Multigene phylogeny and taxonomic revision of yeasts and related fungi in the Ustilaginomycotina

Abstract

The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi (smuts). Some of the lineages possess cultivable unicellular stages that are usually classified as yeast or yeast-like species in a largely artificial taxonomic system which is independent from and largely incompatible with that of the smut fungi. Here we performed phylogenetic analyses based on seven genes including three nuclear ribosomal RNA genes and four protein coding genes to address the molecular phylogeny of the ustilaginomycetous yeast species and their filamentous counterparts. Taxonomic revisions were proposed to reflect this phylogeny and to implement the ‘One Fungus = One Name’ principle. The results confirmed that the yeast-containing classes Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes are monophyletic, whereas Exobasidiomycetes in the current sense remains paraphyletic. Four new genera, namely Dirkmeia gen. nov., Kalmanozyma gen. nov., Golubevia gen. nov. and Robbauera gen. nov. are proposed to accommodate Pseudozyma and Tilletiopsis species that are distinct from the other smut taxa and belong to clades that are separate from those containing type species of the hitherto described genera. Accordingly, new orders Golubeviales ord. nov. with Golubeviaceae fam. nov. and Robbauerales ord. nov. with Robbaueraceae fam. nov. are proposed to accommodate the sisterhood of Golubevia gen. nov. and Robbauera gen. nov. with other orders of Exobasidiomycetes. The majority of the remaining anamorphic yeast species are transferred to corresponding teleomorphic genera based on strongly supported phylogenetic affinities, resulting in the proposal of 28 new combinations. The taxonomic status of a few Pseudozyma species remains to be determined because of their uncertain phylogenetic positions. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the single-species lineages that are temporarily maintained.

Introduction

The subphylum Ustilaginomycotina (Basidiomycota, Fungi) comprises mainly plant pathogenic fungi usually known as smuts, which are mostly dimorphic and present a yeast stage during part of their life cycle (Bauer et al., 2001a, Begerow et al., 2014). As this yeast stage sometimes not only consists of unicellular budding cells, but also includes cultures that might eventually produce hyphae or divide in other modes than budding, these fungi are often summarised as yeasts or yeast-like fungi. For simplicity of reading we will refer to ‘yeasts’ only, as long a differentiation is not necessary. A considerable number of ustilaginomycetous fungi known from yeast states only are described as asexual yeast species that are currently classified into 12 genera with 71 species (Boekhout et al., 2011, Begerow et al., 2014, Nasr et al., 2014, Wang et al., 2014). These genera are Acaromyces, Farysizyma, Fereydounia, Jaminaea, Malassezia, Meira, Moniliella, Pseudozyma, Rhodotorula (pro parte), Sympodiomycopsis, Tilletiaria and Tilletiopsis (Stolk and Dakin, 1966, Gokhale, 1972, Boekhout, 1991, Boekhout, 1995, Boekhout et al., 1995, Boekhout et al., 2003, Boekhout et al., 2011, Begerow et al., 2000, Begerow et al., 2006, Inácio et al., 2008, Sipiczki and Kajdacsi, 2009, Nasr et al., 2014, Wang et al., 2014). Species of these 12 genera occur in four classes currently recognised in Ustilaginomycotina, namely Exobasidiomycetes, Malasseziomycetes, Moniliellomycetes and Ustilaginomycetes (Bauer et al. 2001a, Begerow et al., 2006, Begerow et al., 2014, Hibbett et al., 2007, Nasr et al., 2014, Wang et al., 2014). Many of ustilaginomycetous genera described from teleomorphic stages are cultivable, like members of Ustilago, Exobasidium and Microstroma, but their yeast stages have not been studied with respect to their physiological characteristics in depth as it is typically done for yeasts.

