Phylogenetic classification of yeasts and related taxa within Pucciniomycotina

Stud Mycol. 2015 Jun;81:149-89. doi: 10.1016/j.simyco.2015.12.002. Epub 2016 Jan 11.

Abstract

Most small genera containing yeast species in the Pucciniomycotina (Basidiomycota, Fungi) are monophyletic, whereas larger genera including Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces are polyphyletic. With the implementation of the "One Fungus = One Name" nomenclatural principle these polyphyletic genera were revised. Nine genera, namely Bannoa, Cystobasidiopsis, Colacogloea, Kondoa, Erythrobasidium, Rhodotorula, Sporobolomyces, Sakaguchia and Sterigmatomyces, were emended to include anamorphic and teleomorphic species based on the results obtained by a multi-gene phylogenetic analysis, phylogenetic network analyses, branch length-based methods, as well as morphological, physiological and biochemical comparisons. A new class Spiculogloeomycetes is proposed to accommodate the order Spiculogloeales. The new families Buckleyzymaceae with Buckleyzyma gen. nov., Chrysozymaceae with Chrysozyma gen. nov., Microsporomycetaceae with Microsporomyces gen. nov., Ruineniaceae with Ruinenia gen. nov., Symmetrosporaceae with Symmetrospora gen. nov., Colacogloeaceae and Sakaguchiaceae are proposed. The new genera Bannozyma, Buckleyzyma, Fellozyma, Hamamotoa, Hasegawazyma, Jianyunia, Rhodosporidiobolus, Oberwinklerozyma, Phenoliferia, Pseudobensingtonia, Pseudohyphozyma, Sampaiozyma, Slooffia, Spencerozyma, Trigonosporomyces, Udeniozyma, Vonarxula, Yamadamyces and Yunzhangia are proposed to accommodate species segregated from the genera Bensingtonia, Rhodosporidium, Rhodotorula, Sporidiobolus and Sporobolomyces. Ballistosporomyces is emended and reintroduced to include three Sporobolomyces species of the sasicola clade. A total of 111 new combinations are proposed in this study.

