T

haxt

er 1

889)

35B

6P

hase

olus

sp.

D

elaw

are,

US

A20

00P

1014

5P

hase

olus

luna

tus

Del

awar

e, U

SA

n.a.

P10

150

Pha

seol

us lu

natu

sD

elaw

are,

US

An.

a.

Page 4: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

358 I M A F U N G U S

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar1

P. n

icot

iana

eP

22F9

1541

0, M

YA-4

037

p23

Nic

otia

na ta

bacu

mN

orth

Car

olin

a,

US

An.

a.(B

reda

de

Haa

n 18

96)

22G

115

409,

MYA

-403

6p2

2N

icot

iana

taba

cum

Nor

th C

arol

ina,

U

SA

n.a.

P10

116

Met

rosi

dero

s ex

cels

aC

alifo

rnia

, US

A20

02P

1452

Citr

us s

p.

Cal

iforn

ia, U

SA

n.a.

2aP.

bot

ryos

aP

22H

8M

YA-4

059

p44

Hea

vae

sp.

Thai

land

n.a.

(Che

e 19

69)

46C

226

481

p384

AH

evea

bra

silie

nsis

Thai

land

n.a.

62C

658

1.69

1369

15P

3425

TH

evea

bra

silie

nsis

Mal

aysi

a19

6613

0422

P69

45H

evea

bra

silie

nsis

Mal

aysi

a19

86P.

citr

opht

hora

P03

E5

p132

Irrig

atio

n w

ater

Virg

inia

, US

A20

00(S

mith

& S

mith

19

06)

26H

3p3

1n.

a.n.

a.n.

a.P.

col

ocas

iae

SP

22F8

MYA

-415

9p4

7C

oloc

asia

esc

ulen

tan.

a.19

92(R

acib

orsk

i 190

0)35

D3

p276

Col

ocas

ia e

scul

enta

Haw

aii,

US

A20

05P.

him

alsi

lva

P61

G2

1287

67T

Que

rcus

le

ucot

ricop

hora

Nep

al20

05(V

ettra

ino

et a

l. 20

11)

61G

312

8753

AQ

uerc

us

leuc

otric

opho

raN

epal

2005

P. m

eadi

iP

22G

5M

YA-4

043

p75

Citr

us s

p.

Indi

a19

92(M

cRae

191

8)61

J921

9.88

1291

85H

evea

bra

silie

nsis

Indi

a19

87P.

occ

ulta

nsS

P65

B9

1015

57T

Bux

us s

empe

rvire

nsTh

e N

ethe

rland

s19

98(M

an In

’t Ve

ld e

t al

. 201

5)P.

term

inal

isS

P65

B8

1338

65T

Pac

hysa

ndra

term

inal

isTh

e N

ethe

rland

s20

10(M

an In

’t Ve

ld e

t al

. 201

5)P.

aff.

citr

opht

hora

P26

H4

p32

An.

a.n.

a.n.

a.n.

a.34

2898

P10

341

AS

yrin

ga s

p.E

ngla

nd, U

K19

90P.

aff.

him

alsi

lva

P61

G4

1287

54A

Cas

tano

psis

sp.

Nep

al20

05n.

a.P.

sp.

46C

3n.

a.46

C3

6676

7P

6713

p385

AH

evea

bra

silie

nsis

Mal

aysi

an.

a.n.

a.P.

sp.

P62

62n.

a.P

6262

AH

evea

bra

silie

nsis

Indi

an.

a.n.

a.P.

sp.

P63

10n.

a.P

6310

ATh

eobr

oma

caca

oIn

done

sia

n.a.

n.a.

2bP.

cap

sici

P22

F415

399,

MYA

-403

4p8

AC

apsi

cum

ann

umN

ew M

exic

o,

US

A19

48(L

eoni

an 1

922)

4601

2P

0253

Theo

brom

a ca

cao

Mex

ico

1964

1216

56P

1038

6C

ucum

is s

ativ

usM

ichi

gan,

US

A19

97P.

glo

vera

SP

31E

5p1

67A

Nic

otia

na ta

bacu

mB

razi

ln.

a.(A

bad

et a

l. 20

11)

62B

412

1969

P11

685

TN

icot

iana

taba

cum

Bra

zil

1995

P. m

enge

iS

P42

B2

MYA

-455

4p3

40T

Per

sea

amer

ican

aC

alifo

rnia

, US

An.

a.(H

ong

et a

l. 20

09)

42B

3M

YA-4

555

p341

AP

erse

a am

eric

ana

Cal

iforn

ia, U

SA

n.a.

P. m

exic

ana

P45

G4

554.

8846

731

9255

0P

0646

p355

Sol

anum

lyco

pers

icum

Arg

entin

an.

a.(H

otso

n &

Har

tge

1923

)

Page 5: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

359V O L U M E 8 · N O . 2

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

arP.

sis

kiyo

uens

isS

P41

B7

1227

79M

YA-4

187

P15

122

TS

tream

wat

erO

rego

n, U

SA

2003

(Ree

ser e

t al.

2007

)41

B8

AS

oil

Ore

gon,

US

A 20

03P.

trop

ical

isP

22H

5p2

7 Va

nila

sp.

Tahi

tin.

a.(A

raga

ki &

Uch

ida

2001

)35

C8

434.

9176

651,

MYA

-421

8p2

72T

Mac

adam

ia in

tegr

ifolia

Haw

aii,

US

An.

a.P.

aff.

cap

sici

P22

F515

427,

MYA

-403

5p9

Nic

otia

na ta

bacu

mN

orth

Car

olin

a,

US

An.

a.n.

a.

P. s

p. b

rasi

liens

isn.

a.46

705

P06

30A

Theo

brom

a ca

cao

Bra

zil

1969

(Oud

eman

s &

C

offe

y 19

91)

2cP.

ace

rina

SP

61H

113

3931

TA

cer p

seud

opla

tanu

sIta

ly20

10(G

inet

ti et

al.

2014

)61

H2

AS

oil

Italy

2010

P. c

apen

sis

SP

62C

112

8319

P18

19T

Cur

tisia

den

tata

Sou

th A

frica

n.a.

(Bez

uide

nhou

t et

al. 2

010)

62C

212

8320

P18

22A

Stre

am w

ater

S

outh

Afri

can.

a.62

C3

1283

21P

1823

AO

lea

cam

pens

isS

outh

Afri

ca19

86P.

citr

icol

aS

P33

H8

221.

8860

440

2117

3P

0716

p3

96T

Citr

us s

inen

sis

Taiw

an19

87(S

awad

a 19

27)

33J2

295.

29p3

75A

Citr

us s

p.Ja

pan

1929

P. m

ultiv

ora

SP

55C

512

4094

TS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2007

(Sco

tt et

al.

2009

)

P. p

achy

pleu

raS

P61

H6

AS

oil

UK

2006

(Hen

ricot

et a

l. 20

14)

61H

750

2404

TA

cuba

japo

nica

UK

2008

61H

8A

Soi

lU

K20

09P.

pin

iS

P22

F1M

YA-3

656

p53

AR

hodo

dend

ron

sp.

Wes

t Virg

inia

, U

SA

1987

(Hon

g et

al.

2011

)

45F1

6453

2p3

43T

Pin

us re

sino

saM

inne

sota

, US

A19

25P.

plu

rivor

aS

P22

E9

MYA

-365

7p1

01K

alm

ia la

tifol

iaW

este

rn

Aus

tralia

, A

ustra

lia

1998

(Jun

g &

Bur

gess

20

09)

22F2

p52

Rho

dode

ndro

n sp

. cv.

“O

lga

Mez

itt”

New

Yor

k, U

SA

n.a.

33H

937

9.61

Rho

dode

ndro

n sp

.G

erm

any

1958

P. s

p. 2

2F3

SP

22F3

p33

An.

a.O

hio,

US

An.

a.n.

a.P.

sp.

28D

1S

P28

D1

p119

AFa

gus

sylv

atic

aN

ew Y

ork,

US

An.

a.n.

a.28

D3

p121

AFa

gus

sylv

atic

aN

ew Y

ork,

US

An.

a.P.

sp.

citr

icol

a VI

IIS

P27

D9

AU

nide

ntifi

ed le

afH

aina

n, C

hina

n.a.

n.a.

P. s

p. p

ini-l

ike

SP

56G

1A

Taxu

s sp

.P

enns

ylva

nia,

U

SA

2011

n.a.

P. ta

xon

emza

nsi

SP

61F2

AA

gath

osm

a be

tulin

aS

outh

Afri

ca20

05(B

ezui

denh

out e

t al

. 201

0)

Page 6: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

360 I M A F U N G U S

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar61

F3A

Aga

thos

ma

betu

lina

Sou

th A

frica

2005

2dP.

bis

heria

SP

29D

2R

ubus

idae

us c

v.

Can

byW

isco

nsin

, US

A19

89(A

bad

et a

l. 20

08)

31E

612

2081

P10

117

TFr

agar

ia ×

anan

assa

Nor

th C

arol

ina,

U

SA

1999

P16

20R

hodo

dend

ron

sp.

Nor

th C

arol

ina,

U

SA

n.a.

P. e

long

ata

SP

33J3

An.

a.A

ustra

lia19

95(R

ea e

t al.

2010

)33

J4A

n.a.

Aus

tralia

1995

55C

412

5799

TS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2004

P. fr

igid

aP

47G

6A

Euc

alyp

tus

smith

iS

outh

Afri

can.

a.(M

asek

o et

al.

2007

)47

G7

AE

ucal

yptu

s sm

ithi

Sou

th A

frica

n.a.

47G

8T

Euc

alyp

tus

smith

iS

outh

Afri

ca20

012e

P. m

ultiv

esic

ulat

aS

P to

NP

29E

354

5.96

P10

410

TC

ymbi

dium

sp.

The

Net

herla

nds

n.a.

(Ilie

va e

t al.

1998

)30

D4

AC

ymbi

dium

sp.

The

Net

herla

nds

n.a.

P. ta

xon

aqua

tilis

SP

38J5

MYA

-457

7A

Stre

am w

ater

Virg

inia

, US

A20

06(H

ong

et a

l. 20

12)

3P.

ilic

isS

P23

A7

5661

5, M

YA-3

897

P39

39p1

13Ile

x sp

. C

anad

an.

a.(B

udde

nhag

en &

Yo

ung

1957

)34

D6

Que

rcus

sp.

Ger

man

y19

9962

A7

1143

48T

Ilex

aqui

foliu

mTh

e N

ethe

rland

sn.

a.P.

nem

oros

aS

P28

J3M

YA-4

061

p141

Um

bellu

laria

cal

iforn

ica

Cal

iforn

ia, U

SA

n.a.

(Han

sen

et a

l. 20

03)

41C

4M

YA-2

948

p320

TLi

thoc

arpu

s de

nsifl

orus

Cal

iforn

ia, U

SA

n.a.

P. p

luvi

alis

SP

60B

3M

YA-4

930

TR

ainw

ater

Ore

gon,

US

A 20

08(R

eese

r et a

l. 20

13)

P. p

seud

osyr

inga

eS

P30

A8

1117

72M

YA-4

222

p284

TQ

uerc

us ro

bur

Ger

man

y19

97(J

ung

et a

l. 20

03)

30B

1P

p285

AQ

uerc

us ro

bur

Ger

man

y19

97P.

psy

chro

phila

SP

29J5

803.

95T

Que

rcus

robu

rG

erm

any

1995

(Jun

g et

al.

2002

)29

J6M

YA-4

083

p288

AQ

uerc

us il

exFr

ance

1996

4P.

alti

cola

P47

G5

1219

39P

1694

8A

Euc

alyp

tus

dunn

iiS

outh

Afri

can.

a.(M

asek

o et

al.

2007

)P.

are

naria

P55

C2

1279

50T

Soi

lW

este

rn

Aus

tralia

, A

ustra

lia

2009

(Rea

et a

l. 20

11)

62B

712

5800

AS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2009

P. m

egak

arya

P22

H7

MYA

-404

0p4

2Th

eobr

oma

caca

oA

frica

n.a.

(Bra

sier

& G

riffin

19

79)

Page 7: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

361V O L U M E 8 · N O . 2

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar61

J523

8.83

4210

020

2077

TTh

eobr

oma

caca

oC

amer

oon

n.a.

61J6

239.

8342

099

1063

27A

Theo

brom

a ca

cao

Nig

eria

n.a.

P. p

alm

ivor

aP

22G

8M

YA-4

039

P10

213

p65

Citr

us s

p.Fl

orid

a, U

SA

n.a.

(But

ler 1

910)

22G

9M

YA-4

038

p26

Theo

brom

a ca

cao

Cos

ta R

ica

n.a.

P. q

uerc

etor

umP

15C

7S

oil

Sou

th C

arol

ina,

U

SA

1997

(Bal

ci e

t al.

2008

)

15C

8S

oil

Sou

th C

arol

ina,

U

SA

1997

P. q

uerc

ina

P30

A4

783.

95A

Que

rcus

robu

rG

erm

any

1995

(Jun

g et

al.

1999

)30

A5

784.

95M

YA-4

084

TQ

uerc

us ro

bur

Ger

man

y19

9530

A7

Que

rcus

sp.

Ser

bia

2003

P. s

p. o

hioe

nsis

n.a.

P16

050

AS

oil

Ohi

o, U

SA

2006

n.a.

5P.

aga

thid

icid

aP

67D

5T

Aga

this

aus

tralis

New

Zea

land

2006

(Wei

r et a

l. 20

15)

P. c

asta

neae

P22

H6

MYA

-406

0p4

5C

asta

nea

sp.

Japa

nn.

a.(K

atsu

ra 1

976)

30E

7S

oil

Hai

nan,

Chi

nan.

a.61

J758

7.85

3681

832

5914

TS

oil

Taiw

ann.

a.P.

coc

ois

P67

D6

TC

ocos

nuc

ifera

Haw

aii,

US

A19

90(W

eir e

t al.

2015

)P.

hev

eae

P22

J118

0616

p28

TH

eava

e sp

. M

alay

sia

n.a.

(Tho

mps

on 1

929)

22J2

1670

1, M

YA-3

895

p17

soil

Tenn

esse

e, U

SA

1964

6aP.

gem

ini

NP

46H

112

3382

A Z

oste

ra m

arin

aTh

e N

ethe

rland

s19

99(M

an in

’t Ve

ld e

t al

. 201

1)46

H2

1233

83A

Zos

tera

mar

ina

The

Net

herla

nds

1999

P. h

umic

ola

NP

32F8

200.

8152

179,

MYA

-408

0P

3826

p198

TS

oil

Taiw

an19

76(K

o &

Ann

198

5)32

F9P

6702

p199

AP

hase

olus

vul

garis

Taiw

ann.

a.P.

inun

data

NP

30J3

3901

21p2

91T

Ole

a sp

.S

pain

1996

(Bra

sier

et a

l. 20

03b)

30J4

3897

51p2

98T

Sal

ix m

atsu

dana

UK

1972

P86

19P

ista

cia

vera

Iran

n.a.

P. ro

sace

arum

NP

22J9

MYA

-366

2p8

2A

Pru

nus

sp.

Cal

iforn

ia, U

SA

1987

(Han

sen

et a

l. 20

09)

41C

1p3

21A

Pru

nus

sp.

Cal

iforn

ia, U

SA

n.a.

47J1

MYA

-445

6T

Mal

us d

omes

tica

Cal

iforn

ia, U

SA

n.a.

P. s

p. 4

8H2

NP

48H

2A

Stre

am w

ater

Virg

inia

, US

A20

08n.

a.P.

sp.

62C

9N

P62

C9

AS

tream

wat

erTa

iwan

2013

n.a.

P. s

p. p

erso

nii

n.a.

P11

555

AN

icot

iana

taba

cum

Nor

th C

arol

ina,

U

SA

n.a.

n.a.

P. ta

xon

wal

nut

NP

40A

7A

Irrig

atio

n w

ater

Virg

inia

, US

A20

06(B

rasi

er e

t al.

2003

a)43

G1

AIrr

igat

ion

wat

erVi

rgin

ia, U

SA

2007

6bP.

am

nico

laN

P61

G6

1316

52T

Stre

am w

ater

Wes

tern

A

ustra

lia,

Aus

tralia

2009

(Cro

us e

t al.

2012

)

Page 8: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

362 I M A F U N G U S

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar62

C5

1338

67P

achy

sand

ra s

p.

The

Net

herla

nds

n.a.

P. b

ilorb

ang

NP

61G

813

1653

TS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2010

(Agh

ighi

et a

l. 20

12)

P. b

orea

lisN

P60

B2

1320

23M

YA-4

881

TS

tream

wat

erA

lask

a, U

SA

2008

(Han

sen

et a

l. 20

12)

P. c

rass

amur

aN

P66

C9

AP

icea

abi

esIta

ly20

12(S

canu

et a

l. 20

15)

66D

114

0357

TS

oil

Italy

2011

P. fl

uvia

lisN

P55

B6

1294

24T

Stre

am w

ater

W

este

rn

Aus

tralia

, A

ustra

lia

2009

(Cro

us e

t al.

2011

)

P. g

ibbo

saN

P to

SP

55B

7A

Soi

lW

este

rn

Aus

tralia

, A

ustra

lia

2009

(Jun

g et

al.

2011

)

62B

812

7951

TS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2009

P. g

onap

odyi

des

NP

21J5

4672

6p1

17W

ater

Eng

land

, UK

n.a.

(Bui

sman

192

7,

Pet

erse

n 19

10)

34A

855

4.67

6035

1P

6872

Res

ervo

ir w

ater

n.a.

1967

P. g

rega

taN

P55

B8

AS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2009

(Jun

g et

al.

2011

)

62B

912

7952

TS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2009

P. la

cust

risN

P61

D6

AS

oil

Ger

man

y20

03(N

echw

atal

et a

l. 20

13)

61D

8A

Soi

lG

erm

any

2003

NP

61E

1A

Soi

lG

erm

any

2006

3897

25P

1033

7T

Sal

ix m

atsu

dana

Eng

land

, UK

1972

P. li

tora

lisN

P55

B9

1279

53T

Soi

lW

este

rn

Aus

tralia

, A

ustra

lia

2008

(Jun

g et

al.

2011

)

P. m

egas

perm

aN

P62

C7

402.

7258

817

3203

5P

3599

TA

lthae

a ro

sea

Was

hing

ton

DC

, U

SA

1931

(Dre

chsl

er 1

931)

P. m

issi

ssip

piae

NP

to S

P57

J1A

Irrig

atio

n w

ater

Mis

siss

ippi

, US

A20

12(Y

ang

et a

l. 20

13)

57J2

AIrr

igat

ion

wat

erM

issi

ssip

pi, U

SA

2012

57J3

MYA

-494

6T

Irrig

atio

n w

ater

Mis

siss

ippi

, US

A20

1257

J4A

Irrig

atio

n w

ater

Mis

siss

ippi

, US

A20

12P.

orn

amen

tata

NP

66D

214

0647

TS

oil

Italy

2012

(Sca

nu e

t al.

2015

)

Page 9: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

363V O L U M E 8 · N O . 2

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar66

D3

AS

oil

Italy

2012

P. p

inifo

liaN

P47

H1

1229

24T

Pin

us ra

diat

aC

hile

2007

(Dur

an e

t al.

2008

)47

H2

1229

22A

Pin

us ra

diat

aC

hile

2007

P. ri

paria

NP

60B

113

2024

MYA

-488

2T

Stre

am w

ater

Ore

gon,

US

A 20

06(H

anse

n et

al.

2012

)P.

ther

mop

hila

NP

55C

112

7954

TS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2004

(Jun

g et

al.

2011

)

P. ×

stag

num

NP

36H

8A

Irrig

atio

n w

ater

Virg

inia

, US

A20

06(Y

ang

et a

l. 20

14c)

36J7

AIrr

igat

ion

wat

erVi

rgin

ia, U

SA

2006

43F3

MYA

-492

6T

Irrig

atio

n w

ater

Virg

inia

, US

A20

0744

F9A

Irrig

atio

n w

ater

Virg

inia

, US

A20

07P.

sp.

26E

1N

P26

E1

p116

AM

alus

dom

estic

aN

ew Y

ork,

US

An.

a.n.

a.P.

sp.

can

alen

sis

n.a.

P10

456

AC

anal

wat

erC

alifo

rnia

, US

A20

02n.

a.P.

sp.

del

awar

eN

P63

H4

AP

ond

wat

erD

elaw

are,

US

A20

14n.

a.63

H7

AP

ond

wat

erD

elaw

are,

US

A20

14P.

sp.

gre

gata

-like

NP

22J5

1669

8p1

6 A

n.a.

n.a.

n.a.

n.a.

P. s

p. m

egas

perm

a-lik

eN

P23

A1

p81

AP

runu

s sp

.C

alifo

rnia

, US

An.

a.n.

a.23

A3

MYA

-366

0p7

9A

Act

inid

ia c

hine

nsis

Cal

iforn

ia, U

SA

1987

6P.

asp

arag

iN

P33

D7

3840

46A

Asp

arag

us o

ffici

nalis

New

Zea

land

1980

(Cro

us e

t al.

2012

)62

C4

1320

95M

YA-4

826

TA

spar

agus

offi

cina

lisM

ichi

gan,

US

A20

06P.

sp.

sul

awes

iens

isn.

a.P

6306

AS

yzyg

ium

aro

mat

icum

Indo

nesi

a19

89n.

a.7a

P. a

ttenu

ata

NP

67C

5T

Soi

lTa

iwan

2013

(Jun

g et

al.

2017

)P.

eur

opae

aN

P30

A3

Que

rcus

sp.

Fran

ce19

98(J

ung

et a

l. 20

02)

34C

2Q

uerc

us s

p.G

erm

any

1999

62A

210

9049

TS

oil

Fran

ce19

98P.

flex

uosa

NP

67C

3T

Soi

lTa

iwan

2013

(Jun

g et

al.

2017

)P.

form

osa

NP

67C

4T

Soi

lTa

iwan

2013

(Jun

g et

al.

2017

)P.

frag

aria

eN

P22

G6

1137

4P

3570

p114

Frag

aria

×an

anas

saM

aryl

and,

US

An.

a.(H

ickm

an 1

940)

30C

5Fr

agar

ia ×

anan

assa

Virg

inia

, US

An.

a.61

J320

9.46

1814

17P

6231

TFr

agar

ia ×

anan

assa

Eng

land

, UK

n.a.

P. in

tric

ata

NP

67B

9T

Soi

lTa

iwan

2013

(Jun

g et

al.

2017

)P.

rubi

NP

30D

7p1

86A

Rub

us s

p.A

ustra

lian.

a.(M

an in

‘t V

eld

2007

)41

D5

Rub

us s

p.N

orw

ay20

0546

C7

9044

2p3

89T

Rub

us id

aeus

cv.

"Gle

n C

lova

"S

cotla

nd, U

Kn.

a.

P. u

ligin

osa

NP

62A

310

9054

P10

413

TS

oil

Pol

and

1998

(Jun

g et

al.

2002

)

Page 10: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

364 I M A F U N G U S

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar62

A4

1090

55P

1032

8A

Soi

lG

erm

any

1998

P. ×

alni

NP

32J6

3923

17M

YA-4

081

p205

AA

lnus

glu

tinos

aFr

ance

1996

(Bra

sier

et a

l. 20

04, H

usso

n et

al

. 201

5)32

J739

2318

p206

AA

lnus

sp.

Aus

tria

1996

47A

739

2314

TA

lnus

sp.

UK

1994

47A

8A

Aln

us s

p.Th

e N

ethe

rland

sn.

a.P.

×ca

mbi

vora

NP

22F6

4671

9, M

YA-4

076

p64

Abi

es s

p.O

rego

n, U

SA

n.a.

(Bui

sman

192

7,

Jung

et a

l. 20

17)

26F8

MYA

-407

5p3

8n.

a.N

ew Y

ork,

US

An.

a.P.

×he

tero

hybr

ida

NP

67C

1T

Stre

am w

ater

Taiw

an20

13(J

ung

et a

l. 20

17)

P. ×

incr

assa

taN

P67

C2

TS

tream

wat

erTa

iwan

2013

(Jun

g et

al.

2017

)P.

sp.

eur

opae

a SW

NP

33F7

p229

AS

oil

Wes

t Virg

inia

, U

SA

2005

n.a.

7bP.

asi

atic

aN

P45

G1

9045

5p3

52A

Rob

inia

pse

udoa

caci

aJi

angs

u, C

hina

n.a.

(Rah

man

et a

l. 20

14a)

46C

656

194

p388

AR

obin

ia p

seud

oaca

cia

Jian

gsu,

Chi

nan.

a.61

H3

1333

47T

Pue

raria

loba

taJa

pan

2005

P. c

ajan

iN

P33

D9

p214

Caj

anus

caj

ani

Indi

an.

a.(A

min

et a

l. 19

78)

45F6

4438

9p3

48A

Caj

anus

caj

ani

Indi

an.

a.45

F744

388

P31

05p3

49T

Caj

anus

caj

ani

Indi

an.

a.P.

mel

onis

NP

32F6

MYA

-407

9P

1371

p196

AC

ucum

is s

ativ

usC

hina

n.a.

(Kat

sura

197

6)41

B4

p318

AC

ucum

is s

ativ

usIra

nn.

a.45

F358

2.69

5285

4T

Cuc

umis

sat

ivus

Japa

nn.

a.P.

nie

derh

ause

riiN

P01

D5

p312

AIrr

igat

ion

wat

erVi

rgin

ia, U

SA

2000

(Aba

d et

al.

2014

)23

J6M

YA-4

163

p57

AU

nkno

wn

orna

men

tal

Isra

eln.

a.31

E7

P10

617

p169

ATh

uja

occi

dent

alis

Nor

th C

arol

ina,

U

SA

2001

P. p

isi

NP

60A

4T

Pea

Sw

eden

2009

(Hey

man

et a

l. 20

13)

60A

5A

Pea

Sw

eden

2009

P. p

ista

ciae

NP

33D

6M

YA-4

082

3866

58p2

16T

Pis

taci

a ve

raIra

n19

86(M

irabo

lfath

y et

al

. 200

1)41

A9

p314

AP

ista

cia

vera

Iran

n.a.

