An expanded phylogeny for the genus Phytophthora

Yang, Xiao; Tyler, Brett M.; Hong, Chuanxue

doi:10.5598/imafungus.2017.08.02.09

IMA Fungus

Table 1 Information regarding isolates used in this study. GenBank accession numbers are listed in Table S1.

From: An expanded phylogeny for the genus Phytophthora

			Isolate identification ^d							Isolate origins
(Sub)clade ^a	Species ^b	Papilla ^c	CH	CBS	ATCC	IMI	WPC	MG	Type ^e	Host or Substrate	Location	Year	Reference
1a	*P. cactorum*	P	22E6				P10194	p25		Rhododendron sp.	Ohio, USA	n.a.^f	(Schröter 1886)
			22E7		16693	21168	P0715	p6		n.a.	UK	n.a.
			22E8		16694, MYA-3653	50470	P10193	p7		Malus sp.	Zimbabwe	n.a.
	*P. hedraiandra*	P	33F3		MYA-4165			p225		Rhododendron sp.	Minnesota, USA	2002	(de Cock & Lévesque 2004)
			38C2							Irrigation water	Virginia, USA	2006
			62A5	111725			P19523		T	Viburnum sp.	The Netherlands	2001
	*P. idaei*	P	34D4	971.95	MYA-4065	313728	P6767	p220	T	Rubus idaeus	Scotland, UK	1987	(Kennedy & Duncan 1995)
			62A1	968.95					A	Rubus idaeus	Scotland, UK	1985
	*P. pseudotsugae*	P			52938	331662	P10339		T	Psendotsuga menziesii	Oregon, USA	n.a.	(Hamm & Hansen 1983)
	*P. aff. hedraiandra*	P	33F4					p226		Rhododendron sp.	Minnesota, USA	2003	n.a.
	*P. aff. Dseudotsugae*	P	29B3					p185	A	Psendotsuga menziesii	Oregon, USA	1975	n.a.
1b	*P. clandestina*	P	32G1	347.86	58713, 60438	278933	P3943	p200	T	Trifolium subterraneum	Australia	1985	(Taylor et al. 1985)
			33D8		MYA-4064	287317		p215	A	Trifolium subterranea	Australia	1985
			38D4					p304		n.a.	Australia	n.a.
	*P. iranica*	P	61J4	374.72	60237	158964	P3882	p218	T	Solanum melongena	Iran	1969	(Ershad 1971)
	*P. tentaculata*	P	29F2	552.96			P8497		A	Chrysanthemum leucanthemum	Germany	n.a.	(Kröber & Marwitz 1993)
			30D5							Bacopa sp.	The Netherlands	2004
			30G8		MYA-3655					Argyranthemum frutescens	Germany	2004
1c	*P. andina*	SP	60A2					p460	A	Solanum betaceum	Ecuador	n.a.	(Oliva et al. 2010)
			60A3					p461	A	Solanum betaceum	Ecuador	n.a.
							P13365		T	Solanum brevifolium	Ecuador	2001
	*P. infestans*	SP	27A8							Solanum tuberosum	Mexico	1992	(De Bary 1876)
							P10650			Solanum tuberosum	Mexico	n.a.
	*P. ipomoeae*	SP	31B4				P10226		A	Ipomoea longipedunculata	Mexico	n.a.	(Flier et al. 2002)
			31B5	109229			P10225		T	Ipomoea	Mexico	1999
			31B6				P10227		A	Iongipedunculata Ipomoea	Mexico	n.a.
										Iongipedunculata
	*P. mirabilis*	SP	30C1		64069, MYA-4062		P3006	p145	A	Mirabilis jalapa	Mexico	n.a.	(Galindo-A & Hohl 1985)
			30C2		64070, MYA-4063		P3007	p153	A	Mirabilis jalapa	Mexico	n.a.
	*P. phaseoli*	SP	23B4					p106		Phaseolus lunatus	Delaware, USA	2000	(Thaxter 1889)
			35B6							Phaseolus sp.	Delaware, USA	2000
							P10145			Phaseolus lunatus	Delaware, USA	n.a.
							P10150			Phaseolus lunatus	Delaware, USA	n.a.
1	*P. nicotianae*	P	22F9		15410, MYA-4037			p23		Nicotiana tabacum	North Carolina, USA	n.a.	(Breda de Haan 1896)
			22G1		15409, MYA-4036			p22		Nicotiana tabacum	North Carolina, USA	n.a.
							P10116			Metrosideros excelsa	California, USA	2002
							P1452			Citrus sp.	California, USA	n.a.
2a	*P. botryosa*	P	22H8		MYA-4059			p44		Heavae sp.	Thailand	n.a.	(Chee 1969)
			46C2		26481			p384	A	Hevea brasiliensis	Thailand	n.a.
			62C6	581.69		136915	P3425		T	Hevea brasiliensis	Malaysia	1966
						130422	P6945			Hevea brasiliensis	Malaysia	1986
	*P. citrophthora*	P	03E5					p132		Irrigation water	Virginia, USA	2000	(Smith & Smith 1906)
			26H3					p31		n.a.	n.a.	n.a.
	*P. colocasiae*	SP	22F8		MYA-4159			p47		Colocasia esculenta	n.a.	1992	(Raciborski 1900)
			35D3					p276		Colocasia esculenta	Hawaii, USA	2005
	*P. himalsilva*	P	61G2	128767					T	Quercus leucotricophora	Nepal	2005	(Vettraino et al. 2011)
			61G3	128753					A	Quercus	Nepal	2005
	*P. meadii*	P	22G5		MYA-4043			p75		leucotricophora Citrus sp.	India	1992	(McRae 1918)
			61J9	219.88		129185				Hevea brasiliensis	India	1987
	*P. occultans*	SP	65B9	101557					T	Buxus sempervirens	The Netherlands	1998	(Man In’t Veld et al. 2015)
	*P. terminalis*	SP	65B8	133865					T	Pachysandra terminalis	The Netherlands	2010	(Man In’t Veld et al. 2015)
	P. aff. citrophthora	P	26H4					p32	A	n.a.	n.a.	n.a.	n.a.
						342898	P10341		A	Syringa sp.	England, UK	1990
	P. aff. himalsilva	P	61G4	128754					A	Castanopsis sp.	Nepal	2005	n.a.
	P. sp. 46C3	n.a.	46C3		66767		P6713	p385	A	Hevea brasiliensis	Malaysia	n.a.	n.a.
	P. sp. P6262	n.a.					P6262		A	Hevea brasiliensis	India	n.a.	n.a.
	P. sp. P6310	n.a.					P6310		A	Theobroma cacao	Indonesia	n.a.	n.a.
2b	*P. capsici*	P	22F4		15399, MYA-4034			p8	A	Capsicum annum	New Mexico, USA	1948	(Leonian 1922)
				121656	46012		P0253 P10386			Theobroma cacao Cucumis sativus	Mexico Michigan, USA	1964 1997
	*P. glovera*	SP	31E5					p167	A	Nicotiana tabacum	Brazil	n.a.	(Abad et al. 2011)
			62B4	121969			P11685		T	Nicotiana tabacum	Brazil	1995
	*P. mengei*	SP	42B2		MYA-4554			p340	T	Persea americana	California, USA	n.a.	(Hong et al. 2009)
			42B3		MYA-4555			p341	A	Persea americana	California, USA	n.a.
	*P. mexicana*	P	45G4	554.88	46731	92550	P0646	p355		Solanum lycopersicum	Argentina	n.a.	(Hotson & Hartge 1923)
	*P. siskiyouensis*	SP	41B7	122779	MYA-4187		P15122		T	Stream water	Oregon, USA	2003	(Reeser et al. 2007)
			41B8						A	Soil	Oregon, USA	2003
	*P. tropicalis*	P	22H5					p27		Vanila sp.	Tahiti	n.a.	(Aragaki & Uchida 2001)
			35C8	434.91	76651, MYA-4218			p272	T	Macadamia integrifolia	Hawaii, USA	n.a.
	P. aff. capsici	P	22F5		15427, MYA-4035			p9		Nicotiana tabacum	North Carolina, USA	n.a.	n.a.
	P. sp. brasiliensis	n.a.			46705		P0630		A	Theobroma cacao	Brazil	1969	(Oudemans & Coffey 1991)
2c	*P. acerina*	SP	61H1	133931					T	Acer pseudoplatanus	Italy	2010	(Ginetti et al. 2014)
			61H2						A	Soil	Italy	2010
	*P. capensis*	SP	62C1	128319			P1819		T	Curtisia dentata	South Africa	n.a.	(Bezuidenhout et al. 2010)
			62C2	128320			P1822		A	Stream water	South Africa	n.a.
			62C3	128321			P1823		A	Olea campensis	South Africa	1986
	*P. citricola*	SP	33H8	221.88	60440	21173	P0716	p396	T	Citrus sinensis	Taiwan	1987	(Sawada 1927)
			33J2	295.29				p375	A	Citrus sp.	Japan	1929
	*P. multivora*	SP	55C5	124094					T	Soil	Western Australia, Australia	2007	(Scott et al. 2009)
	*P. pachypleura*	SP	61H6						A	Soil	UK	2006	(Henricot et al. 2014)
			61H7			502404			T	Acuba japonica	UK	2008
			61H8						A	Soil	UK	2009
	*P. pini*	SP	22F1		MYA-3656			p53	A	Rhododendron sp.	West Virginia, USA	1987	(Hong et al. 2011)
			45F1		64532			p343	T	Pinus resinosa	Minnesota, USA	1925
	*P. plurivora*	SP	22E9		MYA-3657			p101		Kalmia latifolia	Western Australia, Australia	1998	(Jung & Burgess 2009)
			22F2					p52		Rhododendron sp. cv. “Olga Mezitt”	New York, USA	n.a.
			33H9	379.61						Rhododendron sp.	Germany	1958
	P. sp. 22F3	SP	22F3					p33	A	n.a.	Ohio, USA	n.a.	n.a.
	P. sp. 28D1	SP	28D1					p119	A	Fagus sylvatica	New York, USA	n.a.	n.a.
			28D3					p121	A	Fagus sylvatica	New York, USA	n.a.