Keywords: B. aurantiaca (Saito) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; B. kluyveri-nielii (van der Walt) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; B. ogasawarensis (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; B. phyllomatis (van der Walt & Y. Yamada) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; B. salicina (B.N. Johri & Bandoni) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; B. syzygii (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; B. taupoensis (Hamam. & Nakase) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout; B. yamatoana (Nakase, M. Suzuki & M. Itoh) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Ballistosporomycessasicola (Nakase & M. Suzuki) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout; Bannoabischofiae (Hamam., Thanh & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Bannozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Bannozymaarctica (Vishniac & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Buckleyzyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Buckleyzymaarmeniaca (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Buckleyzymaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. diffluens (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. eucalyptica (C.H. Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. falcata (Nakase, M. Itoh & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. foliorum (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. griseoflava (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. lophatheri (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. philyla (van der Walt, Klift & D.B. Scott) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. retinophila (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; C. terpenoidalis (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Chrysozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Chrysozymaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Chrysozymafushanensis (Nakase, F.L. Lee & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Colacogloeaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Colacogloeacycloclastica (Thanh, M.S. Smit, Moleleki & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Cystobasidiopsislactophilus (Nakase, M. Itoh, M. Suzuki & Bandoni) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Cystobasidiumportillonense (F. Laich, I. Vaca & R. Chávez) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; E. yunnanense (F.Y. Bai, M. Takash., Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Erythrobasidiumelongatum (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Fellozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Fellozymainositophila (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Fungi; GMYC approach; H. singularis (Phaff & do Carmo-Sousa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Hamamotoa Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Hamamotoalignophila (Dill, C. Ramírez & González) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Hasegawazyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Hasegawazymalactosa (Hasegawa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Jianyunia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Jianyuniasakaguchii (Sugita, M. Takash., Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; K. miscanthi (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout; K. phyllada (van der Walt & Y. Yamada) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout; K. sorbi (F.Y. Bai & Q.M. Wang) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout; K. subrosea (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout; K. thailandica (Fungsin, Hamam. & Nakase ) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout; K. yuccicola (Nakase & M. Suzuki) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout; Kondoachangbaiensis (F.Y. Bai & Q.M. Wang) Q.M. Wang, M. Groenew., F.Y. Bai & Boekhout; M. magnisporus (Nakase, Tsuzuki, F.L. Lee, Sugita, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; M. orientis (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; M. pini (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Microsporomyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Microsporomycesbloemfonteinensis (Pohl, M.S. Smit & Albertyn) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Microsporomycetaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Molecular phylogeny; O. straminea (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; O. yarrowii (Á. Fonseca & van Uden) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Oberwinklerozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Oberwinklerozymasilvestris (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. buffonii (C. Ramírez) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. corallina (N. Furuya & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. dimennae (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. glacialis (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. himalayensis (Shivaji, Bhadra & Rao) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. linderae (Nakase, M. Takash. & Hamam.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. musae (M. Takash., S.O. Suh & Nakase) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout; P. novozealandica (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. producta (N. Furuya & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. psychrophila (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. pustula (Buhagiar) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; P. subbrunnea (Nakase & M. Suzuki) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Phenoliferia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Phenoliferiapsychrophenolica (Margesin & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Phyllozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Phyllozymacoprosmicola (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Phylogenetic rank boundary optimisation; Pseudobensingtonia F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout; Pseudobensingtoniaingoldii (Nakase & Itoh.) F.Y. Bai, Q.M. Wang, M. Groenew. & Boekhout; Pseudohyphozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Pseudohyphozymabogoriensis (Deinema) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Pucciniomycotina; R. azoricus (J.P. Samp. & Gadanho) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. babjevae (Golubev) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. colostri (T. Castelli) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. diobovata (S.Y. Newell & I.L. Hunter) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. diospyroris (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. dracophylli (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. kratochvilovae (Hamam., Sugiy. & Komag.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. lusitaniae (Á. Fonseca & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. microsporus (Higham ex Fell, Blatt & Statzell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. nylandii (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. odoratus (J.P. Samp., Á. Fonseca & Valério) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. paludigena (Fell & Tallman) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. poonsookiae (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. pyrrosiae (Nakase, Tsuzuki, F.L. Lee, Jindam. & M. Takash.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. rubra (Nakase, Oakada & Sugiy.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. ruineniae (Holzschu, Tredick & Phaff) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. sphaerocarpa (S.Y. Newell & Fell) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; R. toruloides (I. Banno) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Rhodosporidiobolus Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Rhodosporidiobolus fluvialis (Fell, Kurtzman, Tallman & J.D. Buck) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Rhodotorulaalborubescens (Derx) Q.M. Wang, F.Y. Bai, Groenew. & Boekhout; Ruinenia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Ruineniaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Ruineniaclavata (F.Y. Bai & Q.M. Wang) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. oryzae (F.Y. Bai & Y.M. Cai) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. foliicola (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. gracilis (Derx) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. johnsonii (Nyland) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. lamellibrachiae (Nagah., Hamam., Nakase & Horikoshi) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. marina (Phaff, Mrak & Williams) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. meli (Libkind, van Broock & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. novozelandica (W.B. Kendr. & X.D. Gong) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout; S. pilati (F.H. Jacob, Faure-Raynaud & Berton) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. pulcherrima (J.E. Wright) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout; S. symmetrica (F.Y. Bai & Q.M. Wang) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. tsugae (Phaff & do Carmo-Sousa) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. vanillica (J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; S. vermiculata (M. Takash. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Sakaguchiaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Sakaguchiacladiensis (Fell, Statzell & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Sampaiozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Sampaiozymaingeniosa (Di Menna) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Slooffia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Slooffia cresolica (Middelhoven & Spaaij) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Spencerozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Spencerozymacrocea (Shifrine & Phaff) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Spiculogloeomycetes Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Sporobolomyceslongiusculus (Libkind, van Broock & J.P. Samp.) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Sterigmatomyceshyphaenes (Har. & Pat.) F.Y. Bai, Q.M. Wang, Groenewald & Boekhout; Symmetrospora Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Symmetrosporaceae Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Symmetrosporacoprosmae (Hamam. & Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Taxonomy; Trigonosporomyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Trigonosporomyceshylophilus (van der Walt, van der Klift & D.B. Scott) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Udeniozyma Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Udeniozymaferulica (J.P. Samp. & van Uden) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Ustilentylomagraminis (Rodr. Mir. & Diem) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Vonarxula Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Vonarxulajavanica (Ruinen) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Y. sonckii (Hopsu-Havu, Tunnela & Yarrow) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Yamadamyces Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Yamadamycesrosulatus (Golubev & Scorzetti) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Yeasts; Yunzhangia Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout; Yunzhangiaauriculariae (Nakase) Q.M. Wang, F.Y. Bai, M. Groenew. & Boekhout.