The genera Acaromyces and Meira contain probably mite-associated species, which are morphologically similar to Pseudozyma species, but phylogenetically belong to different lineages within Exobasidiomycetes (Boekhout et al., 2003, Boekhout et al., 2011, Rush and Aime, 2013). The genus Pseudozyma is a polyphyletic anamorphic genus with species occurring in various clusters together with teleomorphic species of Ustilago, Sporisorium and Moesziomyces in the Ustilaginaceae (Ustilaginales) (Begerow et al., 2000, Begerow et al., 2006, Begerow et al., 2014, Stoll et al., 2003, Stoll et al., 2005, Liou et al., 2009, McTaggart et al., 2012a, McTaggart et al., 2012b, Chamnanpa et al., 2013, Shivas et al., 2013, Oliveira et al., 2014). The genus Farysizyma is an anamorphic genus in the Anthracoideaceae (Ustilaginales) described by Inácio et al. (2008) that clusters with teleomorphic species of the genus Farysia containing dimorphic smut fungi. The genus Fereydounia represents the first yeast lineage within Urocystidales (Nasr et al. 2014). The genus Jaminaea represents a basal lineage in the Microstromatales (Exobasidiomycetes) based on ribosomal RNA (rRNA) gene sequence analysis (Sipiczki & Kajdacsi 2009). Sympodiomycopsis is an anamorphic genus and its basidiomycetous affinity was discussed for a long time based on the ubiquinone system, type of cell wall and septal pore ultrastructure (Sugiyama et al. 1991). Sequence analyses of the small subunit ribosomal RNA (SSU rRNA) and the large subunit rRNA (LSU rRNA) D1/D2 domains indicated that Sympodiomycopsis is a member of Exobasidiomycetes (Suh and Sugiyama, 1994, Fell et al., 2000). Tilletiaria is a teleomorphic genus characterised by the presence of teliospores and narrow hyphae without clamp connections (Bandoni & Johri 1972). This genus was tentatively placed in the Tilletiales (Boekhout et al. 1992), but was later proposed to represent the family Tilletiariaceae in the Georgefischerales (Exobasidiomycetes) based on molecular phylogenetic analyses and morphology of its basidium (Begerow et al., 2006, Boekhout et al., 2006, Hibbett et al., 2007, Boekhout et al., 2011). Tilletiopsis species occur in different orders of Exobasidiomycetes and this genus was often used as a ‘catch all’ genus for anamorphic members of Exobasidiomycetes (Begerow et al., 2000, Begerow et al., 2006, Begerow et al., 2014, Fell et al., 2000, Boekhout et al., 2011). Although most Rhodotorula species belong to Pucciniomycotina, four still occur in Ustilaginomycotina (Fell et al., 2000, Sampaio, 2011). In addition to Rhodotorula acheniorum which has been transferred to Farysizyma (Inácio et al. 2008), three other Rhodotorula species are located in the Microstromatales (Exobasidiomycetes) (Sampaio, 2004, Sampaio, 2011, Boekhout et al., 2011, Begerow et al., 2014). Recently, multiple gene sequence analyses showed that the genera Malassezia and Moniliella represent two deeply rooted lineages within Ustilaginomycotina and, subsequently, two classes Malasseziomycetes and Moniliellomycetes were proposed to accommodate them (Wang et al. 2014).

Based on several studies, it has been clear that many anamorphic yeast species are phylogenetically closely related with teleomorphic smut fungi and that some of the former represent a saprophytic stage of the latter (Begerow et al., 2000, Begerow et al., 2014, Boekhout et al., 2011). However, as is the case in other groups of Basidiomycota, ustilaginomycetous yeasts have been conventionally classified mainly based on physiological and biochemical criteria, resulting in a taxonomic system independent from, and largely incompatible with that of the smut fungi, which were classified mainly based on morphological characters and host range of the teleomorphic stage (Boekhout, 1991, Boekhout et al., 2011, Begerow et al., 2014). Additionally, although many species of smut fungi are cultivable only very few teleomorphic species are available as reference cultures. Integrated taxonomic revisions of Ustilaginomycotina unifying anamorphic and teleomorphic taxa have been made in recent years based on molecular data (Begerow et al., 2000, Begerow et al., 2006, Begerow et al., 2014, Bauer et al., 2001a, Weiß et al., 2004, Matheny et al., 2006, Boekhout et al., 2011). The process is, however, hampered by the lack of a robust and integrated phylogenetic analysis and by use of the dual nomenclature code for pleomorphic fungi. Recent studies have shown that the Exobasidiomycetes may not represent a monophyletic group (Begerow et al., 2006, Begerow et al., 2014, Hibbett et al., 2007, Boekhout et al., 2011, Wang et al., 2014) and a considerable number of currently recognised genera of both yeasts and dimorphic smut fungi in Ustilaginomycotina are polyphyletic (Begerow et al., 2000, Begerow et al., 2014, Boekhout et al., 2011, McTaggart et al., 2012a, McTaggart et al., 2012b). The fine phylogenetic relationships between the yeast and filamentous taxa remain to be resolved. Here we used phylogenetic analyses of seven genes to address the phylogenetic relationships of ustilaginomycetous yeast species with each other and with their filamentous counterparts. Consequently, taxonomic revisions for the majority of the ustilaginomycetous yeasts employed were proposed according to the ‘One Fungus = One Name’ principle (Hawksworth, 2011, Taylor, 2011, McNeill et al., 2012).

Materials and methods

Taxon sampling

All ustilaginomycetous yeast species listed in the 5^th edition of The Yeasts, A Taxonomic Study (Kurtzman et al. 2011) were employed (Table 1, Table 2). The yeast and smut culture strains used came from the CBS Fungal Biodiversity Centre (CBS-KNAW), Utrecht, Netherlands; the China General Microbiological Culture Collection Center (CGMCC), Institute of Microbiology, Chinese Academy of Sciences, Beijing, China; and Ruhr-Universität Bochum, AG Geobotanik, Germany.

Table 1.

Taxa and sequence accession numbers employed in the combined seven genes sequence analysis (those in bold are determined in this study).

Species	Strains number	D1D2	ITS	SSU	RPB1	RPB2	EF1	CytB
Exobasidiomycetes
Georgefischeriales
Tilletiaria anomala	CBS 436.72T	AJ235284	DQ234558	AY803752	DQ234571	AY803750	DQ835991	KP323046
Tilletiopsis derxii	CBS 110078 T	AB052823	AB045707	AB045704	KP322926	KP323086	KP323138	KP323020
Tilletiopsis flavus	CBS 401.84 T	AJ235285	KP322987	KP322970	—	—	KP323126	KP323004
Tilletiopsis fulvescens	CBS 607.83 T	AJ235282	KP322988	KP322971	—	—	—	KP323045
Tilletiopsis minor	CBS 543.50 T	AJ235287	KP322989	KP322972	KP322938	KP323097	KP323114	KP323008
Tilletiopsis penniseti	CBS 110032 T	AB052825	—	KP322975	KP322917	KP323085	KP323143	KP322995
Microstromatales
Jaminaea angkorensis	CBS 10918 T	EU587489	EU604147	EU604148	KP322907	KP323082	KP323152	KC628747
Jaminaea lanaiensis	CBS 10858 T	DQ990016	DQ990017	KP322964	—	KP323080	KP323144	KP323021
Microstroma juglandis	CBS 287.63	AF009867	DQ789988	DQ789987	DQ789990	DQ789989	DQ789991	—
Microstroma albiziae	CMW 36935	KP322982	KP322982	KP322947	—	KP323079	KP323150	KP323016
Quambalaria cyanescens	CBS 876.73	DQ317616	DQ317623	KF706440	—	KF706531	KF706485	KP323031
Rhodotorula bacarum	CGMCC 2.3190 T	AF190002	DQ317629	AJ496257	KP322937	KP323098	KP323120	AB040618
Rhodotorula hinnulea	JCM 9030 T	AF190003	AB038130	AB038130	KP322905	KP323062	KP323121	AB041050
Rhodotorula phylloplana	JCM 9035 T	AF190004	AB038131	AJ496258	KP322906	KP323063	KP323116	AB041051
Sympodiomycopsis kandeliae	CBS 11676	GU047881	GQ465043	KP322963	KP322925	KP323077	KP323149	KP323047
Sympodiomycopsis paphiopedili	CGMCC 2.1398 T	AF352054	DQ317631	DQ832239	KP322941	KP323099	KP323117	—
Tilletiales
Erratomyces patelii	CBS 669.70	DQ094784	DQ846894	DQ846895	DQ846897	DQ846896	DQ846898	—
Tilletia goloskokovii	LMC 321	AY818998	DQ832248	DQ832247	DQ832250	DQ832249	DQ832251	—
Entylomatales
Entyloma arnoseridis	CBS 203.36	DQ645528	DQ911609	DQ645529	—	DQ645530	DQ645531	—
Entyloma calendulae	CBS 746.85	DQ663687	DQ663689	KP322948	—	DQ663690	KP323124	KP323056
Entyloma ficariae	CBS 480.91	AJ235295	JQ586199	KP322949	KP322944	—	KP323125	—
Tilletiopsis cremea	CBS 605.83 T	AJ235279	AB025690	KP322969	—	KP323108	KP323129	KP323006
Tilletiopsis lilacina	CBS 435.92 T	KP322984	KP322984	KP322966	—	KP323110	KP323112	KP323002
Tilletiopsis washingtonensis	CBS 544.50 T	AJ235278	DQ835994	KP322976	—	DQ835995	DQ835996	KP322997
Doassansiales
Rhamphospora nymphaeae	CBS 72.38	DQ831032	DQ831034	DQ831033	—	DQ831035	DQ831036	—
Exobasidiales
Acaromyces ingoldii	CBS 110050 T	AY158665	AY158671	?	KP322920	KP323078	KP323145	KP323019
Exobasidium gracile	DSM 4460	DQ663699	DQ663700	DQ785786	DQ663702	DQ663701	DQ663703	—
Exobasidium rhododendri	CBS 101457	DQ667151	DQ667153	DQ667152	DQ667155	DQ667154	DQ667156	—
Exobasidium vaccinii	DB 160d	KP322983	KP322983	KP866248	KP322924	KP323076	KP323146	—
Meira argovae	CBS 110053 T	AY158669	AY158675	KP322953	KP322922	KP323081	KP323139	KP323017
Meira geulakonigii	CBS 110052 T	AY158668	AY158674	KP322954	KP322919	KP323083	KP323141	KP323011
Meira nashicola	CBS 117161 T	AB185157	AB185159	KP322955	KP322921	KP323084	KP323140	KP323014
Species incertae sedis in the Exobasidiomycetes
Tilletiopsis albescens	CBS 608.83 T	AJ235289	KP322986	KP322968	KP322942	KP323095	KP323127	KP323028
Tilletiopsis pallescens	CBS 364.85 T	AJ235292	DQ317636	KP322973	KP322943	KP323101	KP323123	KP322992
Ustilaginomycetes
Urocystales
Urocystis colchici	CBS 283.28	DQ838576	DQ839596	DQ839595	—	DQ839597	DQ839598	—
Urocystis eranthidis	HMK 2921	JN367324	JN367299	JN367352	JN367428	—	JN367375	—
Ustilaginales
Anthracoideaceae
Cintractia axicola	MP 3490	DQ631906	DQ631908	DQ631907	—	DQ631909	DQ631910	—
Cintractia limitata	HAJB 10488	DQ645506	DQ645508	DQ645507	DQ645510	DQ645509	DQ645511	—
Farysizyma acheniorum	CGMCC 2.3198 T	AF190001	AB038128	AJ496256	KP322927	KP323064	KP323131	AB041047
Farysizyma itapuensis	CBS 10428 T	DQ767831	DQ767831	DQ767831	KP322915	KP323075	KP323161	KP323054
Farysizyma setubalensis	CBS 10241 T	EU002857	EU002888	KP322950	KP322913	KP323073	KP323147	KP323013
Farysizyma taiwniana	CBS 9927 T	AY551270	AY555071	KP322951	KP322914	KP323071	KP323148	KP323033
Schizonella melanogramma	CBS 174.42	DQ832210	DQ832212	DQ832211	DQ832214	DQ832213	DQ832215	—
Ustanciosporium gigantosporum	CBS 131478	JN367325	JN367300	KP322977	JN367429	KP323072	JN367376	KP322994
Ustanciosporium standleyanum	JAG 73	DQ846888	DQ846890	DQ846889	DQ846892	DQ846891	DQ846893	—
Ustilaginaceae
Anthracocystis anthracoideispora	HUV 183501	JN367315	JN367290	JN367344	JN367420	—	JN367367	—
Anthracocystis apludae	KVU 9671	JN367319	JN367294	JN367348	JN367424	—	JN367371	—
Anthracocystis walkeri	KVU 9751	JN367322	JN367297	JN367350	JN367426	—	JN367373	—
Anthracocystis pampara	JCM 2007	KP322980	KP322980	KP322961	KP322908	KP323066	—	—
Langdonia aristidae	HUV 191451	JN367317	JN367292	JN367346	JN367422	—	JN367369	—
Macalpinomyces eriachnes	CBS 131454	JN367312	JN367287	JN367340	JN367417	KP323074	KP323142	KP323022
Macalpinomyces spermophorus	HUV 207171/F 565	AY740171	AY740171	JN367358	JN367433	—	JN367381	—
Melanopsichium pennsylvanicum	UMa7041	JN367313	JN367288	JN367341	JN367418	—	JN367364	—
Ustilago maydis	CBS 504.76	AF453938	AY854090	KP322979	KP322928	KP323090	KP323130	KP322996
Ustilago maydis	FB1	KP866233	KP866233	KP322952	KP322912	KP323067	KP323154	KP323003
Moesziomyces bullatus	CBS 425.34	DQ831011	DQ831013	DQ831012	DQ831015	DQ831014	—	—
Sporisorium andropogonis	CBS 192.26/KVU 8411	AY740095	AY740042	KP322962	JN367419	KP323065	JN367366	—
Sporisorium exsertum	KVU 9651	JN367318	JN367293	JN367347	JN367423	—	JN367370	—
Sporisorium reilianum	CBS 131460	KF706430	KF706438	KF706441	KP322910	KF706511	KF706472	KP323058
Sporisorium scitamineum	CBS 131463	JN367321	JN367296	KP322965	JN367425	KP323070	JN367372	KP323057
Sporisorium sorghi	CBS 104.17	AY745726	DQ200931	DQ234548	DQ785784	KP323105	DQ028590	KP323060
Stollia bursa	KVU 8441	JN367316	JN367291	JN367345	JN367421	—	JN367368	—
Pseudozyma abaconensis	CBS 8380 T	FJ008047	FJ008053	KP322956	KP322916	KP323092	KP323159	KP323051
Pseudozyma antarctica	CBS 5955	AJ235302	AB089358	KP322960	KP322935	KP323093	KP323118	KP323048
Pseudozyma flocculosa	CBS 167.88 T	AJ235299	AF294690	AF294717	KP322931	KP323106	KP323135	KP323059
Pseudozyma hubeiensis	CGMCC 2.2493 T	DQ008953	DQ008954	KP322957	—	KP323103	KP323111	KP322990
Pseudozyma parantarctica	CBS 10005 T	AB089357	AB089356	JN940457	JN992528	KP323069	KP323151	KP322991
Pseudozyma prolifica	CBS 319.87 T	AJ235298	AF294700	AF294724	DQ352825	KP323089	DQ352831	KP323009
Pseudozyma pruni	CBS 10937 T	EU379943	EU379942	KP322958	KP322911	KP323087	KP323155	KP323050
Pseudozyma rugulosa	JCM 10323 T	JN940523	JN942670	JN940458	JN992524	KP323091	KP323133	KP323049
Pseudozyma shanxiensis	CGMCC 2.2523 T	DQ008955	DQ008956	KP866247	KP322932	KP323104	KP323113	KP323005
Pseudozyma thailandica	CBS 10006 T	AB089355	AB089354	KP322959	KP322909	KP323088	KP323157	KP322999
Tranzscheliella hypodytes	RK0741	JN367323	JN367298	JN367351	JN367427	—	JN367374	—
Tranzscheliella williamsii	CBS 131475	JN367338	JN367310	KP322974	KP322923	KP323068	KP323156	KP323052
Ustilago cynodontis	HRK 040/MS 1	AY740168	AY740168	JN367355	JN367430	—	JN367378	—
Ustilago filiformis	HRK 0251	JN367328	JN367302	JN367356	JN367431	—	JN367379	—
Ustilago hordei	CBS 131470	KF706429	KF706437	KP322978	KF706498	KF706521	KF706473	KP323055
Ustilago hordei	DB 1526	JN367329	JN367303	JN367357	JN367432	—	JN367380	—
Ustilago striiformis	HUV 182861	DQ875375	AY740172	JN367359	JN367434	—	JN367382	—
Ustilago tritici	CBS 669.70	DQ094784	DQ846894	DQ846895	DQ846897	DQ846896	DQ846898	—
Ustilago xerochloae	KVU 10001	JN367339	JN367311	JN367362	JN367436	—	JN367385	—
Ustilago vetiveriae	HUV 179541	JN367337	AY345011	JN367360	JN367435	—	JN367383	—
Malasseziomycetes
Malasseziales
Malassezia caprae	CBS 10434 T	AY743616	AY743656	KF706456	KF706495	KF706513	KF706467	KP323001
Malassezia dermatis	CBS 9169 T	AB070365	AY390284	KF706452	KF706490	KF706532	KF706461	KP323000
Malassezia equina	CBS 9969 T	AY743621	KF706439	KF706454	KF706492	KF706515	KP323160	KP323010
Malassezia furfur	CBS 1878NT	AF063214	AY743634	KF706457	KF706497	KF706516	KF706469	KP323024
Malassezia globosa	CBS 7966 T	AF064025	AY387132	—	KF706493	KF706518	KF706465	KP323018
Malassezia japonica	CBS 9431 T	EF140672	EF140669	KF706458	—	KF706514	KP323153	KP323026
Malassezia nana	CBS 9558	EF140673	EF140667	KF706453	KF706491	KF706510	KF706462	KP323015
Malassezia obtusa	CBS 7876 T	AB105197	AY387137	KF706455	—	KF706519	KF706470	KP323030
Malassezia pachydermatis	CBS 1879 T	AY743605	AB118941	DQ457640	DQ785792	DQ408140	DQ028594	—
Malassezia restricta	CBS 7877 NT	AF064026	AY743636	EU192367	KF706496	KF706520	KF706471	KP323027
Malassezia slooffiae	CBS 7956 T	AJ249956	AY743633	KF706459	—	—	—	KP323025
CBS 9986
Malassezia sympodialis	CBS 7222 T	AF064024	AY743632	KF706460	—	KP323094	KP323158	KP323023
CBS 8334
Malassezia yamatoensis	CBS 9725 T	AB125263	AB125261	—	KF706494	KF706512	KF706466	KP323012
Moniliellomycetes
Moniliellales
Moniliella acetoabutens	CBS 169.66 T	AF335523	EU252153	KF706443	KF706500	KF706523	KF706476	KP323032
Moniliella madida	CBS 240.79 T	AF335522	—	KF706447	KF706502	KF706525	KF706478	KP323038
Moniliella megachiliensis	CBS 190.92 T	EF137916	KF706433	KF706448	KF706501	KF706524	KF706477	KP323037
Moniliella mellis	CBS 350.33 T	EU545185	—	KF706446	—	KF706528	KF706481	KP323041
Moniliella nigrescens	CBS 269.81 T	AF335527	KF706436	—	KF706504	KF706527	KF706480	KP323040
Moniliella oedocephalis	CBS 649.66 T	AF335521	KF706435	KF706449	KP322939	KP323107	KF706484	KP323042
Moniliella pollinis	CBS 461.67 T	AF335525	KF706434	KF706450	KF706505	KF706529	KF706482	KP323039
Moniliella spathulata	CBS 241.79 T	AF335526	KF706432	KF706444	KF706503	KF706526	KF706479	KP323036
Moniliella suaveolens	CBS 126.42 T	AF335520	KF706431	KF706445	—	—	KF706475	KP323043

¹Cultures and herbarium specimen are available from the respective collections (CBS, Centraalbureau voor Schimmelcultures; CGMCC, the China General Microbiological Culture Collection Center; CMW, DB, DSM, and FB, Dominik Begerow, Ruhr-Universität Bochum; F, Herbarium Franz Oberwinkler; HAJB, Herbarium Havanna Jardín botánico; HMK, Herbarium Martin Kemler; HRK, Herbarium Ronny Kellner; HUV, Herbarium Ustilaginales Vánky; JAG, Herbarium J.A. Gossmann; JCM: the Japan Collection of Microorganisms (JCM); KVU: Kálmán Vánky Ustilaginales; LMC: Herbarium L. M. Carris; MP, Herbarium Meike Piepenbring; RK, strain collection Ronny Kellner; UMa, Marco Thines).

Table 2.

Overview of the classification of the ustilaginomycetous yeasts and related fungi in the Ustilaginomycotina. Only the species compared in this study are included. For the details on the taxonomy of teliomorphs see Vanky (2012) and Begerow et al. (2014). Type species of genera, genera, families, orders and classes are in bold.

Species	Basionym or important synonym	Strain/Herbarium number	D1/D2	ITS
Exobasidiomycetes
Doassansiales
Rhamphosporaceae
Rhamphospora
Rhamphospora nymphaeae		CBS 72.38	DQ831032	DQ831034
Entylomatales
Entylomataceae
Entyloma
E. arnoseridis		CBS 203.36	DQ645528	DQ911609
E. calendulae	Protomyces calendulae	CBS 746.85	DQ663687	DQ663689
E. ficariae		CBS 480.91	AJ235295	JQ586199
Tilletiopsis1
T. cremea1		CBS 605.83T	AJ235279	AB025690
T. lilacina1		CBS 435.92T	KP322984	KP322984
T. washingtonensis1		CBS 544.50T	AJ235278	DQ835994
Exobasidiales
Brachybasidiaceae
Meira1
M. argovae1		CBS 110053T	AY158669	AY158675
M. geulakonigii1		CBS 110052T	AY158668	AY158674
M. miltonrushii1		MCA 3882T	JX432962	JX432962
M. nashicola1		CBS 117161T	AB185157	AB185159
Cryptobasidiaceae
Acaromyces1
A. ingoldii1		CBS 110050T	AY158665	AY158671
Laurobasidium
L. lauri	Exobasidium lauri	MAFF238665	AB177562	AB180359
Exobasidiaceae
Exobasidium
E. gracile	Exobasidium camelliae var. gracile	DSM4460	DQ663699	DQ663700
E. rhododendri	Exobasidium vaccinii var. rhododendri	CBS 101457	DQ667151	DQ667153
E. vaccinii		TUB019109	FJ644526	AB180362
DB160d	KP322983	KP322983
Georgefischeriales
Gjaerumiaceae
Gjaerumia
G. penniseti comb. nov.1	Tilletiopsis penniseti1	CBS 110032T	AB052825	—
G. minor comb. nov.1	Tilletiopsis minor1	CBS 543.50T	AJ235287	KP322989
Tilletiariaceae
Phragmotaenium
P. derxii comb. nov.1	Tilletiopsis derxii1	CBS 110078T	AB052823	AB045707
P. flavum comb. nov.1	Tilletiopsis flava1	CBS 401.84T	AJ235285	KP322987
P. fulvescens comb. nov.1	Tilletiopsis fulvescens1	CBS 607.83T	AJ235282	KP322988
P. oryzicola comb. nov.1	Tilletiopsis oryzicola1	CBS 110079T	AB052825	AB045708
Tilletiaria1
Tilletiaria anomala1		CBS 436.72T	AJ235284	DQ234558
Golubeviales ord. nov.1
Golubeviaceae fam. nov.1
Golubevia gen. nov.1
G. pallescens comb. nov.1	Tilletiopsis pallescens1	CBS 111626	AY879271	AY879278
CBS 364.85T	AJ235292	DQ317636
Microstromatales
Microstromataceae
Microstroma
M. albiziae		CMW 36935	KP322982	KP322982
M. album	Fusisporium album	RB2072	AF352052	DQ317624
Rhodotorula bacarum	CGMCC 2.3190T	AF190002	DQ317629
Torulopsis bacarum
M. phylloplanum comb. nov.1	Cryptococcus phylloplanus1	JCM 9035T	AF190004	AB038131
Rhodotorula phylloplana1
	Cryptococcus hinnuleus1	JCM 9030T	AF190003	AB038130
Rhodotorula hinnulea1
M. juglandis	Fusidium juglandis	CBS 287.63	AF009867	DQ789988
Volvocisporiaceae
Volvocisporium
V. triumfetticola	Muribasidiospora triumfetticola	RB2070	AF352053	DQ317637
Quambalariaceae
Quambalaria
Q. cyanescens	Sporothrix cyanescens	CBS 876.73	DQ317616	DQ317623
Microstromatales incertae sedis
Jaminaea1
J. angkorensis1		CBS 10918T	EU587489	EU604147
J. lanaiensis1	Sympodiomycopsis lanaiensis1	CBS 11676T	GU047881	GQ465043
Sympodiomycopsis1
S. kandeliae1		CBS 10858T	DQ990016	DQ990017
S. paphiopedili1		AS 2.1398T	AF352054	DQ317631
Robbauerales ord. nov.1
Robbaueraceae fam. nov.1
Robbauera gen. nov.1
R. albescens comb. nov.1	Tilletiopsis albescens1	CBS 608.83T	AJ235289	KP322986
Tilletiales
Tilletiaceae
Erratomyces
E. patelii	Protomycopsis patelii	CBS 669.70	DQ094784	DQ846894
Tilletia
T. caries	Uredo caries	CBS 160.85	AJ235307	AY496450
T. controversa	Tilletia controversa	MP2525	DQ832244	DQ832246
T. goloskokovii		LMC321	AY818998	DQ832248
T. iowensis	Neovossia iowensis	BPI863664	AY818988	DQ832253
Ustilaginomycetes
Urocystales
Doassansiopsaceae
Doassansiopsis
D. limnocharidis	Doassansia limnocharidis	HUV15198	AF009850	DQ875344
Fereydouniaceae1
Fereydounia1
F. khargensis1		IBRCM30116T	KJ490642	KJ490641
Glomosporiaceae
Thecaphora
T. spilanthis		JAG53	DQ832241	DQ832243
Urocystaceae
Melanoxa
M. oxalidiellae		TUB 015007	EF635905	EF635906
M. oxalidis	Melanotaenium oxalidis	HUV1436	EF635908	EF635907
Mundkurella
M. kalopanacis		HUV16732	AF009869	DQ875351
Urocystis
U. colchici	Caeoma colchici	CBS 283.28	DQ838576	DQ839596
U. eranthidis	Urocystis pompholygodes f. eranthidis	hmk292	JN367324	JN367299
Ustacystis
U. waldsteiniae	Urocystis waldsteiniae	FO38439	AF009880	DQ875356
Vankya
V. heufleri	Ustilago heufleri	HUV15007	EF653981	EF667965
V. ornithogali	Uredo ornithogali	TUB015993	EF210712	EF635910
Ustilaginales
Anthracoideaceae
Cintractia
C. amazonica		MP200	AJ236142	DQ875342
C. axicola	Ustilago axicola Berk.	MP3490	DQ631906	DQ631908
C. limitata	Cintractia limitata	HAJB10488	DQ645506	DQ645508
Dermatosorus
D. cyperi		HUV15991	AJ236157	DQ875343
Farysia
F. acheniorum comb. nov.1	Farysizyma acheniorum1	AS 2.3198T	AF190001	AB038128
Rhodotorula acheniorum1, Sterigmatomyces acheniorum1
F. chardoniana		MP2062	AF009859	AY344968
F. itapuensis comb. nov.1	Farysizyma itapuensis1	CBS 10428T	DQ767831	DQ767831
F. setubalensis comb. nov.1	Farysizyma setubalensis1	CBS 10241T	EU002857	EU002888
F. taiwaniana comb. nov.1	Farysizyma taiwniana1	CBS 9927T	AY551270	AY555071
Leucocintractia
L. leucodermoides		MS482	DQ875363	DQ875346
L. scleriae	Uredo scleriae	MP2074	AJ236154	AY740025
Moreaua
M. bulbostylidis		56581 (M)	DQ875366	DQ875349
M. fimbristylidis		56582 (M)	DQ875367	DQ875350
Schizonella
S. melanogramma	Uredo melanogramma	FO37174	AF009870	DQ191252
Stegocintractia
S. luzulae	Ustilago luzulae	MP2340	AJ236148	DQ875353
Tolyposporium
T. isolepidis	Schizonella isolepidis	HUV14720	EU246949	EU246950
T. neillii	Sorosporium neillii	HUV18533	EU246952	EU246951
T. junci	Sorosporium junci	HUV17168	AF009876	AY344994
Ustanciosporium
U. gigantosporum	Cintractia gigantospora	HRK023	JN367325	JN367300
U. standleyanