Pythium Pringsh., Jb. wiss. Bot. 1: 304 (1858)


Pythium is the largest and most comprehensively studied genus in Pythiaceae sensu lato, order Peronosporales sensu lato, class Peronosporomycetes, phylum Oomycota, and kingdom Straminipila (Beakes et al. 2014). Pringsheim (1858) described the genus. However, the initial classification of Pythium has changed many times based on several studies using morphological characteristics (Uzuhashi et al. 2010). Pythium comprises of more than 230 extant species (Hyde et al. 2014), however, identification of species has always been problematic due to limited morphological characters, difficulty in isolating some taxa and lack of molecular data for certain species (Lévesque and de Cock 2004).

Classification – Oomycota, Pythiales, Pythiaceae

Type species Pythium monospermum Pringsh. (Pringsheim 1858)

Distribution – worldwide

Disease symptoms – generally cause rot of fruit, roots and stem including pre- or post-emergence damping-off of seeds and seedlings.

Pythium causes crown and root rot in mature plants, where plants suddenly wilt during warm and sunny weather and when plants have their first heavy fruit load. Often, upper leaves of infected plants wilt in the day and recover overnight. However, plants eventually die (Craft and Nelson 1996; Postma et al. 2000). The first symptoms of Pythium root infections include stunting. In the root system, initial symptoms are brown to dark-brown lesions on root tips and feeder roots. As the disease progresses, symptoms are soft, brown, stubby roots and lack of feeder roots. In larger roots, the outer root tissue or cortex peels away, leaving the string-like vascular bundles underneath (Postma et al. 2000; Moorman et al. 2002; Al-Mahmooli et al. 2015). Pythium rot also occurs in the crown at the stem base. In cucumber, diseased crowns turn orange-brown, often with a soft rot at the base, while in strawberry seedling roots have dark brown, water-soaked rot and rotten crowns (Columbia and English 1988; Ishiguro et al. 2014). Several species of Pythium cause blight of turfgrass, which initially appears as “greasy” water-soaked areas, but later turn brown and grey (Vencelli and Powell 2008).

Several Pythium species are capable of causing fruit rot in numerous crops (Martin and Loper 1999). Pythium fruit rot is commonly known as a cottony leak or watery rot and occurs during wet weather or in poorly drained areas of fields (Ho and Abd-Elsalam 2020; Sharma et al. 2020a). Initial symptoms of the fruit rot are brownish, water-soaked lesions that quickly become large, watery, soft and rotten. The rot generally begins on the parts of fruit in contact with the soil. In cucumber, a brown to dark green blister can be seen on fruit before they become watery and rot. Later, white cottony mycelium can be seen on rotten tissues, especially during humid weather. Pythium fruit rot is most severe in poorly-drained fields during wet weather. The disease can render fruit unmarketable (Ho 2009; Sharma et al. 2020a).

Pre-emergence damping-off causes seeds and young seedlings to rot before they emerge from the growing medium in greenhouses, while post-emergence damping-off kills newly emerged seedlings. In the latter, the pathogen causes a water-soaked, soft brown lesion at the stem base, near the soil line, that pinches off the stem causing the seedling to topple over and die (Weiland et al. 2012).

HostsPythium has a wide range of hosts including species of Cucurbitaceae and Poaceae, Ananas comosus, Arachis hypogaea, Brassica sp., Carica papaya, Beta vulgaris, Daucus carota subsp. sativus, Dendrobium sp, Solanum sp. and Zingiber officinale. Some species are pathogens of algae, fungi, other oomycetes, nematodes, insects, animals and humans (Van der Plaäts-Niterink1981; Czeczuga et al. 2005; Kawamura et al. 2005; Hwang et al. 2009; Li et al. 2010; Weiland et al. 2012; Ho 2013; Hyde et al 2014). Several species inhabit different soils in cultivated and uncultivated fields including forest (Uzuhashi et al 2010). Pythium arrhenomanes, P. dissotocum, P. elongatum, P. myriotylum, and P. spinosum are important pathogens of rice seedlings (Hendrix and Campbell 1973; Hsieh 1978; Ventura et al. 1981; Chun and Schneider 1998; Eberle et al. 2007; Kreye et al. 2009; Oliva et al. 2010; Banaay et al. 2012; Van Buyten and Höfte 2013). Pythium insidiosum causes pythiosis in mammals including humans (Van der Plaats-Niterink 1981; de Cock et al. 1987). Some species target below-ground plant parts and some species can cause fruit rot, however, some Pythium species can also benefit plants as endophytes by acting as biocontrol agents (Benhamou et al. 1997) and by stimulating plant growth (Martin and Looper 1999; Mazzola et al. 2002).

Pathogen biology, disease cycle and epidemiology

Pythium species grow and colonize a plant by producing hyphae which extract nutrients from the host. Once the hyphae from opposite mating types meet, they produce thick-walled oospores which serve as overwintering structures. Upon germination, an oospore may produce more hyphae, or develop a zoosporangium, which produces motile zoospores that swim to and infect plants. Zoosporangia can also germinate and directly infect plants (Ho 2009; van West et al. 2003).

Fig. 1 Disease cycle of a Pythium species (redrawn from van West et al. 2003)


Morphological based identification and diversity

Pythium has hyaline hyphae which are coenocytic without cross septa (van der Plaäts-Niterink 1981). Filamentous and globose sporangia are present, and zoospores develop in a vesicle, which is formed at the tip of a discharge tube from a sporangium. After fertilization with paragynous or hypogynous antheridia, oospores are formed in smooth or ornamented oogonia. The oospore can fill the whole organism or can have space between the walls of the oogonia and oospore. The process of zoospore formation within a vesicle is a characteristic feature of the genus, which distinguishes it from morphologically similar genera such as Phytophthora and Halophytophthora. However, the formation of zoospores is similar to Lagenidium, which features endobiotic and holocarpic features not observed in Pythium (Dick 2001). Species delimitation based on morphological characteristics such as shape and size of sporangia and oogonia is difficult as these characteristics are often shared among different species.


Molecular based identification and diversity

Lévesque and de Cock (2004) separated the genus into 11 clades (A-K) using phylogenies of ITS and 28S. Clade K, which includes P. vexans was transferred to a new genus Phytopythium with Phytopythium sindhum as type species (Bala et al. 2010), while the remaining clades can be divided into two groups: species with filamentous sporangia (clades A-D) and species with globose sporangia (clades E-J). Identification of Pythium isolates to species level is recommended based on cox1 and ITS gene regions. The use of ITS region alone cannot accurately identify all Pythium species. Several species are indistinguishable based on both ITS and cox1 sequences. Lévesque and de Cock (2004) provided the first extensive study of Pythium, accepting 116 species. Additional species have recently been described for example P. alternatum (Rahman et al. 2015), P. biforme, P. brachiatum, P. junctum, P. utonaiense (Uzuhashi et al. 2015), P. cedri (Chen et al. 2017a), P. heteroogonium, P. longipapillum, P. oryzicollum (Salmaninezhad et al. 2019). Currently, there are more than 130 accepted species in the genus (Arafa et al. 2020). The phylogenetic tree constructed is presented in Fig. 2 and the information of species are given in table 1.

Recommended genetic markers (generic level within Pythium sensu lato) – 18S (small subunit, SSU) and 28S (large subunit, LSU) nuclear rRNA genes

Recommended genetic markers (sub-generic, inter- and intra-specific level) – The internal transcribed spacers (ITS including ITS1, 5.8S rRNA, and ITS2), cytochrome c oxidase subunit 2 (cox2)

Accepted number of species – There are 330 epithets listed in Index Fungorum (2020), however only 157 species have DNA sequence data (Table 1).

References – van der Plaäts-Niterink 1981, Dick 2001 (morphology), Lévesque and de Cock 2004, Hyde et al. 2014, Arafa et al. 2020 (phylogeny and accepted species numbers).

Table 1 DNA barcodes available for Pythium. Ex-type/ex-epitype/ex-neotype/ex-lectotype strains and voucher strains are in bold. Species confirmed with pathogenicity studies are marked with #. (VdPN) are strains used by Van der Plaäts-Niterink (1981) for descriptions.