	P. sp. citricola VIII	SP	27D9						A	Unidentified leaf	Hainan, China	n.a.	n.a.
	P. sp. pini-like	SP	56G1						A	Taxus sp.	Pennsylvania, USA	2011	n.a.
	P. taxon emzansi	SP	61F2						A	Agathosma betulina	South Africa	2005	(Bezuidenhout et al. 2010)
			61F3						A	Agathosma betulina	South Africa	2005
2d	*P. bisheria*	SP	29D2							Rubus idaeus cv. Canby	Wisconsin, USA	1989	(Abad et al. 2008)
			31E6	122081			P10117		T	Fragaria ×ananassa	North Carolina, USA	1999
							P1620			Rhododendron sp.	North Carolina, USA	n.a.
	*P. elongata*	SP	33J3						A	n.a.	Australia	1995	(Rea et al. 2010)
			33J4						A	n.a.	Australia	1995
			55C4	125799					T	Soil	Western Australia, Australia	2004
	*P. frigida*	P	47G6						A	Eucalyptus smithi	South Africa	n.a.	(Maseko et al. 2007)
			47G7						A	Eucalyptus smithi	South Africa	n.a.
			47G8						T	Eucalyptus smithi	South Africa	2001
2e	*P. multivesiculata*	SP to NP	29E3	545.96			P10410		T	Cymbidium sp.	The Netherlands	n.a.	(Ilieva et al. 1998)
			30D4						A	Cymbidium sp.	The Netherlands	n.a.
	P. taxon aquatilis	SP	38J5		MYA-4577				A	Stream water	Virginia, USA	2006	(Hong et al. 2012)
3	*P. ilicis*	SP	23A7		56615, MYA-3897		P3939	p113		Ilex sp.	Canada	n.a.	(Buddenhagen & Young 1957)
			34D6							Quercus sp.	Germany	1999
			62A7	114348					T	Ilex aquifolium	The Netherlands	n.a.
	*P. nemorosa*	SP	28J3		MYA-4061			p141		Umbellularia californica	California, USA	n.a.	(Hansen et al. 2003)
			41C4		MYA-2948			p320	T	Lithocarpus densiflorus	California, USA	n.a.
	*P. pluvialis*	SP	60B3		MYA-4930				T	Rainwater	Oregon, USA	2008	(Reeser et al. 2013)
	*P. pseudosyringae*	SP	30A8	111772	MYA-4222			p284	T	Quercus robur	Germany	1997	(Jung et al. 2003)
			30B1					Pp285	A	Quercus robur	Germany	1997
	*P. psychrophila*	SP	29J5	803.95					T	Quercus robur	Germany	1995	(Jung et al. 2002)
			29J6		MYA-4083			p288	A	Quercus ilex	France	1996
4	*P. alticola*	P	47G5	121939			P16948		A	Eucalyptus dunnii	South Africa	n.a.	(Maseko et al. 2007)
	*P. arenaria*	P	55C2	127950					T	Soil	Western Australia, Australia	2009	(Rea et al. 2011)
			62B7	125800					A	Soil	Western Australia, Australia	2009
	*P. megakarya*	P	22H7		MYA-4040			p42		Theobroma cacao	Africa	n.a.	(Brasier & Griffin 1979)
			61J5	238.83	42100	202077			T	Theobroma cacao	Cameroon	n.a.
			61J6	239.83	42099	106327			A	Theobroma cacao	Nigeria	n.a.
	*P. palmivora*	P	22G8		MYA-4039		P10213	p65		Citrus sp.	Florida, USA	n.a.	(Butler 1910)
			22G9		MYA-4038			p26		Theobroma cacao	Costa Rica	n.a.
	*P. quercetorum*	P	15C7							Soil	South Carolina, USA	1997	(Balci et al. 2008)
			15C8							Soil	South Carolina, USA	1997
	*P. quercina*	P	30A4	783.95					A	Quercus robur	Germany	1995	(Jung et al. 1999)
			30A5	784.95	MYA-4084				T	Quercus robur	Germany	1995
			30A7							Quercus sp.	Serbia	2003
	P. sp. ohioensis	n.a.					P16050		A	Soil	Ohio, USA	2006	n.a.
5	*P. agathidicida*	P	67D5						T	Agathis australis	New Zealand	2006	(Weir et al. 2015)
	*P. castaneae*	P	22H6		MYA-4060			p45		Castanea sp.	Japan	n.a.	(Katsura 1976)
			30E7							Soil	Hainan, China	n.a.
			61J7	587.85	36818	325914			T	Soil	Taiwan	n.a.
	*P. cocois*	P	67D6						T	Cocos nucifera	Hawaii, USA	1990	(Weir et al. 2015)
	*P. heveae*	P	22J1			180616		p28	T	Heavae sp.	Malaysia	n.a.	(Thompson 1929)
			22J2		16701, MYA-3895			p17		soil	Tennessee, USA	1964
6a	*P. gemini*	NP	46H1	123382					A	Zostera marina	The Netherlands	1999	(Man in’t Veld et al. 2011)
			46H2	123383					A	Zostera marina	The Netherlands	1999
	*P. humicola*	NP	32F8	200.81	52179, MYA-4080		P3826	p198	T	Soil	Taiwan	1976	(Ko & Ann 1985)
			32F9				P6702	p199	A	Phaseolus vulgaris	Taiwan	n.a.
	*P. inundata*	NP	30J3			390121		p291	T	Olea sp.	Spain	1996	(Brasier et al. 2003b)
			30J4			389751		p298	T	Salix matsudana	UK	1972
							P8619			Pistacia vera	Iran	n.a.
	*P. rosacearum*	NP	22J9		MYA-3662			p82	A	Prunus sp.	California, USA	1987	(Hansen et al. 2009)
			41C1					p321	A	Prunus sp.	California, USA	n.a.
			47J1		MYA-4456				T	Malus domestica	California, USA	n.a.
	P. sp. 48H2	NP	48H2						A	Stream water	Virginia, USA	2008	n.a.
	P. sp. 62C9	NP	62C9						A	Stream water	Taiwan	2013	n.a.
	P. sp. personii	n.a.					P11555		A	Nicotiana tabacum	North Carolina, USA	n.a.	n.a.
	P. taxon walnut	NP	40A7						A	Irrigation water	Virginia, USA	2006	(Brasier et al. 2003a)
			43G1						A	Irrigation water	Virginia, USA	2007
6b	*P. amnicola*	NP	61G6	131652					T	Stream water	Western Australia, Australia	2009	(Crous et al. 2012)
			62C5	133867						Pachysandra sp.	The Netherlands	n.a.	^]
	*P. bilorbang*	NP	61G8	131653					T	Soil	Western Australia, Australia	2010	(Aghighi et al. 2012)
	*P. borealis*	NP	60B2	132023	MYA-4881				T	Stream water	Alaska, USA	2008	(Hansen et al. 2012)
	*P. crassamura*	NP	66C9						A	Picea abies	Italy	2012	(Scanu et al. 2015)
			66D1	140357					T	Soil	Italy	2011
	*P. fluvialis*	NP	55B6	129424					T	Stream water	Western Australia, Australia	2009	(Crous et al. 2011)
	*P. gibbosa*	NP to SP	55B7						A	Soil	Western Australia, Australia	2009	(Jung et al. 2011)
			62B8	127951					T	Soil	Western Australia, Australia	2009
	*P. gonapodyides*	NP	21J5		46726			p117		Water	England, UK	n.a.	(Buisman 1927, Petersen 1910)
			34A8	554.67	60351		P6872			Reservoir water	n.a.	1967
	*P. gregata*	NP	55B8						A	Soil	Western Australia, Australia	2009	(Jung et al. 2011)
			62B9	127952					T	Soil	Western Australia, Australia	2009
	*P. lacustris*	NP	61D6						A	Soil	Germany	2003	(Nechwatal et al. 2013)
			61D8						A	Soil	Germany	2003
		NP	61E1						A	Soil	Germany	2006
						389725	P10337		T	Salix matsudana	England, UK	1972
	*P. litoralis*	NP	55B9	127953					T	Soil	Western Australia, Australia	2008	(Jung et al. 2011)
	*P. megasperma*	NP	62C7	402.72	58817	32035	P3599		T	Althaea rosea	Washington DC, USA	1931	(Drechsler 1931)
	*P. mississippiae*	NP to SP	57J1						A	Irrigation water	Mississippi, USA	2012	(Yang et al. 2013)
			57J2						A	Irrigation water	Mississippi, USA	2012
			57J3		MYA-4946				T	Irrigation water	Mississippi, USA	2012
			57J4						A	Irrigation water	Mississippi, USA	2012
	*P. ornamentata*	NP	66D2	140647					T	Soil	Italy	2012	(Scanu et al. 2015)
			66D3						A	Soil	Italy	2012
	*P. pinifolia*	NP	47H1	122924					T	Pinus radiata	Chile	2007	(Duran et al. 2008)
			47H2	122922					A	Pinus radiata	Chile	2007
	*P. riparia*	NP	60B1	132024	MYA-4882				T	Stream water	Oregon, USA	2006	(Hansen et al. 2012)
	*P. thermophila*	NP	55C1	127954					T	Soil	Western Australia, Australia	2004	(Jung et al. 2011)
	*P. ×stagnum*	NP	36H8						A	Irrigation water	Virginia, USA	2006	(Yang et al. 2014c)