P. s

ojae

NP

22D

831

2.62

1670

5, M

YA-3

899

1313

75p1

9G

lyci

ne m

axO

ntar

io, C

anad

a19

59(K

aufm

ann

&

Ger

dem

ann

1958

)28

F9p2

36G

lyci

ne m

axM

issi

ssip

pi, U

SA

1970

P. v

igna

eN

P45

G6

4673

5p3

57A

Gly

cine

max

n.a.

n.a.

(Pur

ss 1

957)

45G

964

832

3161

96P

3420

p379

Vign

a un

guic

ulat

aS

ri La

nka

n.a.

46C

111

2.76

6412

9p3

80Vi

gna

sine

nsis

n.a.

n.a.

7cP.

cin

nam

omi

NP

23B

115

400,

MYA

-405

7p1

0C

amel

lia ja

poni

caS

outh

Car

olin

a,

US

An.

a.(R

ands

192

2)

Page 11: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

365V O L U M E 8 · N O . 2

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar23

B2

1540

1, M

YA-4

058

p11

Per

sea

amer

ican

aP

uerto

Ric

o19

6061

J114

4.22

4667

122

938

P21

10T

Cin

nam

omum

bu

rman

nii

Indo

nesi

a19

22

P. p

arvi

spor

aN

P30

G9

MYA

-407

8p1

78A

Bea

ucar

nea

sp.

Ger

man

y19

91(S

canu

et a

l. 20

14)

46F6

AB

eauc

arne

a sp

.G

erm

any

1992

66C

713

2771

AA

rbut

us u

nedo

Italy

2008

66C

813

2772

TA

rbut

us u

nedo

Italy

2011

P. s

p. a

xN

P46

H5

AIle

x gl

abra

cv.

“S

ham

rock

”Vi

rgin

ia, U

SA

2008

n.a.

7dP.

frag

aria

efol

iaN

P61

H4

1357

47T

Frag

aria

×an

anas

saJa

pan

2005

(Rah

man

et a

l. 20

14b)

P. n

agai

iN

P61

H5

1332

48T

Ros

a sp

.Ja

pan

1968

(Rah

man

et a

l. 20

14b)

8aP.

cry

ptog

eaN

P61

H9

113.

1918

0615

P17

38T

Sol

anum

lyco

pers

icum

Irela

ndn.

a.(P

ethy

brid

ge &

La

fferty

191

9)P.

dre

chsl

eri

NP

15E

5S

oil

Sou

th C

arol

ina,

U

SA

1997

(Tuc

ker 1

931)

15E

6S

oil

Sou

th C

arol

ina,

U

SA

1998

23J5

292.

3546

724

P10

87p4

1T

Bet

a vu

lgar

is v

ar.

altis

sim

aC

alifo

rnia

, US

An.

a.

P10

331

Ger

bera

jam

eson

iiN

ew H

amps

hire

, U

SA

2003

P. e

ryth

rose

ptic

aN

P61

J212

9.23

3468

4P

1693

TS

olan

um tu

bero

sum

Irela

ndn.

a.(P

ethy

brid

ge

1913

)P.

med

icag

inis

NP

23A

4M

YA-3

900

p37

Med

icag

o sa

tiva

Ohi

o, U

SA

n.a.

(Han

sen

&

Max

wel

l 199

1)28

F144

390

P10

57p1

24M

edic

ago

sativ

aC

alifo

rnia

, US

A19

75P.

pse

udoc

rypt

ogea

NP

5240

2P

3103

Sol

anum

mar

gina

tum

Ecu

ador

n.a.

(Saf

aief

arah

ani e

t al

. 201

5)P.

rich

ardi

aeN

P31

E8

P10

355

p170

Zant

edes

chia

sp.

Japa

n19

89(B

uism

an 1

927)

45F5

240.

3060

353,

467

3432

5930

p347

TZa

nted

esch

ia

aeth

iopi

caU

SA

n.a.

P10

811

Zant

edes

chia

ae

thio

pica

Japa

n19

89

P. s

anso

mea

naN

P47

H3

MYA

-445

5T

Gly

cine

sp.

Indi

ana,

US

An.

a.(H

anse

n et

al.

2009

)47

H4

AG

lyci

ne s

p.In

dian

a, U

SA

n.a.

47H

5A

Gly

cine

sp.

Indi

ana,

US

An.

a.P.

trifo

liiN

P29

B2

MYA

-390

1p1

42A

Trifo

lium

ves

icul

osum

Mis

siss

ippi

, US

A19

78(H

anse

n &

M

axw

ell 1

991)

62A

911

7687

TTr

ifoliu

m s

p.M

issi

ssip

pi, U

SA

n.a.

P. a

ff. c

rypt

ogea

NP

22G

230

8.62

1540

2, M

YA-4

161

3259

07p1

2A

ster

sp.

Cal

iforn

ia, U

SA

n.a.

n.a.

Page 12: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

366 I M A F U N G U S

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

arP.

aff.

ery

thro

sept

ica

NP

22J4

MYA

-404

1p5

0n.

a.O

hio,

US

An.

a.n.

a.33

A1

p207

Sol

anum

tube

rosu

mM

aine

, US

A20

04P.

sp.

kel

man

iaN

P24

A7

MYA

-416

2p1

02

AA

bies

con

colo

rW

est V

irgin

ia,

US

A19

98n.

a.

31E

4P

1061

3p1

66A

Abe

s fra

seri

Nor

th C

arol

ina,

U

SA

2002

8bP.

bra

ssic

aeS

P29

D8

686.

95A

Bra

ssic

a ol

erac

eaTh

e N

ethe

rland

s19

95(M

an in

’t Ve

ld e

t al

. 200

2)61

J817

9.87

P75

17,

P19

521

TB

rass

ica

oler

acea

The

Net

herla

nds

1986

P. c

icho

riiS

P62

A8

1150

29T

Cic

horiu

m in

tybu

s va

r. fo

liosu

mTh

e N

ethe

rland

s20

04(B

ertie

r et a

l. 20

13)

P. d

auci

SP

61E

512

7102

TD

aucu

s ca

rota

Fran

ce20

09(B

ertie

r et a

l. 20

13)

32E

5D

uscu

s ca

rota

Fran

ce20

0432

E6

P10

728

Dus

cus

caro

taFr

ance

2004

32E

7p1

94D

uscu

s ca

rota

Fran

ce20

04P.

lact

ucae

SP

61F4

TLa

ctuc

a sa

tiva

Gre

ece

2001

(Ber

tier e

t al.

2013

)61

F7A

Lact

uca

sativ

aG

reec

e20

0261

F8A

Lact

uca

sativ

aG

reec

e20

03P.

prim

ulae

SP

29E

962

0.97

p286

Prim

ula

acau

lisG

erm

any

1997

(Tom

linso

n 19

52)

29F1

p287

Prim

ula

sp.

The

Net

herla

nds

1998

P. a

ff. b

rass

icae

-2n.

a.11

2968

P62

07A

Alli

um c

epa

Sw

itzer

land

n.a.

n.a.

P. a

ff. c

icho

riiS

P61

E3

1338

15A

Cic

horiu

m in

tybu

s va

r. fo

liosu

mU

K19

99n.

a.

P. s

p. 2

9E7

SP

29E

7A

Alli

um p

orru

mTh

e N

ethe

rland

sn.

a.n.

a.P.

taxo

n ca

stiti

sS

P61

E7

1312

46A

Frag

aria

×an

anas

saS

wed

en19

95(B

ertie

r et a

l. 20

13)

P. ta

xon

pars

ley

SP

61G

1A

Pet

rose

linum

cris

pum

Gre

ece

2006

(Ber

tier e

t al.

2013

)8c

P. fo

lioru

mS

P49

J812

1655

MYA

-363

8P

1097

4T

Rho

dode

ndro

n sp

.Te

nnes

see,

US

A20

04(D

onah

oo e

t al.

2006

)P.

hib

erna

lisS

P22

H1

270.

3160

352

3690

6P

6871

p115

Citr

us s

inen

sis

Por

tuga

l19

31(C

arne

192

5)32

F711

4104

5635

3, M

YA-3

896

1347

60P

3822

p197

Citr

us s

inen

sis

Wes

tern

A

ustra

lia,

Aus

tralia

1958

P. la

tera

lisN

P to

SP

22H

9M

YA-3

898

p51

AC

ham

aecy

paris

la

wso

nian

aO

rego

n, U

SA

n.a.

(Tuc

ker &

Milb

rath

19

42)

29A

920

1856

p128

Cha

mae

cypa

ris

law

soni

ana

Cal

iforn

ia, U

SA

1997

P. ra

mor

umS

P32

G2

Cam

ellia

japo

nica

Sou

th C

arol

ina,

U

SA

n.a.

(Wer

res

et a

l. 20

01)

Page 13: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

367V O L U M E 8 · N O . 2

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

ar33

F2Q

uerc

us a

grifo

liaC

alifo

rnia

, US

An.

a.8d

P. a

ustr

oced

rae

SP

41B

5M

YA-4

073

AA

ustro

cedr

us c

hile

nsis

Arg

entin

an.

a.(G

resl

ebin

et a

l. 20

07)

41B

612

2911

MYA

-407

4T

Aus

troce

drus

chi

lens

isA

rgen

tina

2005

P. o

bscu

raS

P60

E9

1292

73T

Soi

lG

erm

any

1994

(Grü

nwal

d et

al.

2012

)60

F1A

Pie

ris s

p.

Ore

gon,

US

A 20

0960

F2A

Kal

mia

latif

olia

Ore

gon,

US

A n.

a.P.

syr

inga

eS

P21

H9

3400

2P

0649

p187

Citr

us s

p.C

alifo

rnia

, US

An.

a.(K

leba

hn 1

905)

23A

6M

YA-3

659

p35

n.a.

New

Yor

k, U

SA

n.a.

8P.

str

icta

NP

58A

1M

YA-4

944

TIrr

igat

ion

wat

erM

issi

ssip

pi, U

SA

2012

(Yan

g et

al.

2014

a)58

A2

AIrr

igat

ion

wat

erM

issi

ssip

pi, U

SA

2012

58A

3A

Irrig

atio

n w

ater

Mis

siss

ippi

, US

A20

1258

A4

AIrr

igat

ion

wat

erM

issi

ssip

pi, U

SA

2012

9a (c

lust

er

9a1)

P. a

quim

orbi

daN

P40

A6

MYA

-457

8T

Irrig

atio

n w

ater

Virg

inia

, US

A20

06(H

ong

et a

l. 20

12)

40E

3A

Irrig

atio

n w

ater

Virg

inia

, US

A20

0644

G9

AIrr

igat

ion

wat

erVi

rgin

ia, U

SA

2007

P. c

hrys

anth

emi

NP

61E

9A

Chr

ysan

them

um s

p.Ja

pan

1998

(Nah

er e

t al.

2011

)61

F112

3163

TC

hrys

anth

emum

×m

orifo

lium

Japa

n20

00

P. h

ydro

gena

NP

44G

8A

Irrig

atio

n w

ater

Virg

inia

, US

A20

07(Y

ang

et a

l. 20

14b)

46A

3M

YA-4

919

TIrr

igat

ion

wat

erVi

rgin

ia, U

SA

2007

46A

4A

Irrig

atio

n w

ater

Virg

inia

, US

A20

07P.

hyd

ropa

thic

aN

P05

D1

MYA

-446

0p3

66T

Irrig

atio

n w

ater

Virg

inia

, US

A20

00(H

ong

et a

l. 20

10)

5C11

MYA

-445

9p3

65A

Irrig

atio

n w

ater

Virg

inia

, US

A20

00P.

irrig

ata

NP

04E

4M

YA-4

458

p335

AIrr

igat

ion

wat

erVi

rgin

ia, U

SA

2000

(Hon

g et

al.

2008

)

23J7

MYA

-445

7p1

08T

Irrig

atio

n w

ater

Virg

inia

, US

A20

0044

E4

AS

tream

wat

erVi

rgin

ia, U

SA

2007

P. m

acile

ntos

aN

P58

A5

AIrr

igat

ion

wat

erM

issi

ssip

pi, U

SA

2012

(Yan

g et

al.

2014

a)58

A6

AIrr

igat

ion

wat

erM

issi

ssip

pi, U

SA

2012

58A

7M

YA-4

945

TIrr

igat

ion

wat

erM

issi

ssip

pi, U

SA

2012

58A

8A

Irrig

atio

n w

ater

Mis

siss

ippi

, US

A20

12P.

par

sian

aN

P47

C3

3953

29T

Ficu

s ca

rica

Iran

1991

(Mos

tow

fizad

eh-

Gha

lam

fars

a et

al

. 200

8)

Page 14: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

368 I M A F U N G U S

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

arP.

virg

inia

naN

P40

A9

AIrr

igat

ion

wat

erVi

rgin

ia, U

SA

2006

(Yan

g &

Hon

g 20

13)

44G

6A

Irrig

atio

n w

ater

Virg

inia

, US

A20

0746

A2

MYA

-492

7T

Irrig

atio

n w

ater

Virg

inia

, US

A20

07

P. a

ff. p

arsi

ana

G1

NP

47C

7A

Pis

taci

a ve

raIra

nn.

a.n.

a.47

C8

AP

ista

cia

vera

Iran

n.a.

3953

28P

8618

AP

ista

cia

vera

Iran

1992

P. a

ff. p

arsi

ana

G2

NP

47C

539

5330

AP

ista

cia

vera

Iran

1992

n.a.

47C

639

5331

AP

ista

cia

vera

Iran

1992

P. a

ff. p

arsi

ana

G3

NP

47D

5A

Pis

taci

a ve

raIra

nn.

a.n.

a.47

D8

AP

ista

cia

vera

Iran

n.a.

47E

1A

Pis

taci

a ve

raIra

nn.

a.P.

sp.

35G

4N

P35

G4

AIrr

igat

ion

wat

erVi

rgin

ia, U

SA

2005

n.a.

P. s

p. 3

8D9

NP

38D

9A

Dia

nthu

s ca

ryop

hyllu

sTa

iwan

n.a.

n.a.

P. s

p. 4

0J5

NP

40J5

AU

nkno

wn

leaf

in

seaw

ater

Hai

nan,

Chi

nan.

a.n.

a.

P. s

p. c

uyab

ensi

sn.

a.P

8213

An.

a.E

cuad

or19

93n.

a.P.

sp.

lago

aria

naN

P60

B4

P82

20A

n.a.

Ecu

ador

n.a.

n.a.

60B

5P

8217

Tn.

a.E

cuad

orn.

a.P

8223

An.

a.E

cuad

or19

939a

(clu

ster

9a

2)P.

mac

roch

lam

ydos

pora

-G1

SP

33E

1P

1026

4G

lyci

ne m

axN

ew S

outh

W

ales

, Aus

tralia

n.

a.(Ir

win

199

1)

P10

267

Gly

cine

max

New

Sou

th

Wal

es, A

ustra

lia

1994

P. m

acro

chla

myd

ospo

ra-G

2S

P31

E9

3514

73P

8017

p171

Gly

cine

max

Que

ensl

and,

A

ustra

lian.

a.(Ir

win

199

1)

33D

524

0.30

6035

334

0618

Zant

edes

chia

ae

thio

pica

The

Net

herla

nds

1927

P. q

uini

nea

NP

45F2

406.

4856

964

p344

AC

inch

ona

offic

inal

isP

eru

n.a.

(Cra

ndal

l 194

7)46

C4

407.

4846

733

p386

TC

inch

ona

offic

inal

isP

eru

n.a.

9a (c

lust

er

9a3)

P. in

solit

aN

P32

7E1

MYA

-407

7p1

23W

ater

fall

wat

erH

aina

n, C

hina

n.a.

(Ann

& K

o 19

80)

38E

169

1.79

3878

928

8805

TS

oil

Taiw

an19

80P

6703

AS

oil

Taiw

ann.

a.P.

pol

onic

aN

P40

G9

Irrig

atio

n w

ater

Virg

inia

, US

A20

06(B

elba

hri e

t al.

2006

)43

F9Irr

igat

ion

wat

erVi

rgin

ia, U

SA

2007

49J9

P15

005

AS

oil

Pol

and

2006

9bP.

cap

tiosa

NP

46H

6A

Euc

alyp

tus

salig

naN

ew Z

eala

nd19

99(D

ick

et a

l. 20

06)

46H

7P

1071

9T

Euc

alyp

tus

salig

naN

ew Z

eala

nd19

9246

H8

AE

ucal

yptu

s sa

ligna

New

Zea

land

2000

Page 15: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

369V O L U M E 8 · N O . 2

Tabl

e 1.

(Con

tinue

d).

(Sub

)cla

dea

Spec

iesb

Papi

llac

Isol

ate

iden

tifica

tiond

Type

e

Isol

ate

orig

ins

Ref

eren

ceC

HC

BS

ATC

CIM

IW

PCM

GH

ost o

r Sub

stra

teLo

catio

nYe

arP

1072

1A

Euc

alyp

tus

salig

naN

ew Z

eala

nd19

98P.

con

stric

taN

P to

SP

55C

312

5801

TS

oil

Wes

tern

A

ustra

lia,

Aus

tralia

2006

(Rea

et a

l. 20

11)

P. fa

llax

NP

46J2

P10

722

TE

ucal

yptu

s de

lega

tens

isN

ew Z

eala

nd19

97(D

ick

et a

l. 20

06)

46J3

AE

ucal

yptu

s ni

tens

New

Zea

land

2000

46J5

AE

ucal

yptu

s ni

tens

New

Zea

land

2000

P10

725

AE

ucal

yptu

s fa

stig

ata

New

Zea

land

2004

10P.

boe

hmer

iae

P45

F929

1.29

1806

14P

6950

TB

oehm

eria

e ni

vea

Taiw

an19

27(S

awad

a 19

27)

P. g

allic

aN

P50

A1

1114

74P

1682

6T

Que

rcus

robu

rFr

ance

1998

(Jun

g &

N

echw

atal

200

8)61

D5

1114

75P

1682

7A

Phr

agm

ites

aust

ralis

Ger

man

y20

04P.

gon

dwan

ensi

sP

22G

7M

YA-3

893

n.a.

Ohi

o, U

SA

n.a.

(Cro

us e

t al.

2015

)P.

inte

rcal

aris

NP

45B

714

0632

TSD

-7T

Stre

am w

ater

Virg

inia

, US

A20

07(Y

ang

et a

l. 20

16)

48A

1A

Stre

am w

ater

Virg

inia

, US

A20

0849

A7

1406

31A

Stre

am w

ater

Virg

inia

, US

A20

09P.

ker

novi

aeP

46C

8P

1095

6p3

90R

hodo

dend

ron

pont

icum

Eng

land

, UK

2004

(Bra

sier

et a

l. 20

05)

46J6

P10

681

Ann

ona

cher

imol

aN

ew Z

eala

nd20

0246

J8P

1067

1S

oil

New

Zea

land

2003

P. m

orin

dae

P62

B5

1219

82T

Mor

inda

citr

ifolia

var

. ci

trifo

liaH

awai

i, U

SA

2005

(Nel

son

& A

bad

2010

)P.

sp.

boe

hmer

iae-

like

P45

F835

7.52

6017

332

199

P13

78p3

50A

Citr

us s

inen

sis

Arg

entin

a19

39n.

a.n.

a.P.

lilii

NP

1357

46T

Liliu

m s

p.Ja

pan

1987

(Rah

man

et a

l. 20

15)

outg

roup

Elon

gisp

oran

gium

un

dula

tum

P10

1728

3372

30P

1034

2T

Larix

sp.

Sco

tland

, UK

1989

(Uzu

hash

i et a

l. 20

10)

Phyt

opyt

hium

vex

ans

P34

0.49

1219

4P

3980

Tn.

a.n.

a.n.

a.(d

e C

ock

et a

l. 20

15)

Hal

ophy

toph

thor

a flu

viat

ilis

P57

A9

MYA

-496

1T

Stre

am w

ater

Virg

inia

, US

A20

11(Y

ang

& H

ong

2014

)a M

olec

ular

(sub

)cla

de a

s de

sign

ated

in F

ig. 1

b Nam

es o

f tax

a in

form

ally

des

igna

ted

for t

he fi

rst t

ime

in th

is s

tudy

are

und

erlin

ed.

C S

pora

ngia

l pap

illat

ion:

NP

= no

n-pa

pilla

te, P

= p

apill

ate,

and

SP

= se

mi-p

apill

ate.

d Iso

late

iden

tifica

tion

abbr

evia

tions

: CH

, Chu

anxu

e H

ong

labo

rato

ry a

t Virg

inia

Pol

ytec

hnic

Inst

itute

and

Sta

te U

nive

rsity

, Virg

inia

Bea

ch, V

A, U

SA

; CB

S, W

este

rdijk

Fun

gal B

iodi

vers

ity In

stitu

te, U

trech

t, Th

e N

ethe

rland

s; A

TCC

, Am

eric

an T

ype

Cul

ture

Col

lect

ion,

Man

assa

s, V

A, U

SA

; IM

I, C

AB

I Bio

scie

nces

, UK

; WP

C, t

he W

orld

Phy

toph

thor

a G

enet

ic R

esou

rce

Col

lect

ion

at U

nive

rsity

of C

alifo

rnia

, Riv

ersi

de, U

SA

; M

G, M

anno

n E

. Gal

legl

y la

bora

tory

at W

est V

irgin

ia U

nive

rsity

, US

A. L

ocal

iden

tifica

tions

of r

espe

ctiv

e is

olat

es a

re p

rovi

ded

in T

able

S1.

e Ex-

type

s (T

) or a

uthe

ntic

(A) i

sola

tes

(des

igna

ted

as re

pres

enta

tive

isol

ates

by

the

orig

inat

ors

of th

e re

spec

tive

spec

ies)

.f n

.a.=

not

ava

ilabl

e.

Page 16: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

370 I M A F U N G U S

all seven phylogenetic markers from 321 isolates were sequenced in this study. Sequences of all markers from 49 isolates by Blair et al. (2008) were also included in the analyses. Additionally, for seven isolates, sequences of one or two genes were newly produced in this study while the remaining gene sequences were from Blair et al. (2008). Sequences from P. lilii (CBS 135746) and P. sp. ohioensis (ST18-37) were obtained from Rahman et al. (2015) and from the Phytophthora Database (Park et al. 2013), respectively.

Phylogenetic analyses Concatenated sequences of all isolates were aligned using Clustal X version 2.1 (Larkin et al. 2007). The alignment was edited in BioEdit version 7.2.5 (Hall 1999) to trim aligned concatenated sequences to an equal size and set missing data to question marks. The edited alignment was then analyzed in jModelTest version 2.1.7 (Posada 2008) to select the most appropriate model for the following phylogenetic analyses. Maximum likelihood (ML) analysis was performed using RAxML version 8.2.0 (Stamatakis 2014) with the selected model and 1000 bootstrap replicates. Maximum parsimony (MP) analysis was conducted using PAUP version 4.0a147 (Swofford 2002) with 1000 bootstrap replicates. Bayesian analysis (BA) was performed using MrBayes version 3.2.6 (Ronquist et al. 2012) for two million generations with the selected model. Phylogenetic trees were viewed and edited in FigTree version 1.4.2. Alignment and phylogenetic trees from all methods have been deposited in TreeBASE (S19303).

Ancestral character state reconstructions of sporangial papillationInformation on the sporangial papillation of individual species was compiled from the literature (Erwin & Ribeiro 1996, Gallegly & Hong 2008, Kroon et al. 2012, Martin et al. 2012) with emphasis given to their respective original descriptions (Table 1). Both likelihood and parsimony ancestral state reconstructions were performed on the ML tree from the phylogenetic analyses using Mesquite version 3.03 (Maddison & Maddison 2017).

RESULTS

Sequences, alignment, and phylogenetic modelPCR amplification and sequencing was successful for almost all isolates and seven genetic markers. Failure to obtain sequences only occurred occasionally for a few isolates,

such as the EF1α gene of Phytophthora bilorbang (61G8), the Enl gene of P. macrochlamydospora (33E1, 31E9, and 33D5), and P. quininea (45F2), and TigA of P. megasperma (62C7) (Supplementary Table 1). These failures were set as missing data in the alignment. After trimming, each isolate was represented by an 8435-bp concatenated sequence in the alignment including gaps and missing data. This included 496 bp for 60S, 1136 bp for Btub, 965 bp for EF1α, 1169 bp for Enl, 1758 bp for HSP90, 1270 bp for 28S, and 1641 bp for TigA (TreeBASE S19303). The general time reversible nucleotide substitution model with gamma-distributed rate variation and a proportion of invariable sites (GTR+I+G) was identified by jModelTest as the most appropriate model for the phylogenetic analyses.

An expanded phylogeny including 10 clades and basal taxa The three phylogenetic analysis methods, including ML, MP, and BA analyses (TreeBASE S19303), resulted in similar tree topologies. The topology and branch lengths of the ML inference are shown in Fig. 1. The monophyly of each of the previously recognized 10 clades was generally well supported with a few exceptions. Specifically, all clades except for clade 4 were highly supported by > 95 % bootstrap values in ML analysis and 100 % posterior probability (PP) in BA analysis (Fig. 1). Clades 1–3, 5, 7, and 10 were also highly supported by > 95 % bootstrap values in the MP analysis (Fig. 1). However, clades 6, 8, and 9, were only moderately supported with bootstrap numbers of 68, 61, and 52 in the MP analysis, respectively (Fig. 1).

As nearly half of all taxa included in this phylogeny were recently described, all clades in this phylogeny are expanded here to various extents compared to previously published phylogenies. The general structure of clades 1, 3, 5, 8 and 10 remained as previously assigned by Blair et al. (2008) and Martin et al. (2014) with additions of new species. For example, clade 1 was divided into three well-supported subclades and P. nicotianae was placed basal to subclades 1b and 1c (Fig. 1). Clade 8 was divided into four generally well-supported subclades, except P. stricta, which was placed basal to all clade 8 species (Fig. 1). New subclades were assigned to clade 2 (Fig. 2), clade 6 (Fig. 3), clade 7 (Fig. 4) and clade 9 (Fig. 5).