Species Isolate Host SSU ITS LSU cox2 tub2
Pythium abappressorium# CBS 110198 Triticum aestivum HQ643408 HQ643408 HQ643408 KJ595409 KJ595533
P. acanthicum# CBS 377.34 Solanum tuberosum AY598617 AY598617 AY598617 KJ595380 KJ595504
P. acanthophoron# CBS 337.29 Ananas sativus AY598711 AY598711 AY598711 KJ595376 KJ595500
P. acrogynum CBS 549.88 Soil (Spinacia oleracea) N/A AY598638 AY598638 AB362324 KJ595458
P. adhaerens CBS 520.74 Soil AY598619 AY598619 AY598619 KJ595386 KJ595510
P. afertile LEV2066 Turf grass N/A HQ643416 HQ643416 KJ595440 KJ595563
P. alternatum GUCC0015 Soil N/A AB998876 N/A N/A
P. amasculinum CBS 552.88 soil (vegetable garden) AY598671 AY598671 AY598671 KJ595390 KJ595514
P. anandrum# CBS 285.31 Rheum rhaponticum AY598650 AY598650 AY598650 AB362328 KJ595450
P. angustatum# CBS 522.74 (VdPN) Soil AY598623 AY598623 AY598623 KJ595387 KJ595511
P. aphanidermatum# CBS 118.80 Unknown AY598622 AY598622 AY598622 KJ595344 KJ595472
P. apiculatum CBS 120945 Soil (Vitis sp.) HQ643443 HQ643443 HQ643443 KJ595422 KJ595547
P. apleroticum CBS 772.81 Nymphyoidespeltata AY598631 AY598631 AY598631 KJ595400 KJ595524
P. aquatile# CBS 215.80 Soil AY598632 AY598632 AY598632 KJ595355 KJ595481
P. aristosporum CBS 263.38 Triticum aestivum AY598627 AY598627 AY598627 AB507410 DQ071297
P. arrhenomanes# CBS 324.62 (VdPN) Zea mays AKXY02050628 AY598628 AY598628 AKXY02053172 KJ595451
P. attrantheridium# DAOM 230386 Prunus serotina HQ643476 HQ643476 HQ643476 AB512889 AB512822
P. biforme UZ00796 Aquatic N/A KJ995584 KJ995601 N/A N/A
P. boreale CBS 551.88 Soil AY598662 AY598662 AY598662 EF408876 EF408882
P. brachiatum UZ00736 Aquatic N/A KJ995581 KJ995603 N/A N/A
P. buismaniae CBS 288.31 Linumusitatissimum AY598659 AY598659 AY598659 KJ595368 KJ595493
P. camurandrum CBS 124059 Hordeum vulgare GQ244426 GQ244426 GQ244426 KJ595433 KJ595558
P. canariense CBS 112353 Soil HQ643482 HQ643482 HQ665069 JX397983 JX397969
P. capillosum CBS 222.94 Soil AY598635 AY598635 AY598635 KJ595360 KJ595485
P. carbonicum# CBS 112544 Soil (spoil heap) HQ643373 HQ643373 HQ643373 AB690678 KJ595464
P. carolinianum# CBS 122659 Soil N/A HQ643484 HQ665111 KJ595427 KJ595551
P. catenulatum# CBS 842.68 (VdPN) Turf grass AY598675 AY598675 AY598675 KJ595404 KJ595528
P. caudatum# CBS 584.85 Xiphinemarivesi HQ643136 HQ643136 HQ665277 AF290309 KJ595459
P. cederbergense# CBS 133716 Aspalathuslinearis N/A JQ412768 KJ716864 JQ412805 JQ412781
P. cedri Chen 30 roots of Cedrus N/A KX423751 N/A N/A N/A
P. chamaehyphon# CBS 259.30 Carica papaya AY598666 AY598666 AY598666 AB257280 KJ595448
P. chondricola# CBS 203.85 Chondruscrispus N/A AY598620 AY598620 KJ595354 KJ595480
P. citrinum CBS 119171 Soil (Vitis sp.) HQ643375 HQ643375 HQ643375 AB690679 KJ595465