			36J7						A	Irrigation water	Virginia, USA	2006
			43F3		MYA-4926				T	Irrigation water	Virginia, USA	2007
			44F9						A	Irrigation water	Virginia, USA	2007
	P. sp. 26E1	NP	26E1					p116	A	Malus domestica	New York, USA	n.a.	n.a.
	P. sp. canalensis	n.a.					P10456		A	Canal water	California, USA	2002	n.a.
	P. sp. delaware	NP	63H4						A	Pond water	Delaware, USA	2014	n.a.
			63H7						A	Pond water	Delaware, USA	2014
	P. sp. gregata-like	NP	22J5		16698			p16	A	n.a.	n.a.	n.a.	n.a.
	P. sp. megasperma-like	NP	23A1					p81	A	Prunus sp.	California, USA	n.a.	n.a.
			23A3		MYA-3660			p79	A	Actinidia chinensis	California, USA	1987
6	*P. asparagi*	NP	33D7			384046			A	Asparagus officinalis	New Zealand	1980	(Crous et al. 2012)
			62C4	132095	MYA-4826				T	Asparagus officinalis	Michigan, USA	2006
	P. sp. sulawesiensis	n.a.					P6306		A	Syzygium aromaticum	Indonesia	1989	n.a.
7a	*P. attenuata*	NP	67C5						T	Soil	Taiwan	2013	(Jung et al. 2017)
	*P. europaea*	NP	30A3							Quercus sp.	France	1998	(Jung et al. 2002)
			34C2							Quercus sp.	Germany	1999
			62A2	109049					T	Soil	France	1998
	*P. flexuosa*	NP	67C3						T	Soil	Taiwan	2013	(Jung et al. 2017)
	*P. formosa*	NP	67C4						T	Soil	Taiwan	2013	(Jung et al. 2017)
	*P. fragariae*	NP	22G6		11374		P3570	p114		Fragaria ×ananassa	Maryland, USA	n.a.	(Hickman 1940)
			30C5							Fragaria ×ananassa	Virginia, USA	n.a.
			61J3	209.46		181417	P6231		T	Fragaria ×ananassa	England, UK	n.a.
	*P. intricata*	NP	67B9						T	Soil	Taiwan	2013	(Jung et al. 2017)
	*P. rubi*	NP	30D7					p186	A	Rubus sp.	Australia	n.a.	(Man in ‘t Veld 2007)
			41D5							Rubus sp.	Norway	2005
			46C7		90442			p389	T	Rubus idaeus cv. “Glen Clova”	Scotland, UK	n.a.
	*P. uliginosa*	NP	62A3	109054			P10413		T	Soil	Poland	1998	(Jung et al. 2002)
			62A4	109055			P10328		A	Soil	Germany	1998
	P. ×*alni*	NP	32J6	392317	MYA-4081			p205	A	Alnus glutinosa	France	1996	(Brasier et al. 2004, Husson et al. 2015)
			32J7	392318				p206	A	Alnus sp.	Austria	1996
			47A7			392314			T	Alnus sp.	UK	1994
			47A8						A	Alnus sp.	The Netherlands	n.a.
	P. ×*cambivora*	NP	22F6		46719, MYA-4076			p64		Abies sp.	Oregon, USA	n.a.	(Buisman 1927, Jung et al. 2017)
			26F8		MYA-4075			p38		n.a.	New York, USA	n.a.
	P. ×*heterohybrida*	NP	67C1						T	Stream water	Taiwan	2013	(Jung et al. 2017)
	P. ×*incrassata*	NP	67C2						T	Stream water	Taiwan	2013	(Jung et al. 2017)
	P. sp. europaea SW	NP	33F7					p229	A	Soil	West Virginia, USA	2005	n.a.
7b	*P. asiatica*	NP	45G1		90455			p352	A	Robinia pseudoacacia	Jiangsu, China	n.a.	(Rahman et al. 2014a)
			46C6		56194			p388	A	Robinia pseudoacacia	Jiangsu, China	n.a.
			61H3	133347					T	Pueraria lobata	Japan	2005
	*P. cajani*	NP	33D9					p214		Cajanus cajani	India	n.a.	(Amin et al. 1978)
			45F6		44389			p348	A	Cajanus cajani	India	n.a.
			45F7		44388		P3105	p349	T	Cajanus cajani	India	n.a.
	*P. melonis*	NP	32F6		MYA-4079		P1371	p196	A	Cucumis sativus	China	n.a.	(Katsura 1976)
			41B4					p318	A	Cucumis sativus	Iran	n.a.
			45F3	582.69	52854				T	Cucumis sativus	Japan	n.a.
	*P. niederhauserii*	NP	01D5					p312	A	Irrigation water	Virginia, USA	2000	(Abad et al. 2014)
			23J6		MYA-4163			p57	A	Unknown ornamental	Israel	n.a.
			31E7				P10617	p169	A	Thuja occidentalis	North Carolina, USA	2001
	*P. pisi*	NP	60A4						T	Pea	Sweden	2009	(Heyman et al. 2013)
			60A5						A	Pea	Sweden	2009
	*P. pistaciae*	NP	33D6		MYA-4082	386658		p216	T	Pistacia vera	Iran	1986	(Mirabolfathy et al. 2001)
			41A9					p314	A	Pistacia vera	Iran	n.a.
	*P. sojae*	NP	22D8	312.62	16705, MYA-3899	131375		p19		Glycine max	Ontario, Canada	1959	(Kaufmann & Gerdemann 1958)
			28F9					p236		Glycine max	Mississippi, USA	1970
	*P. vignae*	NP	45G6		46735			p357	A	Glycine max	n.a.	n.a.	(Purss 1957)
			45G9		64832	316196	P3420	p379		Vigna unguiculata	Sri Lanka	n.a.
			46C1	112.76	64129			p380		Vigna sinensis	n.a.	n.a.
7c	*P. cinnamomi*	NP	23B1		15400, MYA-4057			p10		Camellia japonica	South Carolina, USA	n.a.	(Rands 1922)
			23B2		15401, MYA-4058			p11		Persea americana	Puerto Rico	1960
			61J1	144.22	46671	22938	P2110		T	Cinnamomum burmannii	Indonesia	1922
	*P. parvispora*	NP	30G9		MYA-4078			p178	A	Beaucarnea sp.	Germany	1991	(Scanu et al. 2014)
			46F6						A	Beaucarnea sp.	Germany	1992
			66C7	132771					A	Arbutus unedo	Italy	2008
			66C8	132772					T	Arbutus unedo	Italy	2011
	P. sp. ax	NP	46H5						A	Ilex glabra cv. “Shamrock”	Virginia, USA	2008	n.a.
7d	*P. fragariaefolia*	NP	61H4	135747					T	Fragaria ×ananassa	Japan	2005	(Rahman et al. 2014b)
	*P. nagaii*	NP	61H5	133248					T	Rosa sp.	Japan	1968	(Rahman et al. 2014b)
8a	*P. cryptogea*	NP	61H9	113.19		180615	P1738		T	Solanum lycopersicum	Ireland	n.a.	(Pethybridge & Lafferty 1919)
	*P. drechsleri*	NP	15E5							Soil	South Carolina, USA	1997	(Tucker 1931)
			15E6							Soil	South Carolina, USA	1998
			23J5	292.35	46724		P1087	p41	T	Beta vulgaris var. altissima	California, USA	n.a.
							P10331			Gerbera jamesonii	New Hampshire, USA	2003
	*P. erythroseptica*	NP	61J2	129.23		34684	P1693		T	Solanum tuberosum	Ireland	n.a.	(Pethybridge 1913)
	*P. medicaginis*	NP	23A4		MYA-3900			p37		Medicago sativa	Ohio, USA	n.a.	(Hansen & Maxwell 1991)
			28F1		44390		P1057	p124		Medicago sativa	California, USA	1975
	*P. pseudocryptogea*	NP			52402		P3103			Solanum marginatum	Ecuador	n.a.	(Safaiefarahani et al. 2015)
	*P. richardiae*	NP	31E8				P10355	p170		Zantedeschia sp.	Japan	1989	(Buisman 1927)
			45 F5	240.30	60353, 46734	325930		p347	T	Zantedeschia aethiopica	USA	n.a.
							P10811			Zantedeschia aethiopica	Japan	1989
	*P. sansomeana*	NP	47H3		MYA-4455				T	Glycine sp.	Indiana, USA	n.a.	(Hansen et al. 2009)
			47H4						A	Glycine sp.	Indiana, USA	n.a.
			47H5						A	Glycine sp.	Indiana, USA	n.a.
	*P. trifolii*	NP	29B2		MYA-3901			p142	A	Trifolium vesiculosum	Mississippi, USA	1978	(Hansen & Maxwell 1991)
			62A9	117687					T	Trifolium sp.	Mississippi, USA	n.a.
	P. aff. cryptogea	NP	22G2	308.62	15402, MYA-4161	325907		p12		Aster sp.	California, USA	n.a.	n.a.
	P. aff. erythroseptica	NP	22J4		MYA-4041			p50		n.a.	Ohio, USA	n.a.	n.a.
			33A1					p207		Solanum tuberosum	Maine, USA	2004
	P. sp. kelmania	NP	24A7		MYA-4162			p102	A	Abies concolor	West Virginia, USA	1998	n.a.
			31E4				P10613	p166	A	Abes fraseri	North Carolina, USA	2002
8b	*P. brassicae*	SP	29D8	686.95					A	Brassica oleracea	The Netherlands	1995	(Man in’t Veld et al. 2002)
			61J8	179.87			P7517, P19521		T	Brassica oleracea	The Netherlands	1986
	*P. cichorii*	SP	62A8	115029					T	Cichorium intybus var. foliosum	The Netherlands	2004	(Bertier et al. 2013)
	*P. dauci*	SP	61E5	127102					T	Daucus carota	France	2009	(Bertier et al. 2013)
			32E5							Duscus carota	France	2004
			32E6				P10728			Duscus carota	France	2004
			32E7					p194		Duscus carota	France	2004
	*P. lactucae*	SP	61F4						T	Lactuca sativa	Greece	2001	(Bertier et al. 2013)
			61F7						A	Lactuca sativa	Greece	2002
			61F8						A	Lactuca sativa	Greece	2003
	*P. primulae*	SP	29E9	620.97				p286		Primula acaulis	Germany	1997	(Tomlinson 1952)
			29F1					p287		Primula sp.	The Netherlands	1998
	P. aff. brassicae-2	n.a.		112968			P6207		A	Allium cepa	Switzerland	n.a.	n.a.
	P. aff. cichorii	SP	61E3	133815					A	Cichorium intybus var. foliosum	UK	1999	n.a.
	P. sp. 29E7	SP	29E7						A	Allium porrum	The Netherlands	n.a.	n.a.
	P. taxon castitis	SP	61E7	131246					A	Fragaria ×ananassa	Sweden	1995	(Bertier et al. 2013)
	P. taxon parsley	SP	61G1						A	Petroselinum crispum	Greece	2006	(Bertier et al. 2013)
8c	*P. foliorum*	SP	49J8	121655	MYA-3638		P10974		T	Rhododendron sp.	Tennessee, USA	2004	(Donahoo et al. 2006)
	*P. hibernalis*	SP	22H1	270.31	60352	36906	P6871	p115		Citrus sinensis	Portugal	1931	(Carne 1925)
			32F7	114104	56353, MYA-3896	134760	P3822	p197		Citrus sinensis	Western Australia, Australia	1958
	*P. lateralis*	NP to SP	22H9		MYA-3898			p51	A	Chamaecyparis lawsoniana	Oregon, USA	n.a.	(Tucker & Milbrath 1942)
			29A9		201856			p128		Chamaecyparis lawsoniana	California, USA	1997
	*P. ramorum*	SP	32G2							Camellia japonica	South Carolina, USA	n.a.	(Werres et al. 2001)
			33F2						Quercus agrifolia	California, USA	n.a.
8d	*P. austrocedrae*	SP	41B5		MYA-4073			A	Austrocedrus chilensis	Argentina	n.a.	(Greslebin et al. 2007)
			41B6	122911	MYA-4074			T	Austrocedrus chilensis	Argentina	2005
	*P. obscura*	SP	60E9	129273				T	Soil	Germany	1994	(Grünwald et al. 2012)
			60F1					A	Pieris sp.	Oregon, USA	2009
			60F2					A	Kalmia latifolia	Oregon, USA	n.a.
	*P. syringae*	SP	21H9		34002	P0649	p187		Citrus sp.	California, USA	n.a.	(Klebahn 1905)
			23A6		MYA-3659		p35		n.a.	New York, USA	n.a.
8	*P. stricta*	NP	58A1		MYA-4944			T	Irrigation water	Mississippi, USA	2012	(Yang et al. 2014a)
			58A2					A	Irrigation water	Mississippi, USA	2012
			58A3					A	Irrigation water	Mississippi, USA	2012
			58A4					A	Irrigation water	Mississippi, USA	2012
9a (cluster 9a1)	*P. aquimorbida*	NP	40A6		MYA-4578			T	Irrigation water	Virginia, USA	2006	(Hong et al. 2012)
			40E3					A	Irrigation water	Virginia, USA	2006
			44G9					A	Irrigation water	Virginia, USA	2007
	*P. Chrysanthemi*	NP	61E9					A	Chrysanthemum sp.	Japan	1998	(Naher et al. 2011)
			61F1	123163				T	Chrysanthemum ×morifolium	Japan	2000
	*P. hydrogena*	NP	44G8					A	Irrigation water	Virginia, USA	2007	(Yang et al. 2014b)
			46A3		MYA-4919			T	Irrigation water	Virginia, USA	2007
			46A4					A	Irrigation water	Virginia, USA	2007
	*P. hydropathica*	NP	05D1		MYA-4460		p366	T	Irrigation water	Virginia, USA	2000	(Hong et al. 2010)
			5C11		MYA-4459		p365	A	Irrigation water	Virginia, USA	2000
	*P. irrigata*	NP	04E4		MYA-4458		p335	A	Irrigation water	Virginia, USA	2000	(Hong et al. 2008)
			23J7		MYA-4457		p108	T	Irrigation water	Virginia, USA	2000
			44E4					A	Stream water	Virginia, USA	2007
	*P. macilentosa*	NP	58A5					A	Irrigation water	Mississippi, USA	2012	(Yang et al. 2014a)
			58A6					A	Irrigation water	Mississippi, USA	2012
			58A7		MYA-4945			T	Irrigation water	Mississippi, USA	2012
			58A8					A	Irrigation water	Mississippi, USA	2012
	*P. parsiana*	NP	47C3			395329		T	Ficus carica	Iran	1991	(Mostowfizadeh-Ghalamfarsa et al. 2008)
	*P. virginiana*	NP	40A9						A	Irrigation water	Virginia, USA	2006	(Yang & Hong 2013)
			44G6						A	Irrigation water	Virginia, USA	2007
			46A2		MYA-4927				T	Irrigation water	Virginia, USA	2007
	P. aff. parsiana G1	NP	47C7						A	Pistacia vera	Iran	n.a.	n.a.
			47C8						A	Pistacia vera	Iran	n.a.
						395328	P8618		A	Pistacia vera	Iran	1992
	P. aff. parsiana G2	NP	47C5			395330			A	Pistacia vera	Iran	1992	n.a.
			47C6			395331			A	Pistacia vera	Iran	1992
	P. aff. parsiana G3	NP	47D5						A	Pistacia vera	Iran	n.a.	n.a.
			47D8						A	Pistacia vera	Iran	n.a.
			47E1						A	Pistacia vera	Iran	n.a.
	P. sp. 35G4	NP	35G4						A	Irrigation water	Virginia, USA	2005	n.a.
	P. sp. 38D9	NP	38D9						A	Dianthus caryophyllus	Taiwan	n.a.	n.a.
	P. sp. 40J5	NP	40J5						A	Unknown leaf in seawater	Hainan, China	n.a.	n.a.
	P. sp. cuyabensis	n.a.					P8213		A	n.a.	Ecuador	1993	n.a.
	P. sp. lagoariana	NP	60B4				P8220		A	n.a.	Ecuador	n.a.	n.a.
			60B5				P8217		T	n.a.	Ecuador	n.a.
							P8223		A	n.a.	Ecuador	1993
9a (cluster 9a2)	*P. macrochlamvdospora*-G1	SP	33E1				P10264			Glycine max	New South Wales, Australia	n.a.	(Irwin 1991)
							P10267			Glycine max	New South Wales, Australia	1994
	*P. macrochlamvdospora* -G2	SP	31E9			351473	P8017	p171		Glycine max	Queensland, Australia	n.a.	(Irwin 1991)
			33D5	240.30	60353	340618				Zantedeschia aethiopica	The Netherlands	1927
	*P. quininea*	NP	45F2	406.48	56964			p344	A	Cinchona officinalis	Peru	n.a.	(Crandall 1947)
			46C4	407.48	46733			p386	T	Cinchona officinalis	Peru	n.a.
9a (cluster 9a3)	*P. insolita*	NP	327E1		MYA-4077			p123		Waterfall water	Hainan, China	n.a.	(Ann & Ko 1980)
			38E1	691.79	38789	288805			T	Soil	Taiwan	1980
							P6703		A	Soil	Taiwan	n.a.
	*P. polonica*	NP	40G9							Irrigation water	Virginia, USA	2006	(Belbahri et al. 2006)
			43F9							Irrigation water	Virginia, USA	2007
			49J9				P15005		A	Soil	Poland	2006
9b	*P. captiosa*	NP	46H6						A	Eucalyptus saligna	New Zealand	1999	(Dick et al. 2006)
			46H7				P10719		T	Eucalyptus saligna	New Zealand	1992
			46H8						A	Eucalyptus saligna	New Zealand	2000
							P10721		A	Eucalyptus saligna	New Zealand	1998
	*P. constricta*	NP to SP	55C3	125801					T	Soil	Western Australia, Australia	2006	(Rea et al. 2011)
	*P. fallax*	NP	46J2				P10722		T	Eucalyptus delegatensis	New Zealand	1997	(Dick et al. 2006)
			46J3						A	Eucalyptus nitens	New Zealand	2000
			46J5						A	Eucalyptus nitens	New Zealand	2000
							P10725		A	Eucalyptus fastigata	New Zealand	2004
10	*P. boehmeriae*	P	45F9	291.29		180614	P6950		T	Boehmeriae nivea	Taiwan	1927	(Sawada 1927)
	*P. gallica*	NP	50A1	111474			P16826		T	Quercus robur	France	1998	(Jung & Nechwatal 2008)
			61D5	111475			P16827		A	Phragmites australis	Germany	2004
	*P. gondwanensis*	P	22G7		MYA-3893					n.a.	Ohio, USA	n.a.	(Crous et al. 2015)
	*P. intercalaris*	NP	45B7	140632	TSD-7				T	Stream water	Virginia, USA	2007	(Yang et al. 2016)
			48A1						A	Stream water	Virginia, USA	2008
			49A7	140631					A	Stream water	Virginia, USA	2009
	*P. kernoviae*	P	46C8				P10956	p390		Rhododendron ponticum	England, UK	2004	(Brasier et al. 2005)
			46J6				P10681			Annona cherimola	New Zealand	2002
			46J8				P10671			Soil	New Zealand	2003
	*P. morindae*	P	62B5	121982					T	Morinda citrifolia var. citrifolia	Hawaii, USA	2005	(Nelson & Abad 2010)
	P. sp. boehmeriae-like	P	45F8	357.52	60173	32199	P1378	p350	A	Citrus sinensis	Argentina	1939	n.a.
n.a.	*P. Iilii*	NP		135746					T	Lilium sp.	Japan	1987	(Rahman et al. 2015)
outgroup	*Elongisporangium undulatum*	P		101728		337230	P10342		T	Larix sp.	Scotland, UK	1989	(Uzuhashi et al. 2010)
	*Phytopythium vexans*	P		340.49	12194		P3980		T	n.a.	n.a.	n.a.	(de Cock et al. 2015)
	*Halophytophthora fluviatilis*	P	57A9		MYA-4961				T	Stream water	Virginia, USA	2011	(Yang & Hong 2014)

^a Molecular (sub)clade as designated in Fig. 1
^b Names of taxa informally designated for the first time in this study are underlined.
^c Sporangial papillation: NP = non-papillate, P = papillate, and SP = semi-papillate.
^d Isolate identification abbreviations: CH, Chuanxue Hong laboratory at Virginia Polytechnic Institute and State University, Virginia Beach, VA, USA; CBS, Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands; ATCC, American Type Culture Collection, Manassas, VA, USA; IMI, CABI Biosciences, UK; WPC, the World Phytophthora Genetic Resource Collection at University of California, Riverside, USA; MG, Mannon E. Gallegly laboratory at West Virginia University, USA. Local identifications of respective isolates are provided in Table S1.
^e Ex-types (T) or authentic (A) isolates (designated as representative isolates by the originators of the respective species).
^f n.a.= not available.

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