Several species were placed basal to other species in their respective clades. First, the cluster of P. quercina and P. sp. ohioensis was placed basal to other species of clade 4 in all three analyses. The bootstrap supports of the ML and MP analyses, and PP (percentage) for the separation of this cluster from that of P. alticola, P. arenaria, P. megakarya, P. palmivora, and P. quercetorum in clade 4 were only 48, 78, and 84, respectively (Fig. 1). Second, P. lilii was excluded from all known clades; it was placed basal to clades 1–5 and 7 (Fig. 1). Third, in clade 6, bootstrap support for the ML and MP analyses, and PP for all species except P. asparagi and P. sp. sulawesiensis were 100/100/100 (Fig. 3). This set of support numbers decreased to 99/92/100 when P. sp. sulawesiensis was included, and to 100/68/100 when further including P. asparagi (Fig. 3). Fourth, the support numbers for clade 8 species excluding P. stricta was 100/100/100, but 96/61/100 when P. stricta was included (Fig. 1). Fifth,

Table 2. Numbers of species and ex-types included in phylogenies for the genus Phytophthora in previous studies and this study.

Phylogeny in

Number of species

Number of ex-typesFormal ProvisionalCooke et al. (2000) 49 2 9Kroon et al. (2004) 46 2 18Blair et al. (2008) 72 10 16Martin et al. (2014) 90 17 31This study 142 43 114

Page 17: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

371V O L U M E 8 · N O . 2

Fig. 1. A phylogeny for the genus Phytophthora based on concatenated sequences of seven nuclear genetic markers. Topology and branch lengths of maximum likelihood analysis are shown. Bootstrap values for maximum likelihood and maximum parsimony, and Bayesian posterior probabilities (percentages) are indicated on individual nodes and separated by a forward slash. An asterisk is used in place of nodes with unambiguous (100 %) support in all three analyses. A dash is used in place of a topology from an analysis ambiguous to the other two analyses and these sets of numbers with ambiguity in one analysis are also highlighted in red. Detailed structures of clades 2, 6, 7, and 9 are shown in Figs 2–5, respectively. Species represented by ex-types and authentic isolates are written in brown and blue, respectively. Branches indicating three hypothesized evolutionary paths with all species producing papillate or semi-papillate sporangia are drawn in red or orange, respectively. Scale bar indicates number of substitutions per site.

Page 18: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

372 I M A F U N G U S

all papillate species in clade 10 (Table 1) formed a well-supported main cluster, while two more recently described non-papillate species, P. gallica and P. intercalaris, were placed basal to the main cluster (Fig. 1).

New subclades in clades 2, 6, 7, and 9

(a) Clade 2 In addition to the previously recognized subclades 2a and 2b, many species, such as P. acerina, P. capensis, P. citricola, P. multivora, P. pachypleura, P. plurivora, and P. pini in the commonly referred to “Phytophthora citricola-complex”

defined a new subclade 2c (Fig. 2). Furthermore, P. bisheria, P. frigida, and P. elongata formed new subclade 2d and the cluster of P. multivesiculata and P. taxon aquatilis formed new subclade 2e, with maximum support values in each case (Fig. 2). (b) Clade 6 Subclade 6a included P. gemini, P. humicola, P. inundata, P. rosacearum, P. sp. personii, P. sp. 48H2, P. sp. 62C9 and P. taxon walnut. The cluster of P. rosacearum and P. taxon walnut could not be separated from that represented by P. gemini with only moderate support values for separation

Fig. 2. Structure of Phytophthora clade 2 in a genus-wide phylogeny for the genus Phytophthora based on concatenated sequences of seven nuclear genetic markers. Topology and branch lengths of maximum likelihood analysis are shown. Bootstrap values for maximum likelihood and maximum parsimony, and Bayesian posterior probabilities (percentages) are indicated on individual nodes and separated by a forward slash. An asterisk is used in place of nodes with unambiguous (100 %) support in all three analyses. A dash is used in place of a topology from an analysis ambiguous to the other two analyses and these sets of numbers with ambiguity in one analysis are also highlighted in red. Species represented by ex-types and authentic isolates are written in brown and blue, respectively. Scale bar indicates number of substitutions per site.

Page 19: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

373V O L U M E 8 · N O . 2

(82/61/100) (Fig. 3). Isolates 62C9 and 48H2, belonging to two new species, had ambiguous placements within subclade 6a among the three analyses (Fig. 3). With approximately 20 species newly included in the present phylogeny, the previously recognized “P. megasperma-P. gonapodyides complex” (Brasier et al. 2003a), subclade II of clade 6 (Jung et al. 2011), or subclade 6b (Kroon et al. 2012) expanded and its separation from subclade 6a was well-supported by 100/100/100 values (Fig. 3). Within subclade 6b, separation of the cluster of P. bilorbang, P. lacustris, and P. riparia from the other subclade 6b species was highly supported by 97/94/100 (Fig. 3), indicating that these three species may define a new subclade, although this is not done in this study. Phytophthora sp. sulawesiensis was placed basal to other clade 6 species except for P. asparagi, while P. asparagi was basal to all other species in clade 6 (Fig. 3). Phytophthora asparagi was previously assigned as subclade 6c (Kroon et al. 2012) and subclade III of clade 6 (Jung et al. 2011);

considering that the support value of MP analysis was only moderate (68 %) when this single taxon was included (Fig. 3), this previous assignation as a subclade was not adopted here. In addition, in order to be consistent with subclade names in other clades, subclades 6a and 6b were used here instead of subclades I and II by Jung et al. (2011). (c) Clade 7 Four subclades were distinguished in clade 7. Separation of the previously assigned subclades 7a and 7b was only moderately supported by values 71/56/100 (Fig. 4). The general structure of subclade 7a remained the same even with the addition of seven new taxa. Six of these new species, including P. attenuata, P. flexuosa, P. formosa, P. intricata, P. ×heterohybrida, and P. ×incrassata were recently recovered from forest soils and streamwater in Taiwan (Jung et al. 2017). On the other hand, P. cinnamomi and P. parvispora were separated from subclade 7b. They,

Fig. 3. Structure of Phytophthora clade 6 in a genus-wide phylogeny for the genus Phytophthora based on concatenated sequences of seven nuclear genetic markers. Topology and branch lengths of maximum likelihood analysis are shown. Bootstrap values for maximum likelihood and maximum parsimony, and Bayesian posterior probabilities (percentages) are indicated on individual nodes and separated by a forward slash. An asterisk is used in place of nodes with unambiguous (100 %) support in all three analyses. A dash is used in place of a topology from an analysis ambiguous to the other two analyses and these sets of numbers with ambiguity in one analysis are also highlighted in red. Species represented by ex-types and authentic isolates are written in brown and blue, respectively. Scale bar indicates number of substitutions per site.

Page 20: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

374 I M A F U N G U S

along with a provisional species, P. sp. ax from Virginia, USA (Table 1), formed a distinct new subclade 7c (Fig. 4). The new subclade 7d, including two recently described species from Japan (Rahman et al. 2014b), P. fragariaefolia and P. nagaii, was placed basal to other subclades in clade 7 (Fig. 4).

(d) Clade 9 The split of clade 9 into two subclades 9a and 9b was highly supported in ML (98 %) and BA (100 %) analyses and moderately supported in the MP (52 %) analysis (Fig. 5). However, monophyly was highly supported for subclade 9b (100/100/100) but not for subclade 9a (44/-/95) (Fig. 5). Within subclade 9a, three monophyletic clusters were formed: 9a1, 9a2, and 9a3. However, support for the separation of these three clusters was moderate or ambiguous. In particular, the MP results did not produce any consistent separation of the three clusters (Fig. 5). Cluster 9a1 included many

recently described high-temperature tolerant species, such as P. aquimorbida, P. chrysanthemi, P. hydropathica, P. macilentosa, P. parsiana, and P. virginiana). The cluster of P. macrochlamydospora (two lineages with two isolates in each lineage, Table 1) and P. quininea constituted 9a2 (Fig. 5). The cluster of two other high-temperature tolerant species P. insolita and P. polonica constituted 9a3 (Fig. 5). The well-supported cluster of P. captiosa, P. constricta, and P. fallax was assigned as subclade 9b (Fig. 5). Evolutionary history of sporangial papillation inferred from ancestral character state reconstructions Sporangial papillation of individual species is indicated in Table 1 and Fig. 6. Due to the size of the cladograms, clusters including species with the same sporangial papillation within each (sub)clade were compressed in Mesquite. Both

Fig. 4. Structure of Phytophthora clade 7 in a genus-wide phylogeny for the genus Phytophthora based on concatenated sequences of seven nuclear genetic markers. Topology and branch lengths of maximum likelihood analysis are shown. Bootstrap values for maximum likelihood and maximum parsimony, and Bayesian posterior probabilities (percentages) are indicated on individual nodes and separated by a forward slash. An asterisk is used in place of nodes with unambiguous (100 %) support in all three analyses. A dash is used in place of a topology from an analysis ambiguous to the other two analyses and these sets of numbers with ambiguity in one analysis are also highlighted in red. Species represented by ex-types and authentic isolates are written in brown and blue, respectively. Scale bar indicates number of substitutions per site.

Page 21: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

375V O L U M E 8 · N O . 2

likelihood and parsimony methods suggested that non-papillate is the progenitor state of Phytophthora species, and that semi-papillate and papillate types were derived from the non-papillate. The analyses indicated three major clusters of semi-papillate and (or) papillate species diverged from the non-papillate ancestors. First, species in clades 1 to 5 (semi-papillate or papillate) diverged from non-papillate species in clade 7 and P. lilii (Fig. 6). Second, species in subclades 8b to 8d (semi-papillate) diverged from non-papillate subclade 8a species (Fig. 6). Third, papillate clade 10 species including P. boehmeriae, P. gondwanensis, P. kernoviae, and P. morindae diverged from the non-papillate P. gallica and P. intercalaris (Fig. 6). Several species such as P. macrochlamydospora, P. mississippiae, P. gibbosa, and P. constricta also evolved to produce partially semi-papillate sporangia (Fig. 6).

DISCUSSION

Here we presented an expanded phylogeny for the genus Phytophthora, encompassing 142 formally named and 43 provisionally recognized species (Table 2). In addition to this comprehensive coverage, this expanded phylogeny features over 1500 signature sequences generated from 278 ex-type and authentic isolates of 162 Phytophthora taxa (Supplementary Table 1). Furthermore, this study provided new insights into the evolutionary history of sporangial papillation in Phytophthora.

The expanded phylogeny provides a sound taxonomic framework for this agriculturally and ecologically important genus. One hundred and fourteen ex-types were included, representing 80 % of the 142 formally named species in this phylogeny. The majority of the 29 species not represented by ex-types, such as P. gonapodyides, P. infestans, P. meadii, P. mexicana, and P. nicotianae, were described long ago without

Fig. 5. Structure of Phytophthora clade 9 in a genus-wide phylogeny for the genus Phytophthora based on concatenated sequences of seven nuclear genetic markers. Topology and branch lengths of maximum likelihood analysis are shown. Bootstrap values for maximum likelihood and maximum parsimony, and Bayesian posterior probabilities (percentages) are indicated on individual nodes and separated by a forward slash. An asterisk is used in place of nodes with unambiguous (100 %) support in all three analyses. A dash is used in place of a topology from an analysis ambiguous to the other two analyses and these sets of numbers with ambiguity in one analysis are also highlighted in red. Species represented by ex-types and authentic isolates are written in brown and blue, respectively. Scale bar indicates number of substitutions per site.

Page 22: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

376 I M A F U N G U S

designation of an ex-type culture. Likewise, almost all the 43 provisional species in this phylogeny were represented by authentic isolates from the originators of the respective species (Table 1 and Supplementary Table 1). This new framework will facilitate identification of new taxa in the future. As the genus continues to rapidly expand, some recently described species were not included in this study: P. mekongensis in subclade 2a (Puglisi et al. 2017), P. amaranthi in subclade 2b (Ann et al. 2016), P. boodjera in clade 4 (Simamora et al. 2015), P. chlamydospora in subclade 6b (Hansen et al.

2015), P. uniformis (basionym: P. alni subsp. uniformis) and P. ×multiformis (basionym: P. alni subsp. multiformis) in subclade 7a (Brasier et al. 2004, Husson et al. 2015), P. pseudolactucae in subclade 8b (Rahman et al. 2015), and P. prodigiosa (Puglisi et al. 2017) and P. pseudopolonica (Li et al. 2017) in subclade 9a. Likewise, some informally designated species also were not included: such as P. taxon humicola-like, P. taxon kwongan, and P. taxon rosacearum-like in subclade 6a (Jung et al. 2011). These and other emerging species are yet to be incorporated in the overall phylogeny of the genus.

Fig. 6. Ancestral state reconstructions of sporangial papillation for the genus Phytophthora based on likelihood (left cladogram) and parsimony (right cladogram). Trace character history analyses were performed on the maximum likelihood phylogeny in Mesquite. Clusters including species of uniform sporangial papillation within individual (sub)clades were compressed in Mesquite.

Page 23: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

377V O L U M E 8 · N O . 2

The generation of over 1500 signature sequences from ex-types and authentic isolates in this study will aid researchers and first responders in correctly identifying Phytophthora cultures to the species level. DNA sequencing of selected genetic markers has become common practice in the identification of Phytophthora cultures (Kang et al. 2010). However, it is recognized that the accuracy of culture identity determined by this approach depends on the quality of the reference sequences used – and currently many sequence deposits are erroneously identified in public repositories, including GenBank (Kang et al. 2010). These errors originated in sequence deposits of cultures that were identified by morphological characters alone, and compounded by those identified through sequence matches to erroneous reference sequences or by single DNA markers (Kang et al. 2010). In this study, 29 isolates were found associated with an erroneous or modified identity (Supplementary Table 2). For instance, isolate 29B3 in clade 1 was identified as P. pseudotsugae and used as a key isolate for this species by Gallegly & Hong (2008). However, its sequences were distinct from those of the P. pseudotsugae ex-type (ATCC 52938). In the phylogenetic tree, it was basal to the cluster of P. cactorum and P. hedraiandra, thus its species identity was changed to P. aff. pseudotsugae (Fig. 1). In clade 2, isolate 26H4 was identified as P. citrophthora (Gallegly & Hong 2008) but sequences and phylogeny showed that it was close to but distinct from P. citrophthora isolates 03E5 and 26H3. It formed a cluster with isolate IMI 342898 (P10341), which was coded as P. sp. aff. colocasiae-1 by Martin et al. (2014). The identity of both isolates was then changed to P. aff. citrophthora (Fig. 2). Similarly, in clade 8, isolate 22G2 had been identified as P. cryptogea, although it was distinct from the P. cryptogea ex-type 61H9 (CBS 113.19). In the phylogenetic tree, it was basal to the cluster of P. cryptogea and P. erythroseptica, and the species identity was consequently changed to P. aff. cryptogea (Fig. 1). Changes in the identifications of these isolates, including the new and original names used, are indicated in Supplementary Table 2. The changes in the naming of these isolates highlights the importance of using signature sequences from ex-type or authentic isolates as references in future culture identification. In order to facilitate this practice, the signature sequences generated from ex-types or authentic isolates in the present study are marked as ‘(ex-type)’ or ‘(authentic)’, respectively, under the ‘isolate’ section in the ‘feature’ table of GenBank deposits. The research, diagnostic and regulatory communities are encouraged to use these sequences as references in future culture identification.

This study provided new insights into the evolutionary history of sporangial morphology in the genus Phytophthora, a subject that has fascinated generations of mycologists and plant pathologists. There have been three major hypotheses regarding the development of papillation, as illustrated in Fig. 7a, b, and c, respectively. First, papillate species were considered as descendants of Pythium-like, non-papillate ancestors and semi-papillation has been considered as intermediate between non-papillation and papillation (Blackwell 1949, Cooke et al. 2000, Erwin & Ribeiro 1996). Second, some semi-papillate species, exemplified by P. primulae in the group III of Waterhouse (1963) are

Fig. 7. Illustration of hypotheses on evolution of Phytophthora and associated changes in sporangial papillation: (a) species producing papillate sporangia evolved from non-papillate ancestors. Semi-papillation is considered as intermediate between non-papillation and papillation (Blackwell 1949, Cooke et al. 2000, Erwin & Ribeiro 1996); (b) some semi-papillate species, exemplified by P. primulae in the group III of Waterhouse (1963), are primitive and evolved to be non-papillate and papillate through two evolutionary paths, by Brasier (1983); (c) papillate species evolved from non-papillate ancestors. Semi-papillate species have been considered as morphological variants of papillate or non-papillate species, by Cooke et al. (2000); (d) a new hypothesis developed in this study that non-papillate ancestors evolved directly to either papillate or semi-papillate species. Some semi-papillate species further evolved to be papillate, or vice versa.

Page 24: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

378 I M A F U N G U S

primitive; they were suggested to have evolved to papillate and non-papillate species through two distinct evolutionary lines (Brasier 1983). Third, semi-papillate sporangia are morphological variants of papillate and non-papillate types (Cooke et al. 2000). Here we suggest that the non-papillate type is ancestral, and that non-papillate species could have evolved directly into either semi-papillate or papillate species (Fig. 7d). The evolution to semi-papillate species is exemplified by those in subclades 8b–d (Fig. 1), while evolution to papillate species is illustrated by P. boehmeriae and other papillate species in clade 10 (Fig. 1).The relationship between semi-papillate and papillate species appears to be more complicated (Fig. 7d). We also hypothesize that some semi-papillate species, such as those in subclade 1c, may have diverged from papillate ancestors, while some papillate species such as P. frigida may have evolved from semi-papillate ancestors of subclade 2d (Fig. 6).

These new hypotheses are supported by the results from phylogeny and ancestral state reconstructions that suggest three major evolutionary paths in sporangial papillation of Phytophthora species (Fig. 1). First, the ancestor of modern species in clades 1–5 evolved to be papillate or semi-papillate (Figs 1, 6) while diverging from the common non-papillate ancestor of clade 7 species (Figs 1, 6). Second, the common ancestor of species in subclades 8b–d diverged from that of subclade 8a species while acquiring semi-papillation (Figs 1, 6). Third, the common ancestor of five clade 10 species in the main cluster including P. boehmeriae, P. gondwanensis, P. kernoviae, P. morindae, and P. sp. boehmeriae-like, acquired papillate sporangia while diverging from two non-papillate clade 10 species, P. gallica and P. intercalaris (Figs 1, 6). Besides these three major groups of papillate or semi-papillate species, a few species may have evolved to acquire semi-papillation independently, such as P. macrochlamydospora in clade 9 (Fig. 6). This evolutionary process may be underway for some other species including P. constricta, P. gibbosa, and P. mississippiae, which all produce both semi-papillate and non-papillate sporangia (Fig. 6). Furthermore, evolutionary reversion to partial production of non-papillate sporangia may have occurred in P. multivesiculata and P. lateralis in two semi-papillate subclades 2e and 8c, respectively (Fig. 6). However, that conclusion is uncertain due to limited and ambiguous data from species in these two subclades. Specifically, P. lateralis was ambiguously reported as non-papillate (Erwin & Ribeiro 1996, Gallegly & Hong 2008, Martin et al. 2012, Tucker & Milbrath 1942) or non- to semi-papillate (Kroon et al. 2012) in different studies. In subclade 2e, the only sister taxon of P. multivesiculata, P. taxon aquatilis, was provisionally described as semi-papillate, but only based on a single isolate (Hong et al. 2012). Evolutionary reversion in the sporangial papillation of these two species requires validation in the future. Also, more studies are warranted to analyze additional characters based on phylogenies with better clade-to-clade resolutions and provide a more comprehensive picture on the evolutionary history of Phytophthora species.

That a number of species were placed basal to other species in their respective clades in this expanded phylogeny presents a significant challenge to the monophyly of their

respective clades and the current 10-clade system. First, P. stricta was initially placed close to other species in subclade 8a based on sequences of the cytochrome c oxidase 1 (cox1) gene, but was not grouped in any ITS clade (Yang et al. 2014a). This species was grouped in clade 8 in our expanded phylogeny by ML and BA analyses (Fig. 1); the monophyly of this clade was only moderately supported (61 %) in the MP analysis (Fig. 1). Second, the monophyly of clade 6 including P. asparagi was only moderately supported (68 %) in the MP analysis (Fig. 3). Third, although the inclusion of P. intercalaris in clade 10 was supported with maximum values, the exact positions of this species and P. gallica were still unresolved since the next node was only moderately supported (53 %) in the ML analysis and ambiguous in the MP analysis (Fig. 1). Fourth, similar to the finding of Blair et al. (2008), support for the monophyly of clade 4 including P. quercina and P. sp. ohioensis was only moderate (48/78/84). Also, similar ambiguity in the placement of the ‘P. quercina – P. sp. ohioensis’ cluster was observed among different phylogenetic approaches, and using different datasets including nuclear, mitochondrial, and combined nuclear and mitochondrial sequences (Martin et al. 2014). Fifth, this phylogeny confirmed the finding by Rahman et al. (2015) that P. lilii was not grouped in any clade of the current 10-clade system (Fig. 1). This species was not assigned as a distinct clade in our study, due to the relatively low clade-to-clade resolutions (Fig. 1). Further analyses are warranted to determine whether this unique species should be assigned as a new clade.

Although many branches in the expanded phylogeny have consistent maximum support in all three methods, some have only moderate to low or inconsistent support. These results highlight the challenges of correctly inferring the evolutionary separation of many closely related Phytophthora species, even when concatenated sequences from seven phylogenetic markers were used. It can be expected that as the cost of gene sequencing drops further, it will become possible to increase phylogenetic resolution among Phytophthora species by using concatenations of much larger numbers of genes. For example, Ye et al. (2016) used 293 concatenated housekeeping proteins to infer a robust phylogeny of seven fully sequenced Phytophthora species and confirmed that downy mildews (represented by three genome sequences) are nested within the genus Phytophthora, close to Phytophthora clade 4 (Ye et al. 2016). However, even with full genome sequences, ambiguity may not be completely resolved in cases where speciation has involved large populations of sexually reproducing individuals, for example, as a result of geographic separation. In these cases, there may be many sequence polymorphisms shared among separated species and these may confound the inference of a reliable phylogeny. Resolution of this level of ambiguity may require sequencing the whole genome of many isolates from the species of interest as well as using improved phylogenetic and coalescent methods.

With the number of described Phytophthora species increasing, recent studies have raised an important concern in the accurate detection of species boundaries using phylogenetic data (Jung & Burgess 2009, Pánek et al. 2016,

Page 25: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

379V O L U M E 8 · N O . 2

Safaiefarahani et al. 2015). One example is the status of P. hedraiandra as a distinct species in subclade 1a (Pánek et al. 2016). As evidenced by the amplified fragment length polymorphism (AFLP) and phylogenetic analysis based on sequences of ITS, phenolic acid decarboxylase, and cox1 genes, a recent study concluded that P. hedraiandra was just one lineage of P. cactorum, while morphological data provided only limited information to delimitate these two species (Pánek et al. 2016). Also, phylogenetic analyses in this study indicated that P. cactorum and P. hedraiandra cluster with strong support (98/100/100), and P. aff. hedraiandra isolate 33F4 (previously identified as P. hedraiandra Supplementary Table 2), was clustered with P. cactorum (Fig. 1). Phylogenies based on nuclear sequences prior to this study also supported P. hedraiandra as closely related to P. cactorum (Blair et al. 2008, Martin et al. 2014). However, in the phylogenies based on concatenated sequences of four mitochondrial loci, and combined seven nuclear and four mitochondrial loci, P. hedraiandra was basal to the cluster of P. cactorum and P. pseudotsugae, and clustered with P. idaei, respectively (Martin et al. 2014). Phytophthora cactorum and P. hedraiandra also have very distinctive single-strand-conformation polymorphism patterns (Gallegly & Hong 2008). Apparently, more investigations are warranted to resolve the P. cactorum complex. Likewise, indistinct boundaries are present among species in other subclades, such as the ‘P. citricola complex’ or subclade 2c (Brazee et al. 2017, Jung & Burgess 2009), the ‘P. cryptogea complex’ in subclade 8a (Safaiefarahani et al. 2015, 2016) and cluster 9a1 in subclade 9a including P. hydropathica (Hong et al. 2010), P. parsiana (Mostowfizadeh-Ghalamfarsa et al. 2008), P. virginiana (Yang & Hong 2013) and other provisionally designated species. Accurately delimiting these closely related species within the genus remains an important task.

This expanded phylogeny has highlighted the importance and difficulty of accurately interpreting the position of hybrid Phytophthora species. As exemplified by P. ×alni (Brasier et al. 2004, Husson et al. 2015), many hybrid species have been identified among emerging plant pathogens (Jung et al. 2017, Man in’t Veld et al. 2012, Nirenberg et al. 2009). Due to the presence of multiple alleles originated from parent species in their nuclear genes, phylogenetic analysis of these hybrids based on nuclear sequences alone may not produce a robust placement. As illustrated in this phylogeny, the placement of hybrid species may be ambiguous. Specifically, in subclade 6b, support values for the placement of P. ×stagnum and its closely related species, P. mississippiae, P. borealis, and P. sp. delaware were moderate in the ML and BA analyses and ambiguous in the MP analysis (Fig. 3). Similarly, in subclade 7a, the placement of P. ×alni, P. ×cambivora, P. ×heterohybrida, and P. ×incrassata’ cluster was not well resolved due to ambiguous placement in the MP analysis and moderate support values in the other two analyses (Fig. 4). Adding mitochondrial sequences into the phylogenetic analyses may be a solution to this problem. However, due to the uniparental inheritance of mitochondria, the hybrids and their maternal parents are inseparable by mitochondrial sequences and their placements could conflict with nuclear analyses (Martin et al. 2014).

ACKNOWLEDGMENTS

This research was supported in part by grants from the USDA-NIFA-Specialty Crop Research Initiative (Agreement no. 2010-51181-21140). We would like to thank all authorities and species originators who provided Phytophthora isolates to our study, including Yilmaz Balci, Zia Banihashemi, Lien Bertier, Karien Bezuidenhout, Clive Brasier, Treena Burgess, Mike Coffey, Mannon Gallegly, Beatrice Ginetti, Niklaus Grünwald, Everett Hansen, Beatrice Henricot, Fredrik Heyman, Hon Ho, Maria Holeva, Steven Jeffers, Thomas Jung, Koji Kageyama, Willem Man in ‘t Veld, Jan Nechwatal, Bruno Scanu, Andrea Vannini, Anna Maria Vettraino, and Irene Vloutoglou. Names of many other contributors are listed in Supplementary Table 1.

REFERENCES

Abad ZG, Abad JA, Cacciola SO, Pane A, Faedda R, et al. (2014) Phytophthora niederhauserii sp. nov., a polyphagous species associated with ornamentals, fruit trees and native plants in 13 countries. Mycologia 106: 431–437.

Abad ZG, Abad JA, Coffey MD, Oudemans PV, Man WA, et al. (2008) Phytophthora bisheria sp. nov., a new species identified in isolates from the Rosaceous raspberry, rose and strawberry in three continents. Mycologia 100: 99–110.

Abad ZG, Ivors KL, Gallup CA, Abad JA, Shew HD (2011) Morphological and molecular characterization of Phytophthora glovera sp. nov. from tobacco in Brazil. Mycologia 103: 341–350.

Aghighi S, Hardy GESJ, Scott JK, Burgess TI (2012) Phytophthora bilorbang sp. nov., a new species associated with the decline of Rubus anglocandicans (European blackberry) in Western Australia. European Journal of Plant Pathology 133: 841–855.

Amin KS, Baldev B, Williams FJ (1978) Phytophthora cajani, a new species causing stem blight on Cajanus cajan. Mycologia 70: 171–176.

Ann PJ, Huang JH, Tsai JN, Ko WH (2016) Morphological, molecular and pathological characterization of Phytophthora amaranthi sp. nov. from Amaranth in Taiwan. Journal of Phytopathology 164: 94–101.

Ann PJ, Ko WH (1980) Phytophthora insolita, a new species from Taiwan. Mycologia 72: 1180–1185.

Aragaki M, Uchida JY (2001) Morphological distinctions between Phytophthora capsici and P. tropicalis sp. nov. Mycologia 93: 137–145.

Balci Y, Balci S, Blair JE, Park SY, Kang S, et al. (2008) Phytophthora quercetorum sp. nov., a novel species isolated from eastern and north-central USA oak forest soils. Mycological Research 112: 906–916.

Belbahri L, Moralejo E, Calmin G, Oszako T, Garcia JA, et al. (2006) Phytophthora polonica, a new species isolated from declining Alnus glutinosa stands in Poland. FEMS Microbiology Letters 261: 165–174.

Bertier L, Brouwer H, De Cock A, Cooke DEL, Olsson CHB, et al. (2013) The expansion of Phytophthora clade 8b: three new species associated with winter grown vegetable crops. Persoonia 31: 63–76.

Bezuidenhout CM, Denman S, Kirk SA, Botha WJ, Mostert L, et al. (2010) Phytophthora taxa associated with cultivated Agathosma, with emphasis on the P. citricola complex and P. capensis sp. nov. Persoonia 25: 32–49.

Page 26: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

380 I M A F U N G U S

Blackwell E (1949) Terminology in Phytophthora. Mycological Papers 30: 1–24.

Blair JE, Coffey MD, Park S-Y, Geiser DM, Kang S (2008) A multi-locus phylogeny for Phytophthora utilizing markers derived from complete genome sequences. Fungal Genetics and Biology 45: 266–277.

Brasier CM (1983) Problems and prospects in Phytophthora research. In: Phytophthora: its Biology, taxonomy, ecology, and pathology (Erwin DC, Bartnicki-Garcia S, Tsao PH, eds): 351–364. St Paul, MN: American Phytopathological Society Press.

Brasier CM, Beales PA, Kirk SA, Denman S, Rose J (2005) Phytophthora kernoviae sp. nov., an invasive pathogen causing bleeding stem lesions on forest trees and foliar necrosis of ornamentals in the UK. Mycological Research 109: 853–859.

Brasier CM, Cooke DEL, Duncan JM, Hansen EM (2003a) Multiple new phenotypic taxa from trees and riparian ecosystems in Phytophthora gonapodyides–P. megasperma ITS Clade 6, which tend to be high-temperature tolerant and either inbreeding or sterile. Mycological Research 107: 277–290.

Brasier CM, Griffin MJ (1979) Taxonomy of ‘Phytophthora palmivora’ on cocoa. Transactions of the British Mycological Society 72: 111–143.

Brasier CM, Kirk SA, Delcan J, Cooke DEL, Jung T, et al. (2004) Phytophthora alni sp. nov. and its variants: designation of emerging heteroploid hybrid pathogens spreading on Alnus trees. Mycological Research 108: 1172–1184.

Brasier CM, Sanchez-Hernandez E, Kirk SA (2003b) Phytophthora inundata sp. nov., a part heterothallic pathogen of trees and shrubs in wet or flooded soils. Mycological Research 107: 477–484.

Brazee NJ, Yang X, Hong C (2017) Phytophthora caryae sp. nov., a new species recovered from streams and rivers in the eastern United States. Plant Pathology 66: 805–817.

Breda De Haan JV (1896) De bibitziekte in de Deli-tabak veroorzaakt door Phytophthora nicotianae. Mededeelingen uit ‘s Lands Plantentuin Batavia 15: 1–107.

Buddenhagen IW, Young RA (1957) A leaf and twig disease of English holly caused by Phytophthora ilicis n. sp. Phytopathology 47: 95–101.

Buisman CJ (1927) Root rots caused by Phycomycetes. Mededelingen Phytopathologisch Laboratorium “Willie Commelin Scholten” 11:1–51.

Butler EJ (1910) The bud-rot of palms in India. Memoirs of the Department of Agriculture in India, Botanical Series 3: 221–280.

Carne WM (1925) A brown rot of citrus in Australia (Phytophthora hibernalis n. sp). Journal of the Royal Society of Western Australia 12: 13–41.

Chee KH (1969) Variability of Phytophthora species from Hevea brasiliensis. Transactions of the British Mycological Society 52: 425–436.

Cooke DEL, Drenth A, Duncan JM, Wagels G, Brasier CM (2000) A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genetics and Biology 30: 17–32.

Crandall BS (1947) A new Phytophthora causing root and collar rot of Cinchona in Peru. Mycologia 39: 218–223.

Crous PW, Groenewald JZ, Shivas RG, Edwards J, Seifert KA, et al. (2011) Fungal Planet description sheets: 69–91. Persoonia 26: 108–156.

Crous PW, Summerell BA, Shivas RG, Burgess TI, Decock CA, et al. (2012) Fungal Planet description sheets: 107–127. Persoonia 28: 138–182.

Crous PW, Wingfield MJ, Le Roux JJ, Richardson DM, Strasberg D, et al. (2015) Fungal Planet description sheets: 371–399. Persoonia 35: 264–327.

De Bary A (1876) Researches into the nature of the potato-fungus, Phytophthora infestans. Journal of the Royal Agricultural Society of England 12: 239–269.

De Cock AW, Lévesque CA (2004) New species of Pythium and Phytophthora. Studies in Mycology 50: 481–487.

De Cock AWAM, Lodhi AM, Rintoul TL, Bala K, Robideau GP, et al. (2015) Phytopythium: molecular phylogeny and systematics. Persoonia 34: 25–39.

Dick MA, Dobbie K, Cooke DEL, Brasier CM (2006) Phytophthora captiosa sp. nov. and P. fallax sp. nov. causing crown dieback of Eucalyptus in New Zealand. Mycological Research 110: 393–404.

Donahoo R, Blomquist CL, Thomas SL, Moulton JK, Cooke DEL, et al. (2006) Phytophthora foliorum sp. nov., a new species causing leaf blight of azalea. Mycological Research 110: 1309–1322.

Drechsler C (1931) A crown-rot of hollyhocks caused by Phytophthora megasperma n. sp. Journal of the Washington Academy of Sciences 21: 513–526.

Duran A, Gryzenhout M, Slippers B, Ahumada R, Rotella A, et al. (2008) Phytophthora pinifolia sp. nov. associated with a serious needle disease of Pinus radiata in Chile. Plant Pathology 57: 715–727.

Ersek T, Ribeiro OK (2010) Mini review article: an annotated list of new Phytophthora species described post 1996. Acta Phytopathologica et Entomologica Hungarica 45: 251–266.

Ershad D (1971) Beitrag zur Kenntnis der Phytophthora-arten in Iran und Ihrer Phytopathologischen Bedeutung. Berlin-Dahlem: Mitteilungen aus der Biologischen Bundesanstalt fur Land- and Forstwirtschaft.

Erwin DC, Ribeiro OK (1996) Phytophthora Diseases Worldwide. St Paul, MN: American Phytopathological Society Press.

Flier WG, Grünwald NJ, Kroon L, Van Den Bosch TBM, Garay-Serrano E, et al. (2002) Phytophthora ipomoeae sp. nov., a new homothallic species causing leaf blight on Ipomoea longipedunculata in the Toluca Valley of central Mexico. Mycological Research 106: 848–856.

Galindo-A J, Hohl HR (1985) Phytophthora mirabilis, a new species of Phytophthora. Sydowia 38: 87–96.

Gallegly ME, Hong C (2008) Phytophthora: identifying species by morphology and DNA fingerprints. St Paul, MN: American Phytopathological Society Press.

Ginetti B, Moricca S, Squires JN, Cooke DEL, Ragazzi A, et al. (2014) Phytophthora acerina sp. nov., a new species causing bleeding cankers and dieback of Acer pseudoplatanus trees in planted forests in northern Italy. Plant Pathology 63: 858–876.

Goheen EM, Hansen EM, Kanaskie A, Mcwilliams MG, Osterbauer N, et al. (2002) Sudden oak death caused by Phytophthora ramorum in Oregon. Plant Disease 86: 441.

Greslebin AG, Hansen EM, Sutton W (2007) Phytophthora austyocedrae sp. nov., a new species associated with Austyocedrus chilensis mortality in Patagonia (Argentina). Mycological Research 111: 308–316.

Grünwald NJ, Werres S, Goss EM, Taylor CR, Fieland VJ (2012) Phytophthora obscura sp. nov., a new species of the novel Phytophthora subclade 8d. Plant Pathology 61: 610–622.

Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, et al. (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461: 393–398.

Page 27: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

381V O L U M E 8 · N O . 2

Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.

Hamm P, Hansen EM (1983) Phytophthora pseudotsugae, a new species causing root rot of Douglas-fir. Canadian Journal of Botany 61: 2626–2631.

Hansen EM, Maxwell DP (1991) Species of the Phytophthora megasperma complex. Mycologia 83: 376–381.

Hansen EM, Reeser P, Sutton W, Brasier CM (2015) Redesignation of Phytophthora taxon Pgchlamydo as Phytophthora chlamydospora sp. nov. North American Fungi 10: 1–14.

Hansen EM, Reeser PW, Davidson JM, Garbelotto M, Ivors K, et al. (2003) Phytophthora nemorosa, a new species causing cankers and leaf blight of forest trees in California and Oregon, U.S.A. Mycotaxon 88: 129–138.

Hansen EM, Reeser PW, Sutton W (2012) Phytophthora borealis and Phytophthora riparia, new species in Phytophthora ITS Clade 6. Mycologia 104: 1133–1142.

Hansen EM, Wilcox WF, Reeser PW, Sutton W (2009) Phytophthora rosacearum and P. sansomeana, new species segregated from the Phytophthora megasperma “complex”. Mycologia 101: 129–135.

Henricot B, Perez Sierra A, Jung T (2014) Phytophthora pachypleura sp. nov., a new species causing root rot of Aucuba japonica and other ornamentals in the United Kingdom. Plant Pathology 63: 1095–1109.

Heyman F, Blair JE, Persson L, Wikstrom M (2013) Root rot of pea and faba bean in southern Sweden caused by Phytophthora pisi sp. nov. Plant Disease 97: 461–471.

Hickman CJ (1940) The red core root disease of the strawberry caused by Phytophthora fragariae n. sp. Journal of Pomology and Horticultural Society 18: 89–118.

Hong C, Gallegly ME, Richardson PA, Kong P (2011) Phytophthora pini Leonian resurrected to distinct species status. Mycologia 103: 351–360.

Hong CX, Gallegly ME, Browne GT, Bhat RG, Richardson PA, et al. (2009) The avocado subgroup of Phytophthora citricola constitutes a distinct species, Phytophthora mengei sp. nov. Mycologia 101: 833–840.

Hong CX, Gallegly ME, Richardson PA, Kong P, Moorman GW (2008) Phytophthora irrigata, a new species isolated from irrigation reservoirs and rivers in Eastern United States of America. FEMS Microbiology Letters 285: 203–211.

Hong CX, Gallegly ME, Richardson PA, Kong P, Moorman GW, et al. (2010) Phytophthora hydropathica, a new pathogen identified from irrigation water, Rhododendron catawbiense and Kalmia latifolia. Plant Pathology 59: 913–921.

Hong CX, Richardson PA, Hao W, Ghimire SR, Kong P, et al. (2012) Phytophthora aquimorbida sp. nov. and Phytophthora taxon ‘aquatilis’ recovered from irrigation reservoirs and a stream in Virginia, USA. Mycologia 104: 1097–1108.

Hotson JW, Hartge L (1923) A disease of tomato caused by Phytophthora mexicana sp. nov. Phytopathology 13: 520–531.

Husson C, Aguayo J, Revellin C, Frey P, Ioos R, et al. (2015) Evidence for homoploid speciation in Phytophthora alni supports taxonomic reclassification in this species complex. Fungal Genetics and Biology 77: 12–21.

Ilieva E, Veld WaM, Veenbaas-Rijks W, Pieters R (1998) Phytophthora multivesiculata, a new species causing rot in Cymbidium. European Journal of Plant Pathology 104: 677–684.

Irwin JaG (1991) Phytophthora macrochlamydospora, a new species from Australia. Mycologia 83: 517–519.

Jung T, Burgess TI (2009) Re-evaluation of Phytophthora citricola isolates from multiple woody hosts in Europe and North America reveals a new species, Phytophthora plurivora sp. nov. Persoonia 22: 95–110.

Jung T, Cooke DEL, Blaschke H, Duncan JM, Oßwald W (1999) Phytophthora quercina sp. nov., causing root rot of European oaks. Mycological Research 103: 785–798.

Jung T, Hansen EM, Winton L, Oßwald W, Delatour C (2002) Three new species of Phytophthora from European oak forests. Mycological Research 106: 397–411.

Jung T, Jung MH, Scanu B, Seress D, Kovács GM, et al. (2017) Six new Phytophthora species from ITS Clade 7a including two sexually functional heterothallic hybrid species detected in natural ecosystems in Taiwan. Persoonia 38: 100–135.

Jung T, Nechwatal J (2008) Phytophthora gallica sp. nov., a new species from rhizosphere soil of declining oak and reed stands in France and Germany. Mycological Research 112: 1195–1205.

Jung T, Nechwatal J, Cooke DEL, Hartmann G, Blaschke M, et al. (2003) Phytophthora pseudosyringae sp. nov., a new species causing root and collar rot of deciduous tree species in Europe. Mycological Research 107: 772–789.

Jung T, Stukely MJC, Hardy GESJ, White D, Paap T, et al. (2011) Multiple new Phytophthora species from ITS Clade 6 associated with natural ecosystems in Australia: evolutionary and ecological implications. Persoonia 26: 13–39.

Kang S, Mansfield MA, Park B, Geiser DM, Ivors KL, et al. (2010) The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes. Phytopathology 100: 732–737.

Katsura K (1976) Two new species of Phytophthora causing damping-off of cucumber and trunk rot of chestnut. Transactions of the Mycological Society of Japan 17: 238–242.

Kaufmann MJ, Gerdemann JW (1958) Root and stem rot of soybean caused by Phytophthora sojae n. sp. Phytopathology 48: 201–208.

Kennedy DM, Duncan JM (1995) A papillate Phytophthora species with specificity to Rubus. Mycological Research 99: 57–68.

Klebahn H (1905) Eine neue Pilzkrankheit der Syringen (A new fungal disease of Syringae). Zentralblatt für Bakteriologie, Parasitenkunde und Infektionskrankheiten 15: 335–336.

Ko WH, Ann PJ (1985) Phytophthora humicola, a new species from soil of a citrus orchard in Taiwan. Mycologia 77: 631–636.

Kröber H, Marwitz R (1993) Phytophthora tentaculata sp. nov. und Phytophthora cinnamomi var. parvispora var. nov., zwei neue Pilze von Zierpflanzen in Deutschland. Zeitschrift Fur Pflanzenkrankheiten Und Pflanzenschutz 100: 250–258.

Kroon LPNM, Bakker FT, Van Den Bosch GBM, Bonants PJM, Flier WG (2004) Phylogenetic analysis of Phytophthora species based on mitochondrial and nuclear DNA sequences. Fungal Genetics and Biology 41: 766–782.

Kroon LPNM, Brouwer H, De Cock AWAM, Govers F (2012) The genus Phytophthora anno 2012. Phytopathology 102: 348–364.

Lara E, Belbahri L (2011) SSU rRNA reveals major trends in oomycete evolution. Fungal Diversity 49: 93–100.

Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947–2948.

Leonian LH (1922) Stem and fruit blight of pepper caused by Phytophthora capsici sp. nov. Phytopathology 12: 401–408.

Page 28: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

382 I M A F U N G U S

Li WW, Zhao WX, Huai WX (2017) Phytophthora pseudopolonica sp. nov., a new species recovered from stream water in subtropical forests of China. International Journal of Systematic and Evolutionary Microbiology 67: 3666-3675.

Maddison WP, Maddison DR (2017) Mesquite: a modular system for evolutionary analysis. http://mesquiteproject.org.

Man In’t Veld WA, De Cock A, Ilieva E, Lévesque CA (2002) Gene flow analysis of Phytophthora porri reveals a new species: Phytophthora brassicae sp. nov. European Journal of Plant Pathology 108: 51–62.

Man In’t Veld WA, Rosendahl KCHM, Brouwer H, De Cock AWAM (2011) Phytophthora gemini sp. nov., a new species isolated from the halophilic plant Zostera marina in the Netherlands. Fungal Biology 115: 724–732.

Man In’t Veld WA, Rosendahl KCHM, Hong C (2012) Phytophthora ×serendipita sp. nov. and P. ×pelgrandis, two destructive pathogens generated by natural hybridization. Mycologia 104: 1390–1396.

Man In’t Veld WA, Rosendahl KCHM, Van Rijswick PCJ, Meffert JP, Westenberg M, et al. (2015) Phytophthora terminalis sp. nov. and Phytophthora occultans sp. nov., two invasive pathogens of ornamental plants in Europe. Mycologia 107: 54–65.

Man In’t Veld WA (2007) Gene flow analysis demonstrates that Phytophthora fragariae var. rubi constitutes a distinct species, Phytophthora rubi comb. nov. Mycologia 99: 222–226.

Martin FN, Abad ZG, Balci Y, Ivors K (2012) Identification and detection of Phytophthora: reviewing our progress, identifying our needs. Plant Disease 96: 1080–1103.

Martin FN, Blair JE, Coffey MD (2014) A combined mitochondrial and nuclear multilocus phylogeny of the genus Phytophthora. Fungal Genetics and Biology 66: 19–32.

Martin FN, Tooley PW (2003) Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes. Mycologia 95: 269–284.

Maseko B, Burgess TI, Coutinho TA, Wingfield MJ (2007) Two new Phytophthora species from South African Eucalyptus plantations. Mycological Research 111: 1321–1338.

Mcrae W (1918) Phytophthora meadii n. sp. on Hevea brasiliensis. Memoirs of the Department of Agriculture in India, Botanical Series 9: 219–273.

Mirabolfathy M, Cooke DEL, Duncan JM, Williams NA, Ershad D, et al. (2001) Phytophthora pistaciae sp. nov. and P. melonis: the principal causes of pistachio gummosis in Iran. Mycological Research 105: 1166–1175.

Mostowfizadeh-Ghalamfarsa R, Cooke DEL, Banihashemi Z (2008) Phytophthora parsiana sp. nov., a new high-temperature tolerant species. Mycological Research 112: 783–794.

Naher M, Motohash K, Watanabe H, Chikuo Y, Senda M, et al. (2011) Phytophthora chrysanthemi sp. nov., a new species causing root rot of chrysanthemum in Japan. Mycological Progress 10: 21–31.

Nechwatal J, Bakonyi J, Cacciola SO, Cooke DEL, Jung T, et al. (2013) The morphology, behaviour and molecular phylogeny of Phytophthora taxon Salixsoil and its redesignation as Phytophthora lacustris sp. nov. Plant Pathology 62: 355–369.

Nelson SC, Abad ZG (2010) Phytophthora morindae, a new species causing black flag disease on noni (Morinda citrifolia L.) in Hawaii. Mycologia 102: 122–134.

Nirenberg HI, Gerlach WF, Graefenhan T (2009) Phytophthora ×pelgrandis, a new natural hybrid pathogenic to Pelargonium grandiflorum hort. Mycologia 101: 220–231.

Oliva RF, Kroon LPNM, Chacon G, Flier WG, Ristaino JB, et al. (2010) Phytophthora andina sp. nov., a newly identified heterothallic pathogen of solanaceous hosts in the Andean highlands. Plant Pathology 59: 613–625.

Oudemans P, Coffey MD (1991) A revised systematics of twelve papillate Phytophthora species based on isozyme analysis. Mycological Research 95: 1025–1046.

Pánek M, Fér T, Mráček J, Tomšovský M (2016) Evolutionary relationships within the Phytophthora cactorum species complex in Europe. Fungal Biology 120: 836–851.

Park B, Martin F, Geiser DM, Kim HS, Mansfield MA, et al. (2013) Phytophthora database 2.0: update and future direction. Phytopathology 103: 1204–1208.

Petersen HE (1910) An account of Danish freshwater-phycomycetes, with biological and systematical remarks. Annales Mycologici 8: 494–560.

Pethybridge GH (1913) On the rotting of potato tubers by a new species of Phytophthora having a method of sexual reproduction hitherto undescribed. Scientific Proceedings of the Royal Dublin Society 13: 529–565.

Pethybridge GH, Lafferty AH (1919) A disease of tomato and other plants caused by a new species of Phytophthora. Scientific Proceedings of the Royal Dublin Society 15: 487–505.

Posada D (2008) jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25: 1253–1256.

Puglisi I, De Patrizio A, Schena L, Jung T, Evoli M, et al. (2017) Two previously unknown Phytophthora species associated with brown rot of Pomelo (Citrus grandis) fruits in Vietnam. PLoS ONE 12: e0172085.

Purss GS (1957) Stem rot: a disease of cowpeas caused by an undescribed species of Phytophthora. Queensland Journal of Agricultural Science 14: 125–154.

Raciborski M (1900) Parasitische Algen und Pilze Java’s. Buitenzorg: Botanisches Institut.

Rahman MZ, Mukobata H, Suga H, Kageyama K (2014a) Phytophthora asiatica sp. nov., a new species causing leaf and stem blight of kudzu in Japan. Mycological Progress 13: 759–769.

Rahman MZ, Uematsu S, Kimishima E, Kanto T, Kusunoki M, et al. (2015) Two plant pathogenic species of Phytophthora associated with stem blight of Easter lily and crown rot of lettuce in Japan. Mycoscience 56: 419–433.

Rahman MZ, Uematsu S, Takeuchi T, Shirai K, Ishiguro Y, et al. (2014b) Two new species, Phytophthora nagaii sp. nov. and P. fragariaefolia sp. nov., causing serious diseases on rose and strawberry plants, respectively, in Japan. Journal of General Plant Pathology 80: 348–365.

Rands RD (1922) Streepkanker van Kaneel, Veroorzaakt Door Phytophthora cinnamomi n. sp. Batavia: Drukkerij Ruygrok.

Rea AJ, Burgess TI, Hardy GESJ, Stukely MJC, Jung T (2011) Two novel and potentially endemic species of Phytophthora associated with episodic dieback of Kwongan vegetation in the south-west of Western Australia. Plant Pathology 60: 1055–1068.

Rea AJ, Jung T, Burgess TI, Stukely MJC, Hardy GESJ (2010) Phytophthora elongata sp. nov., a novel pathogen from the Eucalyptus marginata forest of Western Australia. Australasian Plant Pathology 39: 477–491.

Reeser P, Sutton W, Hansen E (2013) Phytophthora pluvialis, a new species from mixed tanoak-Douglas-fir forests of western Oregon, U.S.A. North American Fungi 8: 1–8.

Page 29: An expanded phylogeny for the genus Phytophthora

Phylogeny of PhytophthoraARTIC

LE

383V O L U M E 8 · N O . 2

Reeser PW, Hansen EM, Sutton W (2007) Phytophthora siskiyouensis, a new species from soil, water, myrtlewood (Umbellularia californica) and tanoak (Lithocarpus densiflorus) in southwestern Oregon. Mycologia 99: 639–643.

Rizzo DM, Garbelotto M, Davidson JM, Slaughter GW, Koike ST (2002) Phytophthora ramorum as the cause of extensive mortality of Quercus spp. and Lithocarpus densiflorus in California. Plant Disease 86: 205–214.

Rizzo DM, Garbelotto M, Hansen EA (2005) Phytophthora ramorum: integrative research and management of an emerging pathogen in California and Oregon forests. Annual Review of Phytopathology 43: 309–335.

Robideau GP, De Cock AWAM, Coffey MD, Voglmayr H, Brouwer H, et al. (2011) DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Molecular Ecology Resources 11: 1002–1011.

Ronquist F, Teslenko M, Van Der Mark P, Ayres DL, Darling A, et al. (2012) MrBayes 3.2: efficient bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542.

Safaiefarahani B, Mostowfizadeh-Ghalamfarsa R, Hardy G, Burgess TI (2015) Re-evaluation of the Phytophthora cryptogea species complex and the description of a new species, Phytophthora pseudocryptogea sp. nov. Mycological Progress 14: 108.

Safaiefarahani B, Mostowfizadeh-Ghalamfarsa R, Hardy GES, Burgess TI (2016) Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize. Fungal Biology 120: 975–987.

Sawada K (1927) Descriptive catalogue of the Formosan fungi III. Report of the Department of Agriculture Government Research Institute of Formosa 27: 1–62.

Scanu B, Hunter GC, Linaldeddu BT, Franceschini A, Maddau L, et al. (2014) A taxonomic re-evaluation reveals that Phytophthora cinnamomi and P. cinnamomi var. parvispora are separate species. Forest Pathology 44: 1–20.

Scanu B, Linaldeddu BT, Deidda A, Jung T (2015) Diversity of Phytophthora species from declining Mediterranean maquis vegetation, including two new species, Phytophthora crassamura and P. ornamentata sp. nov. PLoS ONE 10: e0143234.

Schröter J (1886) Die Pilze Schlesiens In: Kryptogamen-Flora von Schlesien (Cohn F, ed.): 3 (1): 1–814. Breslau: J U Kern’s Verlag.

Scott PM, Burgess TI, Barber PA, Shearer BL, Stukely MJC, et al. (2009) Phytophthora multivora sp. nov., a new species recovered from declining Eucalyptus, Banksia, Agonis and other plant species in Western Australia. Persoonia 22: 1–13.

Simamora AV, Stukely MJC, Hardy GES, Burgess TI (2015) Phytophthora boodjera sp. nov., a damping-off pathogen in production nurseries and from urban and natural landscapes, with an update on the status of P. alticola. IMA Fungus 6: 319–335.

Smith RE, Smith EH (1906) A new fungus of economic importance. Botanical Gazette 42: 215–221.

Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30: 1312–1313.

Swofford DL (2002) PAUP*: phylogenetic analysis using parsimony (*and other methods). Sunderland, MA: Sinauer Associates.

Taylor PA, Pascoe IG, Greenhalgh FC (1985) Phytophthora clandestina sp. nov. in roots of subterranean clover. Mycotaxon 22: 77–85.

Thaxter R (1889) A new American Phytophthora. Botanical Gazette 14: 273–274.

Thompson A (1929) Phytophthora species in Malaya. The Malayan Agricultural Journal 17: 53–100.

Tomlinson JA (1952) Brown core root rot of Primula caused by Phytophthora primulae n. sp. Transactions of the British Mycological Society 35: 221–235.

Tucker CM (1931) Taxonomy of the Genus Phytopthora de Bary. Research Bulletin of the Missouri Agricultural Experiment Station 153: 1–208.

Tucker CM, Milbrath JA (1942) Root rot of Chamaecyparis caused by a species of Phytophthora. Mycologia 34: 94–103.

Turner RS (2005) After the famine: Plant pathology, Phytophthora infestans, and the late blight of potatoes, 1845–1960. Historical Studies in the Physical and Biological Sciences 35: 341–370.

Tyler BM, Tripathy S, Zhang XM, Dehal P, Jiang RHY, et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313: 1261–1266.

Uzuhashi S, Tojo M, Kakishima M (2010) Phylogeny of the genus Pythium and description of new genera. Mycoscience 51: 337–365.

Vettraino AM, Brasier CM, Brown AV, Vannini A (2011) Phytophthora himalsilva sp. nov. an unusually phenotypically variable species from a remote forest in Nepal. Fungal Biology 115: 275–287.

Villa NO, Kageyama K, Asano T, Suga H (2006) Phylogenetic relationships of Pythium and Phytophthora species based on ITS rDNA, cytochrome oxidase II and beta-tubulin gene sequences. Mycologia 98: 410–422.

Waterhouse GM (1963) Key to the species of Phytophthora de Bary. Mycological Papers 92: 1–22.

Weir BS, Paderes EP, Anand N, Uchida JY, Pennycook SR, et al. (2015) A taxonomic revision of Phytophthora Clade 5 including two new species, Phytophthora agathidicida and P. cocois. Phytotaxa 205: 21–38.

Werres S, Marwitz R, Man in’t Veld WA, De Cock AW, Bonants PJ, et al. (2001) Phytophthora ramorum sp. nov., a new pathogen on Rhododendron and Viburnum. Mycological Research 105: 1155–1165.

Yang X (2014) New Species and Phylogeny of the Genus Phytophthora. PhD thesis, Virginia Tech.

Yang X, Balci Y, Brazee NJ, Loyd AL, Hong C (2016) A unique species in Phytophthora clade 10, Phytophthora intercalaris sp. nov., recovered from stream and irrigation water in the eastern USA. International Journal of Systematic and Evolutionary Microbiology 66: 845–855.

Yang X, Copes WE, Hong CX (2013) Phytophthora mississippiae sp. nov., a new species recovered from irrigation reservoirs at a plant nursery in Mississippi. Journal of Plant Pathology & Microbiology 4: 180.

Yang X, Copes WE, Hong CX (2014a) Two novel species representing a new clade and cluster of Phytophthora. Fungal Biology 118: 72–82.

Yang X, Gallegly ME, Hong CX (2014b) A high-temperature tolerant species in clade 9 of the genus Phytophthora: P. hydrogena sp. nov. Mycologia 106: 57–65.

Yang X, Hong C (2014) Halophytophthora fluviatilis sp. nov. from freshwater in Virginia. FEMS Microbiology Letters 352: 230–237.

Yang X, Hong CX (2013) Phytophthora virginiana sp. nov., a high-temperature tolerant species from irrigation water in Virginia. Mycotaxon 126: 167–176.

Page 30: An expanded phylogeny for the genus Phytophthora

Yang et al.ARTICLE

384 I M A F U N G U S

Yang X, Richardson PA, Hong C (2014c) Phytophthora ×stagnum nothosp. nov., a new hybrid from irrigation reservoirs at ornamental plant nurseries in Virginia. PLoS ONE 9: e103450.

Ye W, Wang Y, Shen D, Li D, Pu T, et al. (2016) Sequencing of the litchi downy blight pathogen reveals it is a Phytophthora species with downy mildew-like characteristics. Molecular Plant-Microbe Interactions 29: 573–583.

Page 31: An expanded phylogeny for the genus Phytophthora

Supplementary Table 1Su

pple

men

tary

Tab

le 1

. Inf

orm

atio

n of

all

isol

ates

incl

uded

in th

e ph

ylog

enet

ic a

naly

ses

incl

udin

g lo

cal,

inte

rnat

iona

l and

alte

rnat

ive

isol

ate

num

bers

, spe

cies

iden

titie

s, h

osts

and

sub

stra

tes,

orig

ins,

yea

r, sp

oran

gial

pap

illat

ion

and

Gen

Ban

k ac

cess

ion

num

bers

.

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

1aP.

cac

toru

m22

E6

P10

194

p25

S81

4 (S

chm

itthe

nner

)K

X25

0369

KX

2503

70K

X25

0371

KX

2503

72K

X25

0373

KX

2503

74K

X25

0375

1aP.

cac

toru

m22

E7

1669

302

1168

P07

15p6

IFO

311

51, N

93, N

CTC

20

82E

U08

0284

EU

0802

85E

U08

0286

EU

0802

87E

U08

0288

EU

0802

89E

U08

0290

1aP.

cac

toru

m22

E8

1669

4, M

YA-3

653

0504

70P

1019

3p7

N94

K

X25

0376

KX

2503

77K

X25

0378

KX

2503

79K

X25

0380

KX

2503

81K

X25

0382

1aP.

hed

raia

ndra

33F3

MYA

-416

5p2

25M

NT8

(Bla

nche

tte)

KX

2503

83K

X25

0384

KX

2503

85K

X25

0386

KX

2503

87K

X25

0388

KX

2503

89

1aP.

hed

raia

ndra

38C

2K

X25

0390

KX

2503

91K

X25

0392

KX

2503

93K

X25

0394

KX

2503

95K

X25

0396

1aP.

hed

raia

ndra

62A

511

1725

P19

523

KX

2503

97K

X25

0398

KX

2503

99K

X25

0400

KX

2504

01K

X25

0402

KX

2504

03

1aP.

idae

i34

D4

971,

95M

YA-4

065

3137

28P

6767

p220

SC

RI R

77, P

D 9

4/95

9E

U08

0129

EU

0801

30E

U08

0131

EU

0801

32E

U08

0133

EU

0801

34E

U08

0135

1aP.

idae

i62

A1

968,

95S

CR

I R23

, ID

A 1

KX

2504

04K

X25

0405

KX

2504

06K

X25

0407

KX

2504

08K

X25

0409

KX

2504

10

1aP.

pse

udot

suga

e52

938

3316

62P

1033

926

8 (H

anse

n)E

U08

0426

EU

0804

27E

U08

0428

EU

0804

29E

U08

0430

EU

0804

31E

U08

0432

1aP.

aff.

hed

raia

ndra

33F4

p226

MN

T63

(Bla

nche

tte)

KX

2504

11K

X25

0412

KX

2504

13K

X25

0414

KX

2504

15K

X25

0416

KX

2504

17

1aP.

aff.

pse

udot

suga

e29

B3

p185

333

(Han

sen)

KX

2504

18K

X25

0419

KX

2504

20K

X25

0421

KX

2504

22K

X25

0423

KX

2504

24

1bP.

cla

ndes

tina

32G

134

7,86

5871

3, 6

0438

2789

33P

3943

p200

DA

R 4

9489

EU

0798

66E

U07

9867

EU

0798

68E

U07

9869

EU

0798

70E

U07

9871

EU

0798

72

1bP.

cla

ndes

tina

33D

8M

YA-4

064

2873

17p2

15S

CR

P19

7 C

LA2

KX

2504

25K

X25

0426

KX

2504

27K

X25

0428

KX

2504

29K

X25

0430

KX

2504

31

1bP.

cla

ndes

tina

38D

4p3

04H

LNat

148

KX

2504

32K

X25

0433

KX

2504

34K

X25

0435

KX

2504

36K

X25

0437

KX

2504

38

1bP.

iran

ica

61J4

374,

7260

237

1589

64P

3882

p218

DC

SC

RP

386,

UQ

2132

KX

2504

39K

X25

0440

KX

2504

41K

X25

0442

KX

2504

43K

X25

0444

KX

2504

45

1bP.

tent

acul

ata

29F2

552,

96P

8497

BB

A 65

520

EU

0799

55E

U07

9956

EU

0799

57E

U07

9958

EU

0799

59E

U07

9960

EU

0799

61

1bP.

tent

acul

ata

30D

5P

D97

/555

2K

X25

0446

KX

2504

47K

X25

0448

KX

2504

49K

X25

0450

KX

2504

51K

X25

0452

1bP.

tent

acul

ata

30G

8M

YA-3

655

KK

6-99

-KT

KX

2504

53K

X25

0454

KX

2504

55K

X25

0456

KX

2504

57K

X25

0458

KX

2504

59

1cP.

and

ina

60A

2p4

60E

C33

94K

X25

0460

KX

2504

61K

X25

0462

KX

2504

63K

X25

0464

KX

2504

65K

X25

0466

1cP.

and

ina

60A

3p4

61E

C34

25K

X25

0467

KX

2504

68K

X25

0469

KX

2504

70K

X25

0471

KX

2504

72K

X25

0473

1cP.

and

ina

P13

365

EC

3365

E

U08

0182

EU

0801

83E

U08

0184

EU

0801

85E

U08

0186

EU

0801

87E

U08

0188

1cP.

infe

stan

s27

A8

KD

T-2C

KX

2504

74K

X25

0475

KX

2504

76K

X25

0477

KX

2504

78K

X25

0479

KX

2504

80

1cP.

infe

stan

sP

1065

0E

U07

9625

EU

0796

26E

U07

9627

EU

0796

28E

U07

9629

EU

0796

30E

U07

9631

1cP.

ipom

oeae

31B

4P

1022

6P

IC99

165

EU

0808

37E

U08

0838

EU

0808

39E

U08

0840

EU

0808

41E

U08

0842

EU

0808

43

1cP.

ipom

oeae

31B

510

9229

P10

225

PIC

9916

9, M

UC

L 30

219

EU

0808

30E

U08

0831

EU

0808

32E

U08

0833

EU

0808

34E

U08

0835

EU

0808

36

1cP.

ipom

oeae

31B

6P

1022

7P

IC99

193

EU

0808

44E

U08

0845

EU

0808

46E

U08

0847

EU

0808

48E

U08

0849

EU

0808

50

1cP.

mira

bilis

30C

164

069,

MYA

-406

2P

3006

p145

Hoh

l NR

188

, M8

KX

2504

81K

X25

0482

KX

2504

83K

X25

0484

KX

2504

85K

X25

0486

KX

2504

87

1cP.

mira

bilis

30C

264

070,

MYA

-406

3P

3007

p153

Hoh

l NR

189

, M9

KX

2504

88K

X25

0489

KX

2504

90K

X25

0491

KX

2504

92K

X25

0493

KX

2504

94

1cP.

pha

seol

i23

B4

p106

KX

2504

95K

X25

0496

KX

2504

97K

X25

0498

KX

2504

99K

X25

0500

KX

2505

01

1cP.

pha

seol

i35

B6

Phy

P13

KX

2505

02K

X25

0503

KX

2505

04K

X25

0505

KX

2505

06K

X25

0507

KX

2505

08

1cP.

pha

seol

iP

1014

5P

hyP

4E

U08

0748

EU

0807

49E

U08

0750

EU

0807

51E

U08

0752

EU

0807

53E

U08

0754

1cP.

pha

seol

iP

1015

0P

hyP

FE

U08

0761

EU

0807

62E

U08

0763

EU

0807

64E

U08

0765

EU

0807

66E

U08

0767

1P.

nic

otia

nae

22F9

1541

0, M

YA-4

037

p23

N25

KX

2505

09K

X25

0510

KX

2505

11K

X25

0512

KX

2505

13K

X25

0514

KX

2505

15

1P.

nic

otia

nae

22G

115

409,

MYA

-403

6p2

2N

15K

X25

0516

KX

2505

17K

X25

0518

KX

2505

19K

X25

0520

KX

2505

21K

X25

0522

1P.

nic

otia

nae

P10

116

EU

0799

62E

U07

9963

EU

0799

64E

U07

9965

EU

0799

66E

U07

9967

EU

0799

68

Page 32: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

1P.

nic

otia

nae

P14

52W

-8E

U08

0503

EU

0805

04E

U08

0505

EU

0805

06E

U08

0507

EU

0805

08E

U08

0509

2aP.

bot

ryos

a22

H8

MYA

-405

9p4

4Ts

ao 6

2-2

KX

2505

23K

X25

0524

KX

2505

25K

X25

0526

KX

2505

27K

X25

0528

KX

2505

29

2aP.

bot

ryos

a46

C2

2648

1p3

84C

hee

1117

KX

2505

30K

X25

0531

KX

2505

32K

X25

0533

KX

2505

34K

X25

0535

KX

2505

36

2aP.

bot

ryos

a62

C6

581,

6913

6915

P34

25C

hee

1075

KX

2505

37K

X25

0538

KX

2505

39K

X25

0540

KX

2505

41K

X25

0542

KX

2505

43

2aP.

bot

ryos

a13

0422

P69

45Ta

n 14

62E

U07

9934

EU

0799

35E

U07

9936

EU

0799

37E

U07

9938

EU

0799

39E

U07

9940

2aP.

citr

opht

hora

03E

5p1

32K

X25

0544

KX

2505

45K

X25

0546

KX

2505

47K

X25

0548

KX

2505

49K

X25

0550

2aP.

citr

opht

hora

26H

3p3

1Ts

ao 5

90K

X25

0551

KX

2505

52K

X25

0553

KX

2505

54K

X25

0555

KX

2505

56K

X25

0557

2aP.

col

ocas

iae

22F8

MYA

-415

9p4

7K

X25

0558

KX

2505

59K

X25

0560

KX

2505

61K

X25

0562

KX

2505

63K

X25

0564

2aP.

col

ocas

iae

35D

3p2

76U

chid

a H

1676

KX

2505

65K

X25

0566

KX

2505

67K

X25

0568

KX

2505

69K

X25

0570

KX

2505

71

2aP.

him

alsi

lva

61G

212

8767

NP

44K

X25

0572

KX

2505

73K

X25

0574

KX

2505

75K

X25

0576

KX

2505

77K

X25

0578

2aP.

him

alsi

lva

61G

312

8753

NP

61K

X25

0579

KX

2505

80K

X25

0581

KX

2505

82K

X25

0583

KX

2505

84K

X25

0585

2aP.

mea

dii

22G

5M

YA-4

043

p75

KX

2505

86K

X25

0587

KX

2505

88K

X25

0589

KX

2505

90K

X25

0591

KX

2505

92

2aP.

mea

dii

61J9

219,

8812

9185

KX

2505

93K

X25

0594

KX

2505

95K

X25

0596

KX

2505

97K

X25

0598

KX

2505

99

2aP.

occ

ulta

ns65

B9

1015

57P

D98

1818

110

KX

2506

00K

X25

0601

KX

2506

02K

X25

0603

KX

2506

04K

X25

0605

KX

2506

06

2aP.

term

inal

is65

B8

1338

65P

D01

0104

8855

12-1

KX

2506

07K

X25

0608

KX

2506

09K

X25

0610

KX

2506

11K

X25

0612

KX

2506

13

2aP.

aff.

citr

opht

hora

26H

4p3

267

8 (T

sao)

KX

2506

14K

X25

0615

KX

2506

16K

X25

0617

KX

2506

18K

X25

0619

KX

2506

20

2aP.

aff.

citr

opht

hora

3428

98P

1034

1E

U08

0384

EU

0803

85E

U08

0386

EU

0803

87E

U08

0388

EU

0803

89E

U08

0390

2aP.

aff.

him

alsi

lva

61G

412

8754

NP

86K

X25

0621

KX

2506

22K

X25

0623

KX

2506

24K

X25

0625

KX

2506

26K

X25

0627

2aP.

sp.

46C

346

C3

6676

7P

6713

p385

Moy

141

3K

X25

0628

KX

2506

29K

X25

0630

KX

2506

31K

X25

0632

KX

2506

33K

X25

0634

2aP.

sp.

P62

62P

6262

Raj

alak

shm

y #4

6E

U07

9887

EU

0798

88E

U07

9889

EU

0798

90E

U07

9891

EU

0798

92n.

a.

2aP.

sp.

P63

10P

6310

#066

EU

0805

37E

U08

0538

EU

0805

39E

U08

0540

EU

0805

41E

U08

0542

EU

0805

43

2bP.

cap

sici

22F4

1539

9, M

YA-4

034

p8N

58K

X25

0635

KX

2506

36K

X25

0637

KX

2506

38K

X25

0639

KX

2506

40K

X25

0641

2bP.

cap

sici

4601

2P

0253

Rom

ero4

018

EU

0808

51E

U08

0852

EU

0808

53E

U08

0854

EU

0808

55E

U08

0856

EU

0808

57

2bP.

cap

sici

1216

56P

1038

6O

P97

, Lam

our 5

1E

U07

9543

EU

0795

44E

U07

9545

EU

0795

46E

U07

9547

EU

0795

48E

U07

9549

2bP.

glo

vera

31E

5p1

67A

bad

1109

1.1

KX

2506

42K

X25

0643

KX

2506

44K

X25

0645

KX

2506

46K

X25

0647

KX

2506

48

2bP.

glo

vera

62B

412

1969

P11

685

Aba

d 11

099

No.

23.

BP

I 87

8720

KX

2506

49K

X25

0650

KX

2506

51K

X25

0652

KX

2506

53K

X25

0654

KX

2506

55

2bP.

men

gei

42B

2M

YA-4

554

p340

M21

8.z1

KX

2506

56K

X25

0657

KX

2506

58K

X25

0659

KX

2506

60K

X25

0661

KX

2506

62

2bP.

men

gei

42B

3M

YA-4

555

p341

M22

0.z1

KX

2506

63K

X25

0664

KX

2506

65K

X25

0666

KX

2506

67K

X25

0668

KX

2506

69

2bP.

mex

ican

a45

G4

554,

8846

731

0925

50P

0646

p355

N31

7 K

X25

0670

KX

2506

71K

X25

0672

KX

2506

73K

X25

0674

KX

2506

75K

X25

0676

2bP.

sis

kiyo

uens

is41

B7

1227

79M

YA-4

187

P15

122

Han

sen

WA

5-03

0403

KX

2506

77K

X25

0678

KX

2506

79K

X25

0680

KX

2506

81K

X25

0682

KX

2506

83

2bP.

sis

kiyo

uens

is41

B8

Han

sen

33-2

-7-0

603

KX

2506

84K

X25

0685

KX

2506

86K

X25

0687

KX

2506

88K

X25

0689

KX

2506

90

2bP.

trop

ical

is22

H5

p27

Tsao

FP

59K

X25

0691

KX

2506

92K

X25

0693

KX

2506

94K

X25

0695

KX

2506

96K

X25

0697

2bP.

trop

ical

is35

C8

434,

9176

651,

MYA

-421

8p2

72U

chid

a H

245

KX

2506

98K

X25

0699

KX

2507

00K

X25

0701

KX

2507

02K

X25

0703

KX

2507

04

2bP.

aff.

cap

sici

22F5

1542

7, M

YA-4

035

p9N

14K

X25

0705

KX

2507

06K

X25

0707

KX

2507

08K

X25

0709

KX

2507

10K

X25

0711

Page 33: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

2bP.

sp.

bra

silie

nsis

4670

5P

0630

GM

11E

U08

0419

EU

0804

20E

U08

0421

EU

0804

22E

U08

0423

EU

0804

24E

U08

0425

2cP.

ace

rina

61H

113

3931

B05

7K

X25

0712

KX

2507

13K

X25

0714

KX

2507

15K

X25

0716

KX

2507

17K

X25

0718

2cP.

ace

rina

61H

2B

080

KX

2507

19K

X25

0720

KX

2507

21K

X25

0722

KX

2507

23K

X25

0724

KX

2507

25

2cP.

cap

ensi

s62

C1

1283

19P

1819

KX

2507

26K

X25

0727

KX

2507

28K

X25

0729

KX

2507

30K

X25

0731

KX

2507

32

2cP.

cap

ensi

s62

C2

1283

20P

1822

KX

2507

33K

X25

0734

KX

2507

35K

X25

0736

KX

2507

37K

X25

0738

KX

2507

39

2cP.

cap

ensi

s62

C3

1283

21P

1823

von

Bro

embs

en

8555

K2B

KX

2507

40K

X25

0741

KX

2507

42K

X25

0743

KX

2507

44K

X25

0745

KX

2507

46

2cP.

citr

icol

a33

H8

221,

8860

440

2117

3P

0716

p3

96N

107

KX

2507

47K

X25

0748

KX

2507

49K

X25

0750

KX

2507

51K

X25

0752

KX

2507

53

2cP.

citr

icol

a33

J229

5,29

p375

KX

2507

54K

X25

0755

KX

2507

56K

X25

0757

KX

2507

58K

X25

0759

KX

2507

60

2cP.

mul

tivor

a55

C5

1240

94W

AC

1320

1K

X25

0775

KX

2507

76K

X25

0777

KX

2507

78K

X25

0779

KX

2507

80K

X25

0781

2cP.

pac

hypl

eura

61H

659

55-2

006

KX

2507

82K

X25

0783

KX

2507

84K

X25

0785

KX

2507

86K

X25

0787

KX

2507

88

2cP.

pac

hypl

eura

61H

750

2404

5359

3-20

08

KX

2507

89K

X25

0790

KX

2507

91K

X25

0792

KX

2507

93K

X25

0794

KX

2507

95

2cP.

pac

hypl

eura

61H

810

5415

/09

KX

2507

96K

X25

0797

KX

2507

98K

X25

0799

KX

2508

00K

X25

0801

KX

2508

02

2cP.

pin

i22

F1M

YA-3

656

p53

KX

2508

03K

X25

0804

KX

2508

05K

X25

0806

KX

2508

07K

X25

0808

KX

2508

09

2cP.

pin

i45

F164

532

p343

KX

2508

10K

X25

0811

KX

2508

12K

X25

0813

KX

2508

14K

X25

0815

KX

2508

16

2cP.

plu

rivor

a22

E9

MYA

-365

7p1

01K

X25

0817

KX

2508

18K

X25

0819

KX

2508

20K

X25

0821

KX

2508

22K

X25

0823

2cP.

plu

rivor

a22

F2p5

2K

X25

0824

KX

2508

25K

X25

0826

KX

2508

27K

X25

0828

KX

2508

29K

X25

0830

2cP.

plu

rivor

a33

H9

379,

61K

X25

0831

KX

2508

32K

X25

0833

KX

2508

34K

X25

0835

KX

2508

36K

X25

0837

2cP.

sp.

22F

322

F3p3

3S

813

KX

2508

45K

X25

0846

KX

2508

47K

X25

0848

KX

2508

49K

X25

0850

KX

2508

51

2cP.

sp.

28D

128

D1

p119

KX

2507

61K

X25

0762

KX

2507

63K

X25

0764

KX

2507

65K

X25

0766

KX

2507

67

2cP.

sp.

28D

128

D3

p121

KX

2507

68K

X25

0769

KX

2507

70K

X25

0771

KX

2507

72K

X25

0773

KX

2507

74

2cP.

sp.

citr

icol

a VI

II27

D9

HH

FLK

X25

0838

KX

2508

39K

X25

0840

KX

2508

41K

X25

0842

KX

2508

43K

X25

0844

2cP.

sp.

pin

i-lik

e56

G1

Moo

rman

11-

1958

aK

X25

0852

KX

2508

53K

X25

0854

KX

2508

55K

X25

0856

KX

2508

57K

X25

0858

2cP.

taxo

n em

zans

i61

F2S

TE-U

627

2K

X25

0859

KX

2508

60K

X25

0861

KX

2508

62K

X25

0863

KX

2508

64K

X25

0865

2cP.

taxo

n em

zans

i61

F3S

TE-U

626

9K

X25

0866

KX

2508

67K

X25

0868

KX

2508

69K

X25

0870

KX

2508

71K

X25

0872

2dP.

bis

heria

29D

2Je

ffers

W.1

16K

X25

0873

KX

2508

74K

X25

0875

KX

2508

76K

X25

0877

KX

2508

78K

X25

0879

2dP.

bis

heria

31E

612

2081

P10

117

Cg

2.3

.3E

U08

0741

EU

0807

42E

U08

0743

EU

0807

44E

U08

0745

EU

0807

46E

U08

0747

2dP.

bis

heria

P16

20B

enso

n 41

1 E

U08

0612

EU

0806

13E

U08

0614

EU

0806

15E

U08

0616

EU

0806

17E

U08

0618

2dP.

elo

ngat

a33

J3S

G1-

1 95

2K

X25

0880

KX

2508

81K

X25

0882

KX

2508

83K

X25

0884

KX

2508

85K

X25

0886

2dP.

elo

ngat

a33

J4S

G1-

1 29

52K

X25

0887

KX

2508

88K

X25

0889

KX

2508

90K

X25

0891

KX

2508

92K

X25

0893

2dP.

elo

ngat

a55

C4

1257

99V

HS

134

82K

X25

0894

KX

2508

95K

X25

0896

KX

2508

97K

X25

0898

KX

2508

99K

X25

0900

2dP.

frig

ida

47G

6C

MW

1943

3K

X25

0901

KX

2509

02K

X25

0903

KX

2509

04K

X25

0905

KX

2509

06K

X25

0907

2dP.

frig

ida

47G

7C

MW

1943

4K

X25

0908

KX

2509

09K

X25

0910

KX

2509

11K

X25

0912

KX

2509

13K

X25

0914

2dP.

frig

ida

47G

8C

MW

2031

1K

X25

0915

KX

2509

16K

X25

0917

KX

2509

18K

X25

0919

KX

2509

20K

X25

0921

2eP.

mul

tives

icul

ata

29E

354

5,96

P10

410

PD

95/

8679

EU

0800

65E

U08

0066

EU

0800

67E

U08

0068

EU

0800

69E

U08

0070

EU

0800

71

2eP.

mul

tives

icul

ata

30D

4P

D 9

5/47

44K

X25

0922

KX

2509

23K

X25

0924

KX

2509

25K

X25

0926

KX

2509

27K

X25

0928

Page 34: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

2eP.

taxo

n aq

uatil

is38

J5M

YA-4

577

KX

2509

29K

X25

0930

KX

2509

31K

X25

0932

KX

2509

33K

X25

0934

KX

2509

35

3P.

ilic

is23

A7

5661

5, M

YA-3

897

P39

39p1

13H

o 18

.1K

X25

0936

KX

2509

37K

X25

0938

KX

2509

39K

X25

0940

KX

2509

41K

X25

0942

3P.

ilic

is34

D6

KX

2509

43K

X25

0944

KX

2509

45K

X25

0946

KX

2509

47K

X25

0948

KX

2509

49

3P.

ilic

is62

A7

1143

48P

D 9

1/59

5K

X25

0950

KX

2509

51K

X25

0952

KX

2509

53K

X25

0954

KX

2509

55K

X25

0956

3P.

nem

oros

a28

J3M

YA-4

061

p141

SP

T42.

51K

X25

0957

KX

2509

58K

X25

0959

KX

2509

60K

X25

0961

KX

2509

62K

X25

0963

3P.

nem

oros

a41

C4

MYA

-294

8p3

20 H

anse

n P

13K

X25

0964

KX

2509

65K

X25

0966

KX

2509

67K

X25

0968

KX

2509

69K

X25

0970

3P.

plu

vial

is60

B3

MYA

-493

0H

anse

n LC

-9.2

-020

508

KX

2509

71K

X25

0972

KX

2509

73K

X25

0974

KX

2509

75K

X25

0976

KX

2509

77

3P.

pse

udos

yrin

gae

30A

811

1772

MYA

-422

2p2

84P

SE

U 6

KX

2509

78K

X25

0979

KX

2509

80K

X25

0981

KX

2509

82K

X25

0983

KX

2509

84

3P.

pse

udos

yrin

gae

30B

1P

p285

PS

EU

9K

X25

0985

KX

2509

86K

X25

0987

KX

2509

88K

X25

0989

KX

2509

90K

X25

0991

3P.

psy

chro

phila

29J5

803,

95P

SY

1K

X25

0992

KX

2509

93K

X25

0994

KX

2509

95K

X25

0996

KX

2509

97K

X25

0998

3P.

psy

chro

phila

29J6

MYA

-408

3p2

88P

SY

2K

X25

0999

KX

2510

00K

X25

1001

KX

2510

02K

X25

1003

KX

2510

04K

X25

1005

4P.

alti

cola

47G

512

1939

P16

948

CM

W19

425

KX

2510

06K

X25

1007

KX

2510

08K

X25

1009

KX

2510

10K

X25

1011

KX

2510

12

4P.

are

naria

55C

212

7950

EN

A 3

KX

2510

13K

X25

1014

KX

2510

15K

X25

1016

KX

2510

17K

X25

1018

KX

2510

19

4P.

are

naria

62B

712

5800

EN

A 1

KX

2510

20K

X25

1021

KX

2510

22K

X25

1023

KX

2510

24K

X25

1025

KX

2510

26

4P.

meg

akar

ya22

H7

MYA

-404

0p4

2 T

sao

2035

32K

X25

1027

KX

2510

28K

X25

1029

KX

2510

30K

X25

1031

KX

2510

32K

X25

1033

4P.

meg

akar

ya61

J523

8,83

4210

020

2077

KX

2510

34K

X25

1035

KX

2510

36K

X25

1037

KX

2510

38K

X25

1039

KX

2510

40

4P.

meg

akar

ya61

J623

9,83

4209

910

6327

KX

2510

41K

X25

1042

KX

2510

43K

X25

1044

KX

2510

45K

X25

1046

KX

2510

47

4P.

pal

miv

ora

22G

8M

YA-4

039

P10

213

p65

KX

2510

48K

X25

1049

KX

2510

50K

X25

1051

KX

2510

52K

X25

1053

KX

2510

54

4P.

pal

miv

ora

22G

9M

YA-4

038

p26

Tsao

489

KX

2510

55K

X25

1056

KX

2510

57K

X25

1058

KX

2510

59K

X25

1060

KX

2510

61

4P.

que

rcet

orum

15C

7 J

effe

rs A

F.01

8K

X25

1062

KX

2510

63K

X25

1064

KX

2510

65K

X25

1066

KX

2510

67K

X25

1068

4P.

que

rcet

orum

15C

8 J

effe

rs A

F.01

8K

X25

1069

KX

2510

70K

X25

1071

KX

2510

72K

X25

1073

KX

2510

74K

X25

1075

4P.

que

rcin

a30

A4

783,

95Q

UE

1K

X25

2647

KX

2526

48K

X25

2649

KX

2526

50K

X25

2651

KX

2526

52K

X25

2653

4P.

que

rcin

a30

A5

784,

95M

YA-4

084

QU

E 3

KX

2526

54K

X25

2655

KX

2526

56K

X25

2657

KX

2526

58K

X25

2659

KX

2526

60

4P.

que

rcin

a30

A7

QU

E 1

64K

X25

2661

KX

2526

62K

X25

2663

KX

2526

64K

X25

2665

KX

2526

66K

X25

2667

4P.

sp.

ohi

oens

isP

1605

0B

alci

ST1

8-37

Phy

toph

thor

a D

atab

ase

Phy

toph

thor

a D

atab

ase

Phy

toph

thor

a D

atab

ase

Phy

toph

thor

a D

atab

ase

Phy

toph

thor

a D

atab

ase

Phy

toph

thor

a D

atab

ase

Phy

toph

thor

a D

atab

ase

5P.

aga

thid

icid

a67

D5

ICM

P 17

027

KX

2510

76K

X25

1077

KX

2510

78K

X25

1079

KX

2510

80K

X25

1081

KX

2510

82

5P.

cas

tane

ae22

H6

MYA

-406

0p4

5Ts

ao P

990

KX

2510

83K

X25

1084

KX

2510

85K

X25

1086

KX

2510

87K

X25

1088

KX

2510

89

5P.

cas

tane

ae30

E7

Ho

FFM

10-

5CK

X25

1090

KX

2510

91K

X25

1092

KX

2510

93K

X25

1094

KX

2510

95K

X25

1096

5P.

cas

tane

ae61

J758

7,85

3681

832

5914

L-2A

KX

2510

97K

X25

1098

KX

2510

99K

X25

1100

KX

2511

01K

X25

1102

KX

2511

03

5P.

coc

ois

67D

6IC

MP

1694

8K

X25

1104

KX

2511

05K

X25

1106

KX

2511

07K

X25

1108

KX

2511

09K

X25

1110

5P.

hev

eae

22J1

1806

16p2

8K

X25

1111

KX

2511

12K

X25

1113

KX

2511

14K

X25

1115

KX

2511

16K

X25

1117

5P.

hev

eae

22J2

1670

1, M

YA-3

895

p17

KX

2511

18K

X25

1119

KX

2511

20K

X25

1121

KX

2511

22K

X25

1123

KX

2511

24

6aP.

gem

ini

46H

112

3382

PD

99/

1347

1K

X25

1125

KX

2511

26K

X25

1127

KX

2511

28K

X25

1129

KX

2511

30K

X25

1131

6aP.

gem

ini

46H

212

3383

PD

99/

1347

2K

X25

1132

KX

2511

33K

X25

1134

KX

2511

35K

X25

1136

KX

2511

37K

X25

1138

Page 35: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

6aP.

hum

icol

a32

F820

0.81

5217

9, M

YA-4

080

P38

26p1

98K

X25

1139

KX

2511

40K

X25

1141

KX

2511

42K

X25

1143

KX

2511

44K

X25

1145

6aP.

hum

icol

a32

F9P

6702

p199

KX

2511

46K

X25

1147

KX

2511

48K

X25

1149

KX

2511

50K

X25

1151

KX

2511

52

6aP.

inun

data

30J3

3901

21p2

91B

rasi

er P

894

KX

2511

53K

X25

1154

KX

2511

55K

X25

1156

KX

2511

57K

X25

1158

KX

2511

59

6aP.

inun

data

30J4

3897

51p2

98B

rasi

er P

246B

KX

2511

60K

X25

1161

KX

2511

62K

X25

1163

KX

2511

64K

X25

1165

KX

2511

66

6aP.

inun

data

P86

19P

H-1

5-21

-93

EU

0802

02E

U08

0203

EU

0802

04E

U08

0205

EU

0802

06E

U08

0207

EU

0802

08

6aP.

rosa

cear

um22

J9M

YA-3

662

p82

Han

sen

62K

X25

1431

KX

2514

32K

X25

1433

KX

2514

34K

X25

1435

KX

2514

36K

X25

1437

6aP.

rosa

cear

um41

C1

p321

Han

sen

63K

X25

1438

KX

2514

39K

X25

1440

KX

2514

41K

X25

1442

KX

2514

43K

X25

1444

6aP.

rosa

cear

um47

J1M

YA-4

456

Han

sen

52, M

ircet

ich

20-3

-9K

X25

1445

KX

2514

46K

X25

1447

KX

2514

48K

X25

1449

KX

2514

50K

X25

1451

6aP.

sp.

48H

248

H2

KX

2514

80K

X25

1481

KX

2514

82K

X25

1483

KX

2514

84K

X25

1485

KX

2514

86

6aP.

sp.

62C

962

C9

Jung

TW

65K

X25

1487

KX

2514

88K

X25

1489

KX

2514

90K

X25

1491

KX

2514

92K

X25

1493

6aP.

sp.

per

soni

iP

1155

5A

bad

P51

.8 P

38X

-SE

U08

0312

EU

0803

13E

U08

0314

EU

0803

15E

U08

0316

EU

0803

17E

U08

0318

6aP.

taxo

n w

alnu

t40

A7

KX

2514

52K

X25

1453

KX

2514

54K

X25

1455

KX

2514

56K

X25

1457

KX

2514

58

6aP.

taxo

n w

alnu

t43

G1

KX

2514

59K

X25

1460

KX

2514

61K

X25

1462

KX

2514

63K

X25

1464

KX

2514

65

6bP.

am

nico

la61

G6

1316

52D

H22

8K

X25

1167

KX

2511

68K

X25

1169

KX

2511

70K

X25

1171

KX

2511

72K

X25

1173

6bP.

am

nico

la62

C5

1338

67P

D 0

1205

3369

71K

X25

1174

KX

2511

75K

X25

1176

KX

2511

77K

X25

1178

KX

2511

79K

X25

1180

6bP.

bilo

rban

g61

G8

1316

53S

A26

2K

X25

1181

KX

2511

82n.

a.K

X25

1183

KX

2511

84K

X25

1185

KX

2511

86

6bP.

bor

ealis

60B

213

2023

MYA

-488

1A

KW

A58

.1-0

708

KX

2511

87K

X25

1188

KX

2511

89K

X25

1190

KX

2511

91K

X25

1192

KX

2511

93

6bP.

cra

ssam

ura

66C

9P

H09

4K

X25

1194

KX

2511

95K

X25

1196

KX

2511

97K

X25

1198

KX

2511

99K

X25

1200

6bP.

cra

ssam

ura

66D

114

0357

PH

138

KX

2512

01K

X25

1202

KX

2512

03K

X25

1204

KX

2512

05K

X25

1206

KX

2512

07

6bP.

fluv

ialis

55B

612

9424

KX

2512

08K

X25

1209

KX

2512

10K

X25

1211

KX

2512

12K

X25

1213

KX

2512

14

6bP.

gib

bosa

55B

7V

HS

2200

7K

X25

1215

KX

2512

16K

X25

1217

KX

2512

18K

X25

1219

KX

2512

20K

X25

1221

6bP.

gib

bosa

62B

812

7951

VH

S21

998

KX

2512

22K

X25

1223

KX

2512

24K

X25

1225

KX

2512

26K

X25

1227

KX

2512

28

6bP.

gon

apod

yide

s21

J546

726

p117

KX

2512

29K

X25

1230

KX

2512

31K

X25

1232

KX

2512

33K

X25

1234

KX

2512

35

6bP.

gon

apod

yide

s34

A8

554,

6760

351

P68

72K

X25

1236

KX

2512

37K

X25

1238

KX

2512

39K

X25

1240

KX

2512

41K

X25

1242

6bP.

gre

gata

55B

8V

HS

2199

2K

X25

1243

KX

2512

44K

X25

1245

KX

2512

46K

X25

1247

KX

2512

48K

X25

1249

6bP.

gre

gata

62B

912

7952

VH

S21

962

KX

2512

50K

X25

1251

KX

2512

52K

X25

1253

KX

2512

54K

X25

1255

KX

2512

56

6bP.

lacu

stris

61D

6U

KN

-Ph1

KX

2512

57K

X25

1258

KX

2512

59K

X25

1260

KX

2512

61K

X25

1262

KX

2512

63

6bP.

lacu

stris

61D

8U

KN

-Ph1

5K

X25

1264

KX

2512

65K

X25

1266

KX

2512

67K

X25

1268

KX

2512

69K

X25

1270

6bP.

lacu

stris

61E

1U

KN

-Ph3

3K

X25

1271

KX

2512

72K

X25

1273

KX

2512

74K

X25

1275

KX

2512

76K

X25

1277

6bP.

lacu

stris

3897

25P

1033

7P

PIH

AS

-P56

6E

U08

0530

EU

0805

31E

U08

0532

EU

0805

33E

U08

0534

EU

0805

35E

U08

0536

6bP.

lito

ralis

55B

912

7953

VH

S 2

0763

KX

2512

78K

X25

1279

KX

2512

80K

X25

1281

KX

2512

82K

X25

1283

KX

2512

84

6bP.

meg

aspe

rma

62C

740

2,72

5881

732

035

P35

99K

X25

1285

KX

2512

86K

X25

1287

KX

2512

88K

X25

1289

KX

2512

90n.

a.

6bP.

mis

siss

ippi

ae57

J1K

X25

1291

KX

2512

92K

X25

1293

KX

2512

94K

X25

1295

KX

2512

96K

X25

1297

6bP.

mis

siss

ippi

ae57

J2K

X25

1298

KX

2512

99K

X25

1300

KX

2513

01K

X25

1302

KX

2513

03K

X25

1304

6bP.

mis

siss

ippi

ae57

J3M

YA-4

946

KX

2513

05K

X25

1306

KX

2513

07K

X25

1308

KX

2513

09K

X25

1310

KX

2513

11

Page 36: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

6bP.

mis

siss

ippi

ae57

J4K

X25

1312

KX

2513

13K

X25

1314

KX

2513

15K

X25

1316

KX

2513

17K

X25

1318

6bP.

orn

amen

tata

66D

214

0647

PH

152

KX

2513

19K

X25

1320

KX

2513

21K

X25

1322

KX

2513

23K

X25

1324

KX

2513

25

6bP.

orn

amen

tata

66D

3P

H15

3K

X25

1326

KX

2513

27K

X25

1328

KX

2513

29K

X25

1330

KX

2513

31K

X25

1332

6bP.

pin

ifolia

47H

112

2924

CM

W26

668

KX

2513

33K

X25

1334

KX

2513

35K

X25

1336

KX

2513

37K

X25

1338

KX

2513

39

6bP.

pin

ifolia

47H

212

2922

CM

W26

669

KX

2513

40K

X25

1341

KX

2513

42K

X25

1343

KX

2513

44K

X25

1345

KX

2513

46

6bP.

ripa

ria60

B1

1320

24M

YA-4

882

VI 3

-100

B9F

KX

2513

47K

X25

1348

KX

2513

49K

X25

1350

KX

2513

51K

X25

1352

KX

2513

53

6bP.

ther

mop

hila

55C

112

7954

VH

S13

530

KX

2513

54K

X25

1355

KX

2513

56K

X25

1357

KX

2513

58K

X25

1359

KX

2513

60

6bP.

×st

agnu

m36

H8

KX

2513

61K

X25

1362

KX

2513

63K

X25

1364

KX

2513

65K

X25

1366

KX

2513

67

6bP.

×st

agnu

m36

J7K

X25

1368

KX

2513

69K

X25

1370

KX

2513

71K

X25

1372

KX

2513

73K

X25

1374

6bP.

×st

agnu

m43

F3M

YA-4

926

KX

2513

75K

X25

1376

KX

2513

77K

X25

1378

KX

2513

79K

X25

1380

KX

2513

81

6bP.

×st

agnu

m44

F9K

X25

1382

KX

2513

83K

X25

1384

KX

2513

85K

X25

1386

KX

2513

87K

X25

1388

6bP.

sp.

26E

126

E1

p116

Tool

ey 3

93K

X25

1389

KX

2513

90K

X25

1391

KX

2513

92K

X25

1393

KX

2513

94K

X25

1395

6bP.

sp.

can

alen

sis

P10

456

UC

39E

U07

9569

EU

0795

70E

U07

9571

EU

0795

72E

U07

9573

EU

0795

74n.

a.

6bP.

sp.

del

awar

e63

H4

Gre

gory

HS

2BK

X25

1396

KX

2513

97K

X25

1398

KX

2513

99K

X25

1400

KX

2514

01K

X25

1402

6bP.

sp.

del

awar

e63

H7

Gre

gory

HS

16A

KX

2514

03K

X25

1404

KX

2514

05K

X25

1406

KX

2514

07K

X25

1408

KX

2514

09

6bP.

sp.

gre

gata

-like

22J5

1669

8p1

6 N

65K

X25

1410

KX

2514

11K

X25

1412

KX

2514

13K

X25

1414

KX

2514

15K

X25

1416

6bP.

sp.

meg

aspe

rma-

like

23A

1p8

1H

anse

n 61

KX

2514

17K

X25

1418

KX

2514

19K

X25

1420

KX

2514

21K

X25

1422

KX

2514

23

6bP.

sp.

meg

aspe

rma-

like

23A

3M

YA-3

660

p79

Han

sen

50K

X25

1424

KX

2514

25K

X25

1426

KX

2514

27K

X25

1428

KX

2514

29K

X25

1430

6P.

asp

arag

i33

D7

3840

46S

CR

P20

KX

2514

66K

X25

1467

KX

2514

68K

X25

1469

KX

2514

70K

X25

1471

KX

2514

72

6P.

asp

arag

i62

C4

1320

95M

YA-4

826

SP

326

KX

2514

73K

X25

1474

KX

2514

75K

X25

1476

KX

2514

77K

X25

1478

KX

2514

79

6P.

sp.

sul

awes

iens

isP

6306

EU

0803

45n.

a.E

U08

0346

EU

0803

47E

U08

0348

EU

0803

49E

U08

0350

7aP.

atte

nuat

a67

C5

Jung

TW

129

KX

2516

09K

X25

1610

KX

2516

11K

X25

1612

KX

2516

13K

X25

1614

KX

2516

15

7aP.

eur

opae

a30

A3

Jung

IFB

-EU

R 4

KX

2515

08K

X25

1509

KX

2515

10K

X25

1511

KX

2515

12K

X25

1513

KX

2515

14

7aP.

eur

opae

a34

C2

Hal

msc

hlag

er A

man

ce 1

KX

2515

15K

X25

1516

KX

2515

17K

X25

1518

KX

2515

19K

X25

1520

KX

2515

21

7aP.

eur

opae

a62

A2

1090

49Ju

ng IF

B-E

UR

2K

X25

1522

KX

2515

23K

X25

1524

KX

2515

25K

X25

1526

KX

2515

27K

X25

1528

7aP.

flex

uosa

67C

3Ju

ng T

W78

KX

2516

16K

X25

1617

KX

2516

18K

X25

1619

KX

2516

20K

X25

1621

KX

2516

22

7aP.

form

osa

67C

4Ju

ng T

W10

7K

X25

1623

KX

2516

24K

X25

1625

KX

2516

26K

X25

1627

KX

2516

28K

X25

1629

7aP.

frag

aria

e22

G6

1137

4P

3570

p114

KX

2515

29K

X25

1530

KX

2515

31K

X25

1532

KX

2515

33K

X25

1534

KX

2515

35

7aP.

frag

aria

e30

C5

KX

2515

36K

X25

1537

KX

2515

38K

X25

1539

KX

2515

40K

X25

1541

KX

2515

42

7aP.

frag

aria

e61

J320

9,46

1814

17P

6231

KX

2515

43K

X25

1544

KX

2515

45K

X25

1546

KX

2515

47K

X25

1548

KX

2515

49

7aP.

intr

icat

a67

B9

Jung

TW

16m

4, T

W25

9K

X25

1630

KX

2516

31K

X25

1632

KX

2516

33K

X25

1634

KX

2516

35K

X25

1636

7aP.

rubi

30D

7p1

86To

oley

397

KX

2515

50K

X25

1551

KX

2515

52K

X25

1553

KX

2515

54K

X25

1555

KX

2515

56

7aP.

rubi

41D

5H

erre

ro 9

255

KX

2515

57K

X25

1558

KX

2515

59K

X25

1560

KX

2515

61K

X25

1562

KX

2515

63

7aP.

rubi

46C

790

442

p389

R49

, CH

21K

X25

1564

KX

2515

65K

X25

1566

KX

2515

67K

X25

1568

KX

2515

69K

X25

1570

7aP.

ulig

inos

a62

A3

1090

54P

1041

3Ju

ng IF

B-U

LI 1

EU

0800

11E

U08

0012

EU

0800

13K

X25

1571

KX

2515

72E

U08

0015

KX

2515

73

Page 37: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

7aP.

ulig

inos

a62

A4

1090

55P

1032

8Ju

ng IF

B-U

LI 2

EU

0796

92E

U07

9693

EU

0796

94E

U07

9695

EU

0796

96E

U07

9697

EU

0796

98

7aP.

×al

ni32

J639

2317

MYA

-408

1p2

05P

834

KX

2515

74K

X25

1575

KX

2515

76K

X25

1577

KX

2515

78K

X25

1579

KX

2515

80

7aP.

×al

ni32

J739

2318

p206

P88

3K

X25

1581

KX

2515

82K

X25

1583

KX

2515

84K

X25

1585

KX

2515

86K

X25

1587

7aP.

×al

ni47

A7

3923

14P

772

KX

2515

88K

X25

1589

KX

2515

90K

X25

1591

KX

2515

92K

X25

1593

KX

2515

94

7aP.

×al

ni47

A8

WM

V20

0109

32K

X25

1595

KX

2515

96K

X25

1597

KX

2515

98K

X25

1599

KX

2516

00K

X25

1601

7aP.

×ca

mbi

vora

22F6

4671

9, M

YA-4

076

p64

Tsa

o P

592

KX

2514

94K

X25

1495

KX

2514

96K

X25

1497

KX

2514

98K

X25

1499

KX

2515

00

7aP.

×ca

mbi

vora

26F8

MYA

-407

5p3

8N

Y21

6K

X25

1501

KX

2515

02K

X25

1503

KX

2515

04K

X25

1505

KX

2515

06K

X25

1507

7aP.

×he

tero

hybr

ida

67C

1Ju

ng T

W30

KX

2516

37K

X25

1638

KX

2516

39K

X25

1640

KX

2516

41K

X25

1642

KX

2516

43

7aP.

×in

cras

sata

67C

2Ju

ng T

W43

m5

KX

2516

44K

X25

1645

KX

2516

46K

X25

1647

KX

2516

48K

X25

1649

KX

2516

50

7aP.

sp.

eur

opae

aSW

33F7

p229

BM

4/6

(Bal

ci)

KX

2516

02K

X25

1603

KX

2516

04K

X25

1605

KX

2516

06K

X25

1607

KX

2516

08

7bP.

asi

atic

a45

G1

9045

5p3

52H

o Lu

625

KX

2516

51K

X25

1652

KX

2516

53K

X25

1654

KX

2516

55K

X25

1656

KX

2516

57

7bP.

asi

atic

a46

C6

5619

4p3

88H

o 52

3 (P

31)

KX

2516

58K

X25

1659

KX

2516

60K

X25

1661

KX

2516

62K

X25

1663

KX

2516

64

7bP.

asi

atic

a61

H3

1333

47N

BR

C10

9140

, Tok

u-1

KX

2516

65K

X25

1666

KX

2516

67K

X25

1668

KX

2516

69K

X25

1670

KX

2516

71

7bP.

caj

ani

33D

9p2

14D

CS

CR

P23

1K

X25

1672

KX

2516

73K

X25

1674

KX

2516

75K

X25

1676

KX

2516

77K

X25

1678

7bP.

caj

ani

45F6

4438

9p3

48E

rwin

P4

KX

2516

79K

X25

1680

KX

2516

81K

X25

1682

KX

2516

83K

X25

1684

KX

2516

85

7bP.

caj

ani

45F7

4438

8P

3105

p349

Erw

in P

2K

X25

1686

KX

2516

87K

X25

1688

KX

2516

89K

X25

1690

KX

2516

91K

X25

1692

7bP.

mel

onis

32F6

MYA

-407

9P

1371

p196

KX

2516

93K

X25

1694

KX

2516

95K

X25

1696

KX

2516

97K

X25

1698

KX

2516

99

7bP.

mel

onis

41B

4p3

18B

anih

ashe

mi

PH

.6.4

2.92

KX

2517

00K

X25

1701

KX

2517

02K

X25

1703

KX

2517

04K

X25

1705

KX

2517

06

7bP.

mel

onis

45F3

582,

6952

854

Ho

H51

3K

X25

1707

KX

2517

08K

X25

1709

KX

2517

10K

X25

1711

KX

2517

12K

X25

1713

7bP.

nie

derh

ause

rii01

D5

p312

KX

2517

14K

X25

1715

KX

2517

16K

X25

1717

KX

2517

18K

X25

1719

KX

2517

20

7bP.

nie

derh

ause

rii23

J6M

YA-4

163

p57

Rib

eiro

Isra

el 2

KX

2517

21K

X25

1722

KX

2517

23K

X25

1724

KX

2517

25K

X25

1726

KX

2517

27

7bP.

nie

derh

ause

rii31

E7

P10

617

p169

Aba

d 52

12K

X25

1728

KX

2517

29K

X25

1730

KX

2517

31K

X25

1732

KX

2517

33K

X25

1734

7bP.

pis

i60

A4

Hey

man

976

03K

X25

1735

KX

2517

36K

X25

1737

KX

2517

38K

X25

1739

KX

2517

40K

X25

1741

7bP.

pis

i60

A5

Hey

man

215

0K

X25

1742

KX

2517

43K

X25

1744

KX

2517

45K

X25

1746

KX

2517

47n.

a.

7bP.

pis

taci

ae33

D6

MYA

-408

238

6658

p216

DC

SC

RP

533,

S16

KX

2517

48K

X25

1749

KX

2517

50K

X25

1751

KX

2517

52K

X25

1753

KX

2517

54

7bP.

pis

taci

ae41

A9

p314

Ban

ihas

hem

i P

H.6

.44.

93K

X25

1755

KX

2517

56K

X25

1757

KX

2517

58K

X25

1759

KX

2517

60K

X25

1761

7bP.

soj

ae22

D8

312.

6216

705,

MYA

-389

913

1375

p19

N9

KX

2517

62K

X25

1763

KX

2517

64K

X25

1765

KX

2517

66K

X25

1767

KX

2517

68

7bP.

soj

ae28

F9p2

36Ty

ler P

6497

KX

2517

69K

X25

1770

KX

2517

71K

X25

1772

KX

2517

73K

X25

1774

KX

2517

75

7bP.

vig

nae

45G

646

735

p357

Pur

ss 9

01, Z

entm

eyer

P

606,

K

X25

1776

KX

2517

77K

X25

1778

KX

2517

79K

X25

1780

KX

2517

81K

X25

1782

7bP.

vig

nae

45G

964

832

3161

96P

3420

p379

KX

2517

83K

X25

1784

KX

2517

85K

X25

1786

KX

2517

87K

X25

1788

KX

2517

89

7bP.

vig

nae

46C

111

2,76

6412

9p3

80K

X25

1790

KX

2517

91K

X25

1792

KX

2517

93K

X25

1794

KX

2517

95K

X25

1796

7cP.

cin

nam

omi

23B

115

400,

MYA

-405

7p1

0N

311

KX

2517

97K

X25

1798

KX

2517

99K

X25

1800

KX

2518

01K

X25

1802

KX

2518

03

7cP.

cin

nam

omi

23B

215

401,

MYA

-405

8p1

1N

33K

X25

1804

KX

2518

05K

X25

1806

KX

2518

07K

X25

1808

KX

2518

09K

X25

1810

Page 38: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

7cP.

cin

nam

omi

61J1

144,

2246

671

2293

8P

2110

KX

2518

11K

X25

1812

KX

2518

13K

X25

1814

KX

2518

15K

X25

1816

KX

2518

17

7cP.

par

visp

ora

30G

9M

YA-4

078

p178

Wer

res

BB

A65

507

KX

2518

18K

X25

1819

KX

2518

20K

X25

1821

KX

2518

22K

X25

1823

KX

2518

24

7cP.

par

visp

ora

46F6

Wer

res

BB

A65

508

KX

2518

25K

X25

1826

KX

2518

27K

X25

1828

KX

2518

29K

X25

1830

KX

2518

31

7cP.

par

visp

ora

66C

713

2771

Sca

nu P

H02

8K

X25

1832

KX

2518

33K

X25

1834

KX

2518

35K

X25

1836

KX

2518

37K

X25

1838

7cP.

par

visp

ora

66C

813

2772

Sca

nu P

H07

2K

X25

1839

KX

2518

40K

X25

1841

KX

2518

42K

X25

1843

KX

2518

44K

X25

1845

7cP.

sp.

ax

46H

5K

X25

1846

KX

2518

47K

X25

1848

KX

2518

49K

X25

1850

KX

2518

51K

X25

1852

7dP.

frag

aria

efol

ia61

H4

1357

47N

BR

C10

9709

, C

H05

NS

U11

, M

AFF

2440

58

KX

2518

53K

X25

1854

KX

2518

55K

X25

1856

KX

2518

57K

X25

1858

KX

2518

59

7dP.

nag

aii

61H

513

3248

NB

RC

1091

31,

CH

04P

HR

12,

MA

FF24

4047

KX

2518

60K

X25

1861

KX

2518

62K

X25

1863

KX

2518

64K

X25

1865

KX

2518

66

8aP.

cry

ptog

ea61

H9

113,

1918

0615

P17

38B

PIC

118

9K

X25

1867

KX

2518

68K

X25

1869

KX

2518

70K

X25

1871

KX

2518

72K

X25

1873

8aP.

dre

chsl

eri

15E

5Je

ffers

AF.

021

KX

2518

74K

X25

1875

KX

2518

76K

X25

1877

KX

2518

78K

X25

1879

KX

2518

80

8aP.

dre

chsl

eri

15E

6Je

ffers

D.2

00K

X25

1881

KX

2518

82K

X25

1883

KX

2518

84K

X25

1885

KX

2518

86K

X25

1887

8aP.

dre

chsl

eri

23J5

292,

3546

724

P10

87p4

1K

X25

1888

KX

2518

89K

X25

1890

KX

2518

91K

X25

1892

KX

2518

93K

X25

1894

8aP.

dre

chsl

eri

P10

331

EU

0795

06E

U07

9507

EU

0795

08E

U07

9509

EU

0795

10E

U07

9511

EU

0795

12

8aP.

ery

thro

sept

ica

61J2

129,

2334

684

P16

93V

KM

F-1

807

KX

2518

95K

X25

1896

KX

2518

97K

X25

1898

KX

2518

99K

X25

1900

KX

2519

01

8aP.

med

icag

inis

23A

4M

YA-3

900

p37

S79

7K

X25

1902

KX

2519

03K

X25

1904

KX

2519

05K

X25

1906

KX

2519

07K

X25

1908

8aP.

med

icag

inis

28F1

4439

0P

1057

p124

Erw

in 9

45-1

2 K

X25

1909

KX

2519

10K

X25

1911

KX

2519

12K

X25

1913

KX

2519

14K

X25

1915

8aP.

pse

udoc

rypt

ogea

5240

2P

3103

6368

9E

U08

0626

EU

0806

27E

U08

0628

EU

0806

29E

U08

0630

EU

0806

31n.

a.

8aP.

rich

ardi

ae31

E8

P10

355

p170

CH

89-

1, S

ugur

o 3-

3K

X25

1916

KX

2519

17K

X25

1918

KX

2519

19K

X25

1920

KX

2519

21K

X25

1922

8aP.

rich

ardi

ae45

F524

0.30

6035

3, 4

6734

3259

30p3

47Ze

ntm

eyer

P64

2K

X25

1923

KX

2519

24K

X25

1925

KX

2519

26K

X25

1927

KX

2519

28K

X25

1929

8aP.

rich

ardi

aeP

1081

1C

H89

-19,

Kam

azak

i1E

U08

0496

EU

0804

97E

U08

0498

EU

0804

99E

U08

0500

EU

0805

01E

U08

0502

8aP.

san

som

eana

47H

3M

YA-4

455

Han

sen

1819

BK

X25

1930

KX

2519

31K

X25

1932

KX

2519

33K

X25

1934

KX

2519

35K

X25

1936

8aP.

san

som

eana

47H

4H

anse

n 23

23K

X25

1937

KX

2519

38K

X25

1939

KX

2519

40K

X25

1941

KX

2519

42K

X25

1943

8aP.

san

som

eana

47H

5H

anse

n 92

-84

KX

2519

44K

X25

1945

KX

2519

46K

X25

1947

KX

2519

48K

X25

1949

KX

2519

50

8aP.

trifo

lii29

B2

MYA

-390

1p1

42H

anse

n 33

KX

2519

51K

X25

1952

KX

2519

53K

X25

1954

KX

2519

55K

X25

1956

KX

2519

57

8aP.

trifo

lii62

A9

1176

87H

anse

n 32

KX

2519

58K

X25

1959

KX

2519

60K

X25

1961

KX

2519

62K

X25

1963

KX

2519

64

8aP.

aff.

cry

ptog

ea22

G2

308,

6215

402,

MYA

-416

132

5907

p12

N57

KX

2519

65K

X25

1966

KX

2519

67K

X25

1968

KX

2519

69K

X25

1970

KX

2519

71

8aP.

aff.

ery

thro

sept

ica

22J4

MYA

-404

1p5

0S

720

KX

2519

72K

X25

1973

KX

2519

74K

X25

1975

KX

2519

76K

X25

1977

KX

2519

78

8aP.

aff.

ery

thro

sept

ica

33A

1p2

07La

mbe

rt 20

04S

-1K

X25

1979

KX

2519

80K

X25

1981

KX

2519

82K

X25

1983

KX

2519

84K

X25

1985

8aP.

sp.

kel

man

ia24

A7

MYA

-416

2p1

02

KX

2519

86K

X25

1987

KX

2519

88K

X25

1989

KX

2519

90K

X25

1991

KX

2519

92

8aP.

sp.

kel

man

ia31

E4

P10

613

p166

Aba

d 02

-119

A, P

h4-1

EU

0796

05E

U07

9606

EU

0796

07E

U07

9608

EU

0796

09E

U07

9610

EU

0796

11

8bP.

bra

ssic

ae29

D8

686,

95M

an in

‘t V

eld

PD

95/

691 K

X25

1993

KX

2519

94K

X25

1995

KX

2519

96K

X25

1997

KX

2519

98K

X25

1999

Page 39: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

8bP.

bra

ssic

ae61

J817

9,87

P75

17,

P19

521

KX

2520

00K

X25

2001

KX

2520

02K

X25

2003

KX

2520

04K

X25

2005

KX

2520

06

8bP.

cic

horii

62A

811

5029

KX

2520

07K

X25

2008

KX

2520

09K

X25

2010

KX

2520

11K

X25

2012

KX

2520

13

8bP.

dau

ci61

E5

1271

02B

orfS

P37

0K

X25

2014

KX

2520

15K

X25

2016

KX

2520

17K

X25

2018

KX

2520

19K

X25

2020

8bP.

dau

ci32

E5

Bre

ton

134-

1K

X25

2021

KX

2520

22K

X25

2023

KX

2520

24K

X25

2025

KX

2520

26K

X25

2027

8bP.

dau

ci32

E6

P10

728

Bre

ton

143-

1K

X25

2028

KX

2520

29K

X25

2030

KX

2520

31K

X25

2032

KX

2520

33K

X25

2034

8bP.

dau

ci32

E7

p194

Bre

ton

148-

1K

X25

2035

KX

2520

36K

X25

2037

KX

2520

38K

X25

2039

KX

2520

40K

X25

2041

8bP.

lact

ucae

61F4

BP

IC 1

985

KX

2520

42K

X25

2043

KX

2520

44K

X25

2045

KX

2520

46K

X25

2047

KX

2520

48

8bP.

lact

ucae

61F7

BP

IC 1

988

KX

2520

49K

X25

2050

KX

2520

51K

X25

2052

KX

2520

53K

X25

2054

KX

2520

55

8bP.

lact

ucae

61F8

BP

IC 1

991

KX

2520

56K

X25

2057

KX

2520

58K

X25

2059

KX

2520

60K

X25

2061

KX

2520

62

8bP.

prim

ulae

29E

962

0,97

p286

Man

in ‘t

Vel

d P

D97

/875

KX

2520

63K

X25

2064

KX

2520

65K

X25

2066

KX

2520

67K

X25

2068

KX

2520

69

8bP.

prim

ulae

29F1

p287

Man

in ‘t

Vel

d P

D98

/8/2

01K

X25

2070

KX

2520

71K

X25

2072

KX

2520

73K

X25

2074

KX

2520

75K

X25

2076

8bP.

aff.

bra

ssic

ae-2

1129

68P

6207

Bol

ay #

8418

2E

U07

9880

EU

0798

81E

U07

9882

EU

0798

83E

U07

9884

EU

0798

85E

U07

9886

8bP.

aff.

cic

horii

61E

313

3815

SC

RA

CE

5388

KX

2520

77K

X25

2078

KX

2520

79K

X25

2080

KX

2520

81K

X25

2082

KX

2520

83

8bP.

sp.

29E

729

E7

Man

in ‘t

Vel

d P

D92

/214

KX

2520

91K

X25

2092

KX

2520

93K

X25

2094

KX

2520

95K

X25

2096

KX

2520

97

8bP.

taxo

n ca

stiti

s61

E7

1312

46C

H11

2K

X25

2098

KX

2520

99K

X25

2100

KX

2521

01K

X25

2102

KX

2521

03K

X25

2104

8bP.

taxo

n pa

rsle

y61

G1

BP

IC 2

584

KX

2521

05K

X25

2106

KX

2521

07K

X25

2108

KX

2521

09K

X25

2110

KX

2521

11

8cP.

folio

rum

49J8

1216

55M

YA-3

638

P10

974

LT19

2K

X25

2112

KX

2521

13K

X25

2114

KX

2521

15K

X25

2116

KX

2521

17K

X25

2118

8cP.

hib

erna

lis22

H1

270,

3160

352

0369

06P

6871

p115

BP

IC 1

137

KX

2521

19K

X25

2120

KX

2521

21K

X25

2122

KX

2521

23K

X25

2124

KX

2521

25

8cP.

hib

erna

lis32

F711

4104

5635

3, M

YA-3

896

1347

60P

3822

p197

Ho

H17

.1, W

A64

8K

X25

2126

KX

2521

27K

X25

2128

KX

2521

29K

X25

2130

KX

2521

31K

X25

2132

8cP.

late

ralis

22H

9M

YA-3

898

p51

CM

P63

1K

X25

2133

KX

2521

34K

X25

2135

KX

2521

36K

X25

2137

KX

2521

38K

X25

2139

8cP.

late

ralis

29A

920

1856

p128

Han

sen

366

KX

2521

40K

X25

2141

KX

2521

42K

X25

2143

KX

2521

44K

X25

2145

KX

2521

46

8cP.

ram

orum

32G

2Je

ffers

04-

4398

KX

2521

47K

X25

2148

KX

2521

49K

X25

2150

KX

2521

51K

X25

2152

KX

2521

53

8cP.

ram

orum

33F2

Gar

belo

tto P

r-10

2K

X25

2154

KX

2521

55K

X25

2156

KX

2521

57K

X25

2158

KX

2521

59K

X25

2160

8dP.

aus

troc

edra

e41

B5

MYA

-407

3G

resl

ebin

195

KX

2521

61K

X25

2162

KX

2521

63K

X25

2164

KX

2521

65K

X25

2166

KX

2521

67

8dP.

aus

troc

edra

e41

B6

1229

11M

YA-4

074

Gre

sleb

in 2

03K

X25

2168

KX

2521

69K

X25

2170

KX

2521

71K

X25

2172

KX

2521

73K

X25

2174

8dP.

obs

cura

60E

912

9273

BB

A 2⁄

94-

IIBK

X25

2175

KX

2521

76K

X25

2177

KX

2521

78K

X25

2179

KX

2521

80K

X25

2181

8dP.

obs

cura

60F1

JP-0

9-05

9 H

H-B

KX

2521

82K

X25

2183

KX

2521

84K

X25

2185

KX

2521

86K

X25

2187

KX

2521

88

8dP.

obs

cura

60F2

P-0

9-01

1K

X25

2189

KX

2521

90K

X25

2191

KX

2521

92K

X25

2193

KX

2521

94K

X25

2195

8dP.

syr

inga

e21

H9

3400

2P

0649

p187

KX

2521

96K

X25

2197

KX

2521

98K

X25

2199

KX

2522

00K

X25

2201

KX

2522

02

8dP.

syr

inga

e23

A6

MYA

-365

9p3

5K

X25

2203

KX

2522

04K

X25

2205

KX

2522

06K

X25

2207

KX

2522

08K

X25

2209

8P.

str

icta

58A

1M

YA-4

944

KX

2522

10K

X25

2211

KX

2522

12K

X25

2213

KX

2522

14K

X25

2215

KX

2522

16

8P.

str

icta

58A

2K

X25

2217

KX

2522

18K

X25

2219

KX

2522

20K

X25

2221

KX

2522

22K

X25

2223

8P.

str

icta

58A

3K

X25

2224

KX

2522

25K

X25

2226

KX

2522

27K

X25

2228

KX

2522

29K

X25

2230

8P.

str

icta

58A

4K

X25

2231

KX

2522

32K

X25

2233

KX

2522

34K

X25

2235

KX

2522

36K

X25

2237

Page 40: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

9a (c

lust

er 9

a1)

P. a

quim

orbi

da40

A6

MYA

-457

8K

X25

2238

KX

2522

39K

X25

2240

KX

2522

41K

X25

2242

KX

2522

43K

X25

2244

9a (c

lust

er 9

a1)

P. a

quim

orbi

da40

E3

KX

2522

45K

X25

2246

KX

2522

47K

X25

2248

KX

2522

49K

X25

2250

KX

2522

51

9a (c

lust

er 9

a1)

P. a

quim

orbi

da44

G9

KX

2522

52K

X25

2253

KX

2522

54K

X25

2255

KX

2522

56K

X25

2257

KX

2522

58

9a (c

lust

er 9

a1)

P. c

hrys

anth

emi

61E

9K

agey

ama

Chr

3,

NB

RC

1049

18K

X25

2259

KX

2522

60K

X25

2261

KX

2522

62K

X25

2263

KX

2522

64K

X25

2265

9a (c

lust

er 9

a1)

P. c

hrys

anth

emi

61F1

1231

63K

agey

ama

GF7

49,

NB

RC

1049

17K

X25

2266

KX

2522

67K

X25

2268

KX

2522

69K

X25

2270

KX

2522

71K

X25

2272

9a (c

lust

er 9

a1)

P. h

ydro

gena

44G

8K

X25

2273

KX

2522

74K

X25

2275

KX

2522

76K

X25

2277

KX

2522

78K

X25

2279

9a (c

lust

er 9

a1)

P. h

ydro

gena

46A

3M

YA-4

919

KX

2522

80K

X25

2281

KX

2522

82K

X25

2283

KX

2522

84K

X25

2285

KX

2522

86

9a (c

lust

er 9

a1)

P. h

ydro

gena

46A

4K

X25

2287

KX

2522

88K

X25

2289

KX

2522

90K

X25

2291

KX

2522

92K

X25

2293

9a (c

lust

er 9

a1)

P. h

ydro

path

ica

05D

1M

YA-4

460

p366

KX

2522

94K

X25

2295

KX

2522

96K

X25

2297

KX

2522

98K

X25

2299

KX

2523

00

9a (c

lust

er 9

a1)

P. h

ydro

path

ica

5C11

MYA

-445

9p3

65K

X25

2301

KX

2523

02K

X25

2303

KX

2523

04K

X25

2305

KX

2523

06K

X25

2307

9a (c

lust

er 9

a1)

P. ir

rigat

a04

E4

MYA

-445

8p3

35K

X25

2308

KX

2523

09K

X25

2310

KX

2523

11K

X25

2312

KX

2523

13K

X25

2314

9a (c

lust

er 9

a1)

P. ir

rigat

a23

J7M

YA-4

457

p108

KX

2523

15K

X25

2316

KX

2523

17K

X25

2318

KX

2523

19K

X25

2320

KX

2523

21

9a (c

lust

er 9

a1)

P. ir

rigat

a44

E4

KX

2523

22K

X25

2323

KX

2523

24K

X25

2325

KX

2523

26K

X25

2327

KX

2523

28

9a (c

lust

er 9

a1)

P. m

acile

ntos

a58

A5

KX

2523

29K

X25

2330

KX

2523

31K

X25

2332

KX

2523

33K

X25

2334

KX

2523

35

9a (c

lust

er 9

a1)

P. m

acile

ntos

a58

A6

KX

2523

36K

X25

2337

KX

2523

38K

X25

2339

KX

2523

40K

X25

2341

KX

2523

42

9a (c

lust

er 9

a1)

P. m

acile

ntos

a58

A7

MYA

-494

5K

X25

2343

KX

2523

44K

X25

2345

KX

2523

46K

X25

2347

KX

2523

48K

X25

2349

9a (c

lust

er 9

a1)

P. m

acile

ntos

a58

A8

KX

2523

50K

X25

2351

KX

2523

52K

X25

2353

KX

2523

54K

X25

2355

KX

2523

56

9a (c

lust

er 9

a1)

P. p

arsi

ana

47C

339

5329

C25

, B

anih

ashe

mi P

H-

21-5

-08

(X-2

-91)

KX

2523

57K

X25

2358

KX

2523

59K

X25

2360

KX

2523

61K

X25

2362

KX

2523

63

9a (c

lust

er 9

a1)

P. v

irgin

iana

40A

9K

X25

2364

KX

2523

65K

X25

2366

KX

2523

67K

X25

2368

KX

2523

69K

X25

2370

9a (c

lust

er 9

a1)

P. v

irgin

iana

44G

6K

X25

2371

KX

2523

72K

X25

2373

KX

2523

74K

X25

2375

KX

2523

76K

X25

2377

9a (c

lust

er 9

a1)

P. v

irgin

iana

46A

2M

YA-4

927

KX

2523

78K

X25

2379

KX

2523

80K

X25

2381

KX

2523

82K

X25

2383

KX

2523

84

9a (c

lust

er 9

a1)

P. a

ff. p

arsi

ana

G1

47C

7B

anih

ashe

mi 1

KX

2523

91K

X25

2392

KX

2523

93K

X25

2394

KX

2523

95K

X25

2396

n.a.

9a (c

lust

er 9

a1)

P. a

ff. p

arsi

ana

G1

47C

8B

anih

ashe

mi 2

KX

2523

97K

X25

2398

KX

2523

99K

X25

2400

KX

2524

01K

X25

2402

n.a.

9a (c

lust

er 9

a1)

P. a

ff. p

arsi

ana

G1

3953

28P

8618

Ban

ihas

hem

i PH

-15-

19-

92, P

H-2

1-4-

08, S

UC

19E

U08

0195

EU

0801

96E

U08

0197

EU

0801

98E

U08

0199

EU

0802

00E

U08

0201

9a (c

lust

er 9

a1)

P. a

ff. p

arsi

ana

G2

47C

539

5330

SU

Rf6

, Ban

ihas

hem

i P

H-2

1-6-

08K

X25

2433

KX

2524

34K

X25

2435

KX

2524

36K

X25

2437

KX

2524

38n.

a.

9a (c

lust

er 9

a1)

P. a

ff. p

arsi

ana

G2

47C

639

5331

SU

Rf1

7, B

anih

ashe

mi

PH

-21-

7-08

K

X25

2439

KX

2524

40K

X25

2441

KX

2524

42K

X25

2443

KX

2524

44n.

a.

9a (c

lust

er 9

a1)

P. a

ff. p

arsi

ana

G3

47D

5B

anih

ashe

mi 8

KX

2524

45K

X25

2446

KX

2524

47K

X25

2448

KX

2524

49K

X25

2450

n.a.

9a (c

lust

er 9

a1)

P. a

ff. p

arsi

ana

G3

47D

8B

anih

ashe

mi 1

1K

X25

2463

KX

2524

64K

X25

2465

KX

2524

66K

X25

2467

KX

2524

68n.

a.

9a (c

lust

er 9

a1)

P. a

ff. p

arsi

ana

G3

47E

1B

anih

ashe

mi 1

3K

X25

2475

KX

2524

76K

X25

2477

KX

2524

78K

X25

2479

KX

2524

80n.

a.

9a (c

lust

er 9

a1)

P. s

p. 3

5G4

35G

4K

X25

2481

KX

2524

82K

X25

2483

KX

2524

84K

X25

2485

KX

2524

86K

X25

2487

Page 41: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

9a (c

lust

er 9

a1)

P. s

p. 3

8D9

38D

9K

o W

KK

X25

2488

KX

2524

89K

X25

2490

KX

2524

91K

X25

2492

KX

2524

93K

X25

2494

9a (c

lust

er 9

a1)

P. s

p. 4

0J5

40J5

Ho

Boa

o 3-

2K

X25

2495

KX

2524

96K

X25

2497

KX

2524

98K

X25

2499

KX

2525

00K

X25

2501

9a (c

lust

er 9

a1)

P. s

p. c

uyab

ensi

sP

8213

103

EU

0806

64E

U08

0665

EU

0806

66E

U08

0667

EU

0806

68E

U08

0669

EU

0803

31

9a (c

lust

er 9

a1)

P. s

p. la

goar

iana

60B

4P

8220

148

EU

0803

58K

X25

2502

EU

0803

59E

U08

0360

EU

0803

61E

U08

0362

EU

0803

63

9a (c

lust

er 9

a1)

P. s

p. la

goar

iana

60B

5P

8217

145

KX

2525

03K

X25

2504

KX

2525

05K

X25

2506

KX

2525

07K

X25

2508

KX

2525

09

9a (c

lust

er 9

a1)

P. s

p. la

goar

iana

P82

2315

5E

U08

0364

EU

0803

65E

U08

0366

EU

0803

67E

U08

0368

EU

0803

69E

U08

0370

9a (c

lust

er 9

a2)

P. m

acro

chla

myd

ospo

ra-G

133E

1P

1026

4U

Q77

8, D

AR

5229

9K

X25

2510

KX

2525

11K

X25

2512

n.a.

KX

2525

13K

X25

2514

KX

2525

15

9a (c

lust

er 9

a2)

P. m

acro

chla

myd

ospo

ra-G

1P

1026

7U

Q11

63, T

1044

6 (Q

DP

I)EU

0800

04E

U08

0005

EU

0800

06E

U08

0007

EU

0800

08E

U08

0009

EU

0800

10

9a (c

lust

er 9

a2)

P. m

acro

chla

myd

ospo

ra-G

231E

935

1473

P80

17p1

71E

U08

0658

EU

0806

59E

U08

0660

n.a.

EU

0806

61E

U08

0662

EU

0806

63

9a (c

lust

er 9

a2)

P. m

acro

chla

myd

ospo

ra-G

233D

524

0.30

6035

334

0618

Coo

ke S

CR

P55

1K

X25

2516

KX

2525

17K

X25

2518

n.a.

KX

2525

19K

X25

2520

KX

2525

21

9a (c

lust

er 9

a2)

P. q

uini

nea

45F2

406,

4856

964

p344

CM

W 3

1061

, Cra

ndal

l N

o. C

-66,

Ho

H35

.1E

U08

0107

EU

0801

08E

U08

0109

n.a.

KX

2525

22E

U08

0110

KX

2525

23

9a (c

lust

er 9

a2)

P. q

uini

nea

46C

440

7,48

4673

3p3

86C

MW

310

62, C

rand

all

No.

C-6

7E

U07

9802

EU

0798

03E

U07

9804

KX

2525

24E

U07

9805

EU

0798

06E

U07

9807

9a (c

lust

er 9

a3)

P. in

solit

a27

E1

MYA

-407

7p1

23H

o H

HW

KX

2525

25K

X25

2526

KX

2525

27K

X25

2528

KX

2525

29K

X25

2530

KX

2525

31

9a (c

lust

er 9

a3)

P. in

solit

a38

E1

691,

7938

789

2888

05K

o TA

I513

1E

U08

0175

EU

0801

76E

U08

0177

EU

0801

78E

U08

0179

EU

0801

80E

U08

0181

9a (c

lust

er 9

a3)

P. in

solit

aP

6703

EU

0802

09E

U08

0210

EU

0802

11E

U08

0212

EU

0802

13E

U08

0214

EU

0802

15

9a (c

lust

er 9

a3)

P. p

olon

ica

40G

9 =

cv0

609-

129

KX

2525

32K

X25

2533

KX

2525

34K

X25

2535

KX

2525

36K

X25

2537

KX

2525

38

9a (c

lust

er 9

a3)

P. p

olon

ica

43F9

= b

c070

1-16

3K

X25

2539

KX

2525

40K

X25

2541

KX

2525

42K

X25

2543

KX

2525

44K

X25

2545

9a (c

lust

er 9

a3)

P. p

olon

ica

49J9

P15

005

GD

7e

EU

0802

56K

X25

2546

EU

0802

58E

U08

0259

EU

0802

60E

U08

0261

EU

0802

62

9bP.

cap

tiosa

46H

6N

ZFS

310

.37

KX

2525

47K

X25

2548

KX

2525

49K

X25

2550

KX

2525

51K

X25

2552

KX

2525

53

9bP.

cap

tiosa

46H

7P

1071

9N

ZFS

310

CE

U07

9658

EU

0796

59E

U07

9660

EU

0796

61E

U07

9662

EU

0796

63E

U07

9664

9bP.

cap

tiosa

46H

8N

ZFS

430

KX

2525

54K

X25

2555

KX

2525

56K

X25

2557

KX

2525

58K

X25

2559

KX

2525

60

9bP.

cap

tiosa

P10

721

NZF

S 3

10.3

5E

U07

9665

EU

0796

66E

U07

9667

EU

0796

68E

U07

9669

EU

0796

70E

U07

9671

9bP.

con

stric

ta55

C3

1258

01V

HS

161

30K

X25

2561

KX

2525

62K

X25

2563

KX

2525

64K

X25

2565

KX

2525

66K

X25

2567

9bP.

falla

x46

J2P

1072

2N

ZFS

310

LK

X25

2568

KX

2525

69K

X25

2570

KX

2525

71K

X25

2572

KX

2525

73K

X25

2574

9bP.

falla

x46

J3N

ZFS

450

KX

2525

75K

X25

2576

KX

2525

77K

X25

2578

KX

2525

79K

X25

2580

KX

2525

81

9bP.

falla

x46

J5N

ZFS

448

KX

2525

82K

X25

2583

KX

2525

84K

X25

2585

KX

2525

86K

X25

2587

KX

2525

88

9bP.

falla

xP

1072

5N

ZFS

171

9E

U08

0034

EU

0800

35E

U08

0036

EU

0800

37E

U08

0038

EU

0800

39E

U08

0040

10P.

boe

hmer

iae

45F9

291,

2918

0614

P69

50E

U08

0161

EU

0801

62E

U08

0163

EU

0801

64E

U08

0165

EU

0801

66E

U08

0167

10P.

gal

lica

50A

111

1474

P16

826

GA

L1, M

B49

7405

KX

2525

89K

X25

2590

KX

2525

91K

X25

2592

KX

2525

93K

X25

2594

KX

2525

95

10P.

gal

lica

61D

511

1475

P16

827

GA

L2K

X25

2596

KX

2525

97K

X25

2598

KX

2525

99K

X25

2600

KX

2526

01K

X25

2602

10P.

gon

dwan

ensi

s22

G7

MYA

-389

3S

833

KX

2526

03K

X25

2604

KX

2526

05K

X25

2606

KX

2526

07K

X25

2608

KX

2526

09

10P.

inte

rcal

aris

45B

714

0632

TSD

-7K

X25

2610

KX

2526

11K

X25

2612

KX

2526

13K

X25

2614

KX

2526

15K

X25

2616

10P.

inte

rcal

aris

48A

1K

X25

2617

KX

2526

18K

X25

2619

KX

2526

20K

X25

2621

KX

2526

22K

X25

2623

10P.

inte

rcal

aris

49A

714

0631

KX

2526

24K

X25

2625

KX

2526

26K

X25

2627

KX

2526

28K

X25

2629

KX

2526

30

Page 42: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

1. (

Con

tinue

d).

(Sub

)cla

deSp

ecie

sIs

olat

e id

entifi

catio

nG

enB

ank

acce

ssio

n nu

mbe

rs

Loca

l (C

H)

CB

SAT

CC

IMI

WPC

M.G

alle

gly

Oth

er60

Sβ-

TUB

EF1a

Enol

ase

HSP

9028

STi

gA

10P.

ker

novi

ae46

C8

P10

956

p390

CS

L 22

86, P

RI 7

12E

U08

0041

EU

0800

42E

U08

0043

EU

0800

44E

U08

0045

EU

0800

46K

X25

2631

10P.

ker

novi

ae46

J6P

1068

1IC

MP

1476

1, H

ill

LYN

701

EU

0796

45E

U07

9646

EU

0796

47E

U07

9648

EU

0796

49E

U07

9650

EU

0796

51

10P.

ker

novi

ae46

J8P

1067

1IC

MP

1508

2E

U08

0027

EU

0800

28E

U08

0029

EU

0800

30E

U08

0031

EU

0800

32K

X25

2632

10P.

mor

inda

e62

B5

1219

82N

elso

n P

h697

.P23

8,

BP

I 878

721

KX

2526

33K

X25

2634

KX

2526

35K

X25

2636

KX

2526

37K

X25

2638

KX

2526

39

10P.

sp.

boe

hmer

iae-

like

45F8

357,

5260

173

3219

9P

1378

p350

KX

2526

40K

X25

2641

KX

2526

42K

X25

2643

KX

2526

44K

X25

2645

KX

2526

46

n.a.

P. li

lii13

5746

EL-

8701

, NB

RC

321

74,

MA

FF 2

3750

0A

B85

6779

AB

8567

82A

B85

6788

AB

8567

91A

B85

6794

AB

8567

97A

B85

6800

outg

roup

Elon

gisp

oran

gium

un

dula

tum

1017

2833

7230

P10

342

EU

0804

40E

U08

0441

EU

0804

42n.

a.E

U08

0443

EU

0804

44E

U08

0445

outg

roup

Phyt

opyt

hium

vex

ans

340,

4912

194

P39

80C

MI 3

2 04

4E

U08

0483

EU

0804

84E

U08

0485

n.a.

EU

0804

86E

U08

0487

EU

0804

88

outg

roup

Hal

ophy

toph

thor

a flu

viat

ilis

57A

9M

YA-4

961

KX

2526

68K

X25

2669

KX

2526

70K

X25

2671

KX

2526

72K

X25

2673

KX

2526

74

Page 43: An expanded phylogeny for the genus Phytophthora

Supplementary Table 2

Supp

lem

enta

ry T

able

2. A

list

of t

he 2

9 is

olat

es fo

und

asso

ciat

ed w

ith a

n er

rone

ous

or m

odifi

ed id

entit

y in

this

stu

dy a

nd th

eir i

dent

ities

as

used

in th

is s

tudy

.

Isol

ate

num

bers

(Sub

)cla

deId

entit

y in

this

stu

dyO

rigin

ial i

dent

ityLo

cal

CB

SAT

CC

IMI

Gal

legl

yW

PCO

ther

33F4

p226

MN

T63

(Bla

nche

tte)

1aP.

aff.

hed

raia

ndra

P. h

edra

iand

ra (G

alle

gly

& H

ong

2008

, Sch

win

gle

et a

l. 20

06)

29B

3p1

8533

3 (H

anse

n)1a

P. a

ff. p

seud

otsu

gae

P. p

seud

otsu

gae

(Gal

legl

y &

Hon

g 20

08, H

amm

& H

anse

n 19

83)

26H

4p3

267

8 (T

sao)

2aP.

aff.

citr

opht

hora

P. c

itrop

htho

ra (G

alle

gly

& H

ong

2008

)

3428

98P

1034

12a

P. a

ff. c

itrop

htho

raP.

sp.

aff.

col

ocas

iae-

1 (M

artin

et a

l. 20

14)

61G

412

8754

NP

862a

P. a

ff. h

imal

silv

aP.

him

alsi

lva

(Vet

train

o et

al.

2011

)

46C

366

767

p385

P67

13M

oy 1

413

2aP.

sp.

46C

3P.

bot

ryos

a

P62

62R

ajal

aksh

my

#46

2aP.

sp.

P62

62P.

sp.

aff.

col

ocas

iae-

2 (M

artin

et a

l. 20

14)

P63

10#0

662a

P. s

p. P

6310

P. c

itrop

htho

ra (

Mar

tin e

t al.

2014

)

22F5

1542

7, M

YA-4

035

p9N

142b

P. a

ff. c

apsi

ciP.

cap

sici

(Gal

legl

y &

Hon

g 20

08)

22F3

p33

S81

32c

P. s

p. 2

2F3

P. p

ini (

Hon

g et

al.

2011

), P.

citr

icol

a C

il I (

Gal

legl

y &

Hon

g 20

08)

P86

19P

H-1

5-21

-93

6aP.

inun

data

P. s

p. d

rech

sler

i-lik

e (B

lair

et a

l. 20

08)

22J5

1669

8p1

6 N

656b

P. s

p. g

rega

ta-li

keP.

ery

thro

sept

ica

(Gal

legl

y &

Hon

g 20

08)

23A

1p8

1H

anse

n 61

6bP.

sp.

meg

aspe

rma-

like

P. m

egas

perm

a M

eg I

(Gal

legl

y &

Hon

g 20

08)

23A

3M

YA-3

660

p79

Han

sen

506b

P. s

p. m

egas

perm

a-lik

eP.

meg

aspe

rma

Meg

I (G

alle

gly

& H

ong

2008

)

33F7

p229

Bal

ci B

M4/

67a

P. s

p. e

urop

aea

SW

P. e

urop

aea

(Gal

legl

y &

Hon

g 20

08)

01D

5p3

127b

P. n

iede

rhau

serii

P. d

rech

sler

i (G

alle

gly

& H

ong

2008

)

23J6

MYA

-416

3p5

7 R

ibei

ro Is

rael

27b

P. n

iede

rhau

serii

P. d

rech

sler

i (G

alle

gly

& H

ong

2008

)

22G

230

8,62

1540

2, M

YA-4

161

3259

07p1

2N

578a

P. a

ff. c

rypt

ogea

P. c

rypt

ogea

(Gal

legl

y &

Hon

g 20

08)

22J4

MYA

-404

1p5

0S

720

8aP.

aff.

ery

thro

sept

ica

P. e

ryth

rose

ptic

a (G

alle

gly

& H

ong

2008

)

33A

1p2

07La

mbe

rt 20

04S

-18a

P. a

ff. e

ryth

rose

ptic

aP.

ery

thro

sept

ica

(Gal

legl

y &

Hon

g 20

08)

32E

6P

1072

8B

reto

n 14

3-1

8bP.

dau

ciP.

sp.

aff.

bra

ssic

ae-1

(Mar

tin e

t al.

2014

)

32E

7p1

94B

reto

n 14

8-1

8bP.

dau

ciP.

por

ri (G

alle

gly

& H

ong

2008

)

61E

313

3815

SC

RA

CE

5388

8bP.

aff.

cic

horii

P. c

icho

rii (B

ertie

r et a

l. 20

13)

29E

7M

an in

’t Ve

ld P

D92

/214

8bP.

sp.

29E

7P.

por

ri (G

alle

gly

& H

ong

2008

)

3953

28P

8618

Ban

ihas

hem

i PH

-15-

19-9

2, P

H-2

1-4-

08, S

UC

199a

P. a

ff. p

arsi

ana

G1

P. p

arsi

ana

(Mos

tow

fizad

eh-G

hala

mfa

rsa

et a

l. 20

08),

P. s

p.

zent

mye

ii (W

PS

)

47C

539

5330

SU

Rf6

, Ban

ihas

hem

i PH

-21-

6-08

9aP.

aff.

par

sian

a G

2P.

par

sian

a (M

osto

wfiz

adeh

-Gha

lam

fars

a et

al.

2008

)

47C

639

5331

SU

Rf1

7, B

anih

ashe

mi P

H-2

1-7-

08

9aP.

aff.

par

sian

a G

2P.

par

sian

a (M

osto

wfiz

adeh

-Gha

lam

fars

a et

al.

2008

)

Page 44: An expanded phylogeny for the genus Phytophthora

Supp

lem

enta

ry T

able

2. (

Con

tinue

d).

Isol

ate

num

bers

(Sub

)cla

deId

entit

y in

this

stu

dyO

rigin

ial i

dent

ityLo

cal

CB

SAT

CC

IMI

Gal

legl

yW

PCO

ther

22G

7M

YA-3

893

S83

310

P. g

ondw

anen

sis

P. b

oehm

eria

e (G

alle

gly

& H

ong

2008

)

45F8

357,

5260

173

3219

9p3

50P

1378

10P.

sp.

boe

hmer

iae-

like

P. b

oehm

eria

e (G

alle

gly

& H

ong

2008

)

Ref

eren

ces:

Ber

tier L

, Bro

uwer

H, D

e C

ock

A, C

ooke

DE

L, O

lsso

n C

HB

, et a

l. (2

013)

The

exp

ansi

on o

f Phy

toph

thor

a cl

ade

8b: t

hree

new

spe

cies

ass

ocia

ted

with

win

ter g

row

n ve

geta

ble

crop

s. P

erso

onia

31:

63–

76.

Bla

ir JE

, Cof

fey

MD

, Par

k S

-Y, G

eise

r DM

, Kan

g S

(200

8) A

mul

ti-lo

cus

phyl

ogen

y fo

r Phy

toph

thor

a ut

ilizi

ng m

arke

rs d

eriv

ed fr

om c

ompl

ete

geno

me

sequ

ence

s. F

unga

l Gen

etic

s an

d B

iolo

gy 4

5: 2

66–2

77.

Gal

legl

y M

E, H

ong

C (2

008)

Phy

toph

thor

a: id

entif

ying

spe

cies

by

mor

phol

ogy

and

DN

A fin

gerp

rints

. St P

aul,

MN

: Am

eric

an P

hyto

path

olog

ical

Soc

iety

Pre

ss.

Ham

m P

, Han

sen

EM

(198

3) P

hyto

phth

ora

pseu

dots

ugae

, a n

ew s

peci

es c

ausi

ng ro

ot ro

t of D

ougl

as-fi

r. C

anad

ian

Jour

nal o

f Bot

any

61: 2

626–

2631

.

Hon

g C

, Gal

legl

y M

E, R

icha

rdso

n PA

, Kon

g P

(201

1) P

hyto

phth

ora

pini

Leo

nian

resu

rrec

ted

to d

istin

ct s

peci

es s

tatu

s. M

ycol

ogia

103

: 351

–360

.

Mar

tin F

N, B

lair

JE, C

offe

y M

D (2

014)

A c

ombi

ned

mito

chon

dria

l and

nuc

lear

mul

tiloc

us p

hylo

geny

of t

he g

enus

Phy

toph

thor

a. F

unga

l Gen

etic

s an

d B

iolo

gy 6

6: 1

9–32

.

Mos

tow

fizad

eh-G

hala

mfa

rsa

R, C

ooke

DE

L, B

anih

ashe

mi Z

(200

8) P

hyto

phth

ora

pars

iana

sp.

nov

., a

new

hig

h-te

mpe

ratu

re to

lera

nt s

peci

es. M

ycol

ogic

al R

esea

rch

112:

783

–794

.

Sch

win

gle

BW

, Sm

ith J

A, B

lanc

hette

RA

, Gou

ld S

, Bla

nche

tte B

L, e

t al.

(200

6) F

irst r

epor

t of d

ieba

ck a

nd le

af le

sion

s on

Rho

dode

ndro

n sp

. cau

sed

by P

hyto

phth

ora

hedr

aian

dra

in th

e U

nite

d S

tate

s. P

lant

Dis

ease

90

: 109

.

Vettr

aino

AM

, Bra

sier

CM

, Bro

wn

AV, V

anni

ni A

(201

1) P

hyto

phth

ora

him

alsi

lva

sp. n

ov. a

n un

usua

lly p

heno

typi

cally

var

iabl

e sp

ecie

s fro

m a

rem

ote

fore

st in

Nep

al. F

unga

l Bio

logy

115

: 275

–287

.


Molecular phylogeny of the Palaearctic butterfly genus

Molecular phylogeny of the Palaearctic butterfly genus

Documents
Molecular phylogeny and a taxonomic proposal for the genus

Molecular phylogeny and a taxonomic proposal for the genus

Documents
Phylogeny and species delimitation in the genus Coprinellus with … PDFs... · 2013. 12. 23. · Phylogeny and species delimitation in the genus Coprinellus with special emphasis

Phylogeny and species delimitation in the genus Coprinellus with … PDFs... · 2013. 12. 23. · Phylogeny and species delimitation in the genus Coprinellus with special emphasis

Documents
Phytophthora and Oak Decline - Impact on Seedlings and ... · 4.1 An introduction to the genus Phytophthora 17 4.2 Occurrence of Phytophthora species in European oak ecosystems and

Phytophthora and Oak Decline - Impact on Seedlings and ... · 4.1 An introduction to the genus Phytophthora 17 4.2 Occurrence of Phytophthora species in European oak ecosystems and

Documents
Phylogeny and biogeography of the dung beetle genus

Phylogeny and biogeography of the dung beetle genus

Documents
Phylogeny and genus-level classification of mantellid frogs

Phylogeny and genus-level classification of mantellid frogs

Documents
Phylogeny and biogeography of the lamioid mint genus Phlomis L

Phylogeny and biogeography of the lamioid mint genus Phlomis L

Documents
Phylogeny of the genus Stephomyia Tavares, 1916 (Diptera ... · Phylogeny of the genus Stephomyia Tavares, ... A monofilia de Stephomyia foi suportada por oito sinapomorfias:

Phylogeny of the genus Stephomyia Tavares, 1916 (Diptera ... · Phylogeny of the genus Stephomyia Tavares, ... A monofilia de Stephomyia foi suportada por oito sinapomorfias:

Documents
Phylogeny and taxonomy of the Prenolepis genus-group of ants

Phylogeny and taxonomy of the Prenolepis genus-group of ants

Documents
Phylogeny of the túngara frog genus Engystomops ......We present a phylogeny of the Neotropical genus Engystomops (DPhysalaemus pustulosus species group) based on sequences of »2.4kb

Phylogeny of the túngara frog genus Engystomops ......We present a phylogeny of the Neotropical genus Engystomops (DPhysalaemus pustulosus species group) based on sequences of »2.4kb

Documents
PHYLOGENY OF THE GENUS PYRAMIMONAS … · J, 30, 991-999 (1994) PHYLOGENY OF THE GENUS PYRAMIMONAS (PRASINOPHYCEAE, CHLOROPHYTA) INFERRED FROM THE rbcL GENET Niels Daugbjerg2 Zoological

PHYLOGENY OF THE GENUS PYRAMIMONAS … · J, 30, 991-999 (1994) PHYLOGENY OF THE GENUS PYRAMIMONAS (PRASINOPHYCEAE, CHLOROPHYTA) INFERRED FROM THE rbcL GENET Niels Daugbjerg2 Zoological

Documents
Phylogeny and biogeography of the genus Cephalenchus ... › publications › Pereira_et_al_2017.pdfPhylogeny and biogeography of the genus Cephalenchus (Tylenchomorpha, Nematoda)

Phylogeny and biogeography of the genus Cephalenchus ... › publications › Pereira_et_al_2017.pdfPhylogeny and biogeography of the genus Cephalenchus (Tylenchomorpha, Nematoda)

Documents
Phylogeny and nomenclature of the genus Talaromyces in Penicillium

Phylogeny and nomenclature of the genus Talaromyces in Penicillium

Documents
Phylogeny of the genus Teloganopsis Teloganopsis media

Phylogeny of the genus Teloganopsis Teloganopsis media

Documents
Toward a Phylogeny of the Kukri Snakes, Genus …labs.eeb.utoronto.ca/murphy/PDFs of papers/2010_Oligodon.pdfNo. 1 Marc D. Green et al. Toward a Phylogeny of the Kukri Snakes, Genus

Toward a Phylogeny of the Kukri Snakes, Genus …labs.eeb.utoronto.ca/murphy/PDFs of papers/2010_Oligodon.pdfNo. 1 Marc D. Green et al. Toward a Phylogeny of the Kukri Snakes, Genus

Documents
PhytoPhthora (root rot) - · PDF filePhytophthora root rot infection ... Bleeding canker caused by Phytophthora cinnamomi. DESCRIPTION Phytophthora is a genus of oomycetes that are

PhytoPhthora (root rot) - · PDF filePhytophthora root rot infection ... Bleeding canker caused by Phytophthora cinnamomi. DESCRIPTION Phytophthora is a genus of oomycetes that are

Documents
A contribution to the ITS-LSU phylogeny of the genus Leucopaxillus

A contribution to the ITS-LSU phylogeny of the genus Leucopaxillus

Documents
PhytoPhthora (root rot)B: Bleeding canker caused by Phytophthora cinnamomi. DESCRIPTION Phytophthora is a genus of oomycetes that are smi ali r to fungi. There are 59 specei s of Phytophthora,

PhytoPhthora (root rot)B: Bleeding canker caused by Phytophthora cinnamomi. DESCRIPTION Phytophthora is a genus of oomycetes that are smi ali r to fungi. There are 59 specei s of Phytophthora,

Documents
Molecular phylogeny and taxonomy of the genus Veloporphyrellus · Molecular phylogeny and taxonomy of the genus Veloporphyrellus Yan-Chun Li Key Laboratory for Plant Diversity and

Molecular phylogeny and taxonomy of the genus Veloporphyrellus · Molecular phylogeny and taxonomy of the genus Veloporphyrellus Yan-Chun Li Key Laboratory for Plant Diversity and

Documents
Phylogeny and species delimitation in the genus Coprinellus

Phylogeny and species delimitation in the genus Coprinellus

Documents
Phylogeny and biogeography of the freshwater crab genus Johora

Phylogeny and biogeography of the freshwater crab genus Johora

Documents
Phylogeny and nomenclature of the genus - Cbs - KNAW

Phylogeny and nomenclature of the genus - Cbs - KNAW

Documents
Phylogeny of leafcutter ants in the genus Atta Fabricius ... · Phylogeny of leafcutter ants in the genus Atta Fabricius (Formicidae: Attini) based on mitochondrial and nuclear DNA

Phylogeny of leafcutter ants in the genus Atta Fabricius ... · Phylogeny of leafcutter ants in the genus Atta Fabricius (Formicidae: Attini) based on mitochondrial and nuclear DNA

Documents
Phylogeny and taxonomy of the genus Arundinaria - Rivercane

Phylogeny and taxonomy of the genus Arundinaria - Rivercane

Documents
Phylogeny of the bee genus Andrena FABRICIUS based on morphology

Phylogeny of the bee genus Andrena FABRICIUS based on morphology

Documents
Phylogeny of the plant genus Pachypodium - Ecology and

Phylogeny of the plant genus Pachypodium - Ecology and

Documents
Taxonomy and Phylogeny of the Genus Lilium · Taxonomy and Phylogeny of the Genus Lilium ... according to different traits: the earliest classifications were typically based on the

Taxonomy and Phylogeny of the Genus Lilium · Taxonomy and Phylogeny of the Genus Lilium ... according to different traits: the earliest classifications were typically based on the

Documents
Phylogeny of slug species of the genus Arion: evidence of

Phylogeny of slug species of the genus Arion: evidence of

Documents
Phylogeny of the coral genus Plesiastrea (Cnidaria ... · Contributions to Zoology, 80 (4) 231-249 (2011) Phylogeny of the coral genus Plesiastrea (Cnidaria, Scleractinia) Francesca

Phylogeny of the coral genus Plesiastrea (Cnidaria ... · Contributions to Zoology, 80 (4) 231-249 (2011) Phylogeny of the coral genus Plesiastrea (Cnidaria, Scleractinia) Francesca

Documents
A Three-Gene Phylogeny of the Genus Solanum (Solanaceae)

A Three-Gene Phylogeny of the Genus Solanum (Solanaceae)

Documents