P. coloratum# CBS 154.64 Soil (tree nursery) AY598633 AY598633 AY598633 KJ595346 KJ595474
P. conidiophorum# CBS 223.88 Soil AY598629 AY598629 AY598629 KJ595361 KJ595486
P. contiguanum CBS 221.94 Soil (salt marsh) HQ643514 HQ643514 HQ665162 KJ595358 KJ595483
P. cryptoirregulare# CBS 118731 Euphorbia pulcherrima HQ643515 HQ643515 HQ643515 GU071763 GU071888
P. cucurbitacearum# CBS 748.96 Unknown AY598667 AY598667 AY598667 AB690680 KJ595460
P. cylindrosporum# CBS 218.94 Soil AY598643 AY598643 AY598643 GU071762 GU071877
P. cystogenes# CBS 675.85 Viciafaba HQ643518 HQ643518 HQ643518 KJ595396 KJ595520
P. debaryanum# CBS 752.96 Tulipa sp. AY598704 AY598704 AY598704 KJ595399 KJ595523
P. delawarense CBS 123040 Glycine max KF853241 EU339312 KF853240 KJ595430 KJ595555
P. deliense# CBS 314.33 Nicotiana tabacum AY598674 AY598674 AY598674 KJ595372 KJ595497
P. diclinum# CBS 664.79 Beta vulgaris N/A AY598690 HQ665282 KJ595394 KJ595518
P. dimorphum# CBS 406.72 Pinus taeda AY598651 AY598651 AY598651 AB362331 KJ595454
P. dissimile CBS 155.64 Pinus radiata AY598681 AY598681 AY598681 KJ595347 KJ595475
P. dissotocum# CBS 166.68 (VdPN) Triticum aestivum AY598634 AY598634 AY598634 KJ595351 KJ595479
P. echinulatum# CBS 281.64 (VdPN) Soil (forest nursery) AY598639 AY598639 AY598639 AB362327 KJ595449
P. emineosum CBS 124057 Juniperus communis N/A GQ244427 GQ244427 KJ595432 KJ595557
P. erinaceum CBS 505.80 Soil N/A AY598694 HQ665243 AB362326 KJ595456
P. ershadii IRAN2379C soil N/A KT894054 N/A N/A
P. flevoense CBS 234.72 Soil AY598691 AY598691 AY598691 KJ595363 KJ595488
P. folliculosum# CBS 220.94 Soil AY598676 AY598676 HQ665160 N/A N/A
P. glomeratum# CBS 122644 Soil N/A HQ643542 HQ665097 KJ595424 KJ595548
P. graminicola# CBS 327.62 Saccharum officinarum AY598625 AY598625 AY598625 AF196593 KJ595452
P. grandisporangium# CBS 286.79 Decaying leaf (Zostera marina) AY598692 AY598692 AY598692 KJ595367 KJ595492
P. helicandrum CBS 393.54 Rumex acetosella AY598653 AY598653 AY598653 AB362329 KJ595453
P. helicoides# CBS 286.31 Phaseolus vulgaris AY598665 AY598665 AY598665 DQ071377 AB511994
P. heteroogonium 079-1 – CBS 141232 Soil N/A KX228103 N/A KX228131 KX228117
P. heterothallicum# CBS 450.67 Soil (Sambucus) AY598654 AY598654 AY598654 AB512919 AB512850
P. hydnosporum# CBS 253.60 (VdPN) Unknown AY598672 AY598672 AY598672 KJ595364 KJ595489
P. hypogynum# CBS 234.94 Soil AY598693 HQ643565 HQ665171 AB362325 KJ595447
P. inflatum# CBS 168.68 (VdPN) Saccharum officinarum AY598626 AY598626 AY598626 KJ595352 N/A
P. insidiosum# CBS 574.85 Equus ferus AF289981 AY598637 AY598637 KJ595391 KJ595515
P. intermedium# CBS 266.38 (VdPN) Agrostis stolonifera AY598647 AY598647 AY598647 AB507410 AB512836
P. irregular# CBS 250.28 Phaseolus vulgaris AY598702 AY598702 AY598702 GU071760 GU071886
P. iwayamai# CBS 156.64 (VdPN) Soil (Pinus sp.) AY598648 AY598648 AY598648 JX397979 JX397965
P. jasmonium CBS 101876 Arabidopsis thaliana HQ643778 HQ643778 HQ643778 KJ595406 KJ595530
P. junctum UZ00732 Aquatic N/A KJ995576 KJ995605 N/A N/A
P. kashmirense# CBS 122908 Soil HQ643671 HQ643671 HQ643671 KJ595429 KJ595553
P. kunmingense# CBS 550.88 Soil (Viciafaba) AY598700 AY598700 HQ665259 KJ595389 KJ595513
P. litorale# CBS 118360 Soil (Phragmites australis) HQ643386 HQ643386 HQ643386 KJ595418 KJ595543
P. longandrum# CBS 112355 Soil HQ643679 HQ643679 HQ665071 KJ595413 KJ595538
P. longipapillum# NRh8* soil N/A KX228105 N/A KX228130 KX228114
P. longisporangium# CBS 122646 Soil (Vitis sp.) N/A HQ643680 HQ665099 KJ595426 KJ595550
P. lucens# CBS 113342 Triticum HQ643681 HQ643681 HQ643681 KJ595415 KJ595540
P. lutarium# CBS 222.88 Soil HQ643682 HQ643682 HQ665163 KJ595359 KJ595484
P. lycopersici# CBS 122909 Soil (Lycopersicum esculentum) N/A HQ643683 HQ665119 KJ595343 KJ595554
P. macrosporum# CBS 574.80 Flower bulb AY598646 AY598646 AY598646 AB512916 AB512842
P. mamillatum# CBS 251.28 (VdPN) Beta vulgaris AY598703 AY598703 HQ665173 AB362325 AB512844
P. marinum# CBS 750.96 Soil N/A AY598689 AY598689 KJ595398 KJ595522
P. marsipium# CBS 773.81 Nymphyoides peltata N/A AY598699 HQ665297 KJ595401 KJ595525
P. mastophorum# CBS 375.72 (VdPN) Apiumgraveolens AY598661 AY598661 AY598661 KJ595378 KJ595502
P. megacarpum CBS 112351 Soil (Vitis sp.) HQ643388 HQ643388 HQ643388 AB690665 KJ595536
P. megalacanthum# CBS 101356 Chrysanthemum N/A HQ643693 KJ716865 KJ595435 N/A
P. mercurial# CBS 122443 Macadamia integrifolia KF853243 DQ916363 KF853236 AB690666 KJ595466
P. middletonii# CBS 528.74(VdPN) Soil N/A AY598640 AY598640 AB362318 KJ595457
P. minus# CBS 226.88 Soil HQ643696 HQ643696 HQ665168 AB362320 KJ595446
P. monospermum# CBS 158.73 (VdPN) Soil HQ643697 HQ643697 HQ643697 KJ595350 KJ595478
P. montanum CBS 111349 Soil (Picea abies) HQ643389 HQ643389 HQ643389 KJ595410 KJ595534
P. multisporum CBS 470.50 Soil AY598641 AY598641 AY598641 AB362319 KJ595455
P. nagaii# CBS 779.96 Soil AY598705 AY598705 AY598705 KJ595402 KJ595526
P. nodosum# CBS 102274 Soil N/A HQ643709 HQ665055 KJ595407 KJ595531
P. nunn# CBS 808.96 Soil AY598709 AY598709 AY598709 AF196609 DQ071325
P. oedochilum# CBS 292.37 Unknown AY598664 AY598664 AY598664 AB108011 EF408883
P. okanoganense# CBS 315.81 Triticum aestivum AY598649 AY598649 AY598649 KJ595373 KJ595498
P. oligandrum# CBS 382.34 (VdPN) Viola sp. AY598618 AY598618 AY598618 KJ595381 KJ595505
P. oopapillum# CBS 124053 Cucumis sativus N/A FJ655174 FJ655174 KJ595431 KJ595556
P. ornacarpum CBS 112350 Soil HQ643721 HQ643721 HQ643721 KJ595411 KJ595535
P. ornamentatum CBS 122665 Soil N/A HQ643722 HQ665117 KJ595428 KJ595552
P. orthogonon# CBS 376.72 Zea mays AY598710 AY598710 HQ665221 KJ595379 KJ595503
P. oryzicollum# Kr7 soil N/A KX228072 N/A KX228125 KX228108
P. ostracodes# CBS 768.73 (VdPN) Soil AY598663 AY598663 AY598663 AB690668 EF408880
P. pachycaule# CBS 227.88 Soil AY598687 AY598687 HQ665169 KJ595362 KJ595487
P. paddicum# CBS 698.83 Triticum and Hordeum AY598707 AY598707 AY598707 JX397982 JX397968
P. paroecandrum# CBS 157.64 (VdPN) Soil AY598644 AY598644 AY598644 DQ071391 DQ071332
P. parvum CBS 225.88 Soil AY598697 AY598697 AY598697 AB362322 KJ595445
P. pectinolyticum CBS 122643 Soil HQ643739 HQ643739 HQ643739 N/A KJ595469
P. periilum# CBS 169.68 (VdPN) Soil AY598683 AY598683 HQ665141 N/A KJ595444
P. periplocum# CBS 289.31 Citrullus vulgaris AY598670 AY598670 AY598670 KJ595369 KJ595494
P. perplexum# CBS 674.85 Viciafaba AY598658 AY598658 AY598658 KJ595395 KJ595519
P. phragmitis# CBS 117104 Soil (Phragmites australis) HQ643746 HQ643746 HQ665081 AJ890351 EU152854
P. pleroticum CBS 776.81 Nymphyoides peltata AY598642 AY598642 AY598642 AB362321 KJ595461
P. plurisporium# CBS 100530 Agrostis AY598684 AY598684 AY598684 KJ595405 KJ595529
P. polare# CBS 118203 Sanionia uncinata KJ716858 AB299390 KJ716859 KJ595417 KJ595542
P. polymastum# CBS 811.70 (VdPN) Lactuca sativa AY598660 AY598660 AY598660 KJ595403 KJ595527
P. porphyrae# CBS 369.79 (VdPN) Porphyrayezoensis AY598673 AY598673 AY598673 KJ595377 KJ595501
P. phragmiticola P56 Soil N/A KC145165 N/A KC145166 KC145167
P. prolatum# CBS 845.68 Rhododendron sp. AY598652 AY598652 AY598652 AB362330 KJ595462
P. pyrioosporum IRAN2382C Soil N/A KT894052 N/A N/A
P. pyrilobum# CBS 158.64 Pinus radiata AY598636 AY598636 AY598636 KJ595349 KJ595477
P. radiosum CBS 217.94 Soil N/A AY598695 HQ665156 KJ595356 N/A
P. recalcitrans# CBS 122440 Soil (Vitis vinifera) N/A DQ357833 KJ716861 KJ595423 EF195143
P. rishiriense GUCC0007 Aquatic N/A AB998878 N/A N/A
P. rhizo-oryzae# CBS 119169 Soil HQ643757 HQ643757 HQ643757 KJ595420 KJ595545
P. rhizosaccharum CBS 112356 Soil (Saccharum officinarum) N/A HQ643760 HQ665072 AB362323 KJ595463
P. rostratifingens# CBS 115464 Soil (Malus sp.) HQ643761 HQ643761 HQ643761 KJ595416 KJ595541
P. rostratum# CBS 533.74 Soil AY598696 AY598696 AY598696 KJ595388 KJ595512
P. salpingophorum# CBS 471.50 (VdPN) Lupinus angustifolius AY598630 AY598630 AY598630 KJ595384 KJ595508
P. schmitthenneri# CBS 129726 Glycine max N/A JF836869 KJ716862 JF895530 KJ595470
P. scleroteichum# CBS 294.37 Ipomoea batatas AY598680 AY598680 AY598680 KJ595370 KJ595495
P. segnitium CBS 112354 Soil HQ643772 HQ643772 HQ643772 KJ595412 KJ595537
P. selbyi# CBS 129728 Zea mays N/A JF836871 KJ716863 JF895532 KJ595471
P. senticosum# CBS 122490 Soil (forest) HQ643773 HQ643773 HQ643773 AB362317 KJ595467
P. solare CBS 119359 Phaseolus vulgaris N/A EF688275 KJ716860 KJ595421 KJ595546
P. spinosum# CBS 275.67 (VdPN) Compost AY598701 AY598701 AY598701 KJ595366 KJ595491
P. splendens# CBS 462.48 (VdPN) Unknown AY598655 AY598655 AY598655 AB512921 AB512852
P. stipitatum DAOM 240293 Soil N/A KJ716866 KJ716866 KJ595437 KJ595560
P. sukuiense CBS 110030 Soil N/A HQ643836 HQ665059 KJ595408 KJ595532
P. sulcatum# CBS 603.73 Daucus carota AY598682 AY598682 HQ665281 KJ595393 KJ595517
P. sylvaticum# CBS 453.67 Soil AY598645 AY598645 AY598645 KJ595383 KJ595507
P. takayamanum CBS 122491 Soil HQ643854 HQ643854 HQ643854 AB362315 KJ595468
P. tardicrescens# LEV1534 Turfgrass N/A HQ643855 HQ643855 KJ595439 KJ595562
P. torulosum# CBS 316.33 (VdPN) Grass AY598624 AY598624 AY598624 KJ595374 KJ595499
P. tracheiphilum# CBS 323.65 Lactuca sativa N/A AY598677 HQ665207 KJ595375 N/A
P. ultimum var. sporangiiferum# CBS 219.65 Chenopodium album AKYB02045405 AY598656 AY598656 KJ595357 KJ595482
P. ultimum var. ultimum# CBS 398.51 Lepidium sativum AY598657 AY598657 AY598657 KJ595382 KJ595506
P. uncinulatum# CBS 518.77 Lactuca sativa AY598712 AY598712 AY598712 KJ595385 KJ595509
P. undulatum# CBS 157.69 (VdPN) Soil (Pinus sp.) AY598708 AY598708 AY598708 KJ595348 KJ595476
P. urmianum IRAN2376C Soil N/A KT894049 N/A N/A
P. utonaiense UZ00769 Aquatic N/A KJ995587 KJ995600 N/A N/A
P. vanterpoolii# CBS 295.37 Triticum aestivum AY598685 AY598685 AY598685 KJ595371 KJ595496
P. vexans# CBS 119.80(VdPN) Soil HQ643400 HQ643400 HQ643400 GU133518 EF426556
P. viniferum# CBS 119168 Soil (Vitis sp.) HQ643956 HQ643956 HQ643956 KJ595419 KJ595544
P. violae# CBS 159.64 (VdPN) Soil AY598706 AY598706 AY598706 JX397980 JX397966
P. wohlseniorum W15-2  Aquatic N/A MH277978 MH289800 MH289798 MH289799
Pythiumsp. rooibos 2 STE-U 7550 Aspalathus linearis N/A JQ412777 N/A JQ412813 JQ412789

Fig 2 Maximum likelihood of Pythium species based on the concatenated SSU, ITS, LSU, cox2 and tub2 regions. The maximumparsimonious dataset consisted of 528 constant, 71 parsimony-informative and 556parsimony-uninformativecharacters. The parsimony analysis of the data matrix resulted in the maximum of ten equally mostparsimonious trees with a length of 1637 steps (CI = 0.200, RI = 0.737, RC = 0.147, HI = 0.800). ML and MP bootstrap support values over 60% are indicated. Type strains are in bold and the 11 clades (A-K) are indicated. Scale bar indicates number of substitutions per site. The tree was rooted with Lagenidium giganteum (CBS 580.84) and Lagenidium sp. (DAOM 242348 and CBS 127283). Likelihood of the best scoring ML tree was -28453.969593. Estimated base frequencies were as follows: A = 0.264872, C = 0.163069, G = 0.213432, T = 0.358627; substitution rates AC = 1.219282, AG = 3.062456, AT = 3.113530, CG = 0.855790, CT = 4.379562, GT = 1.000000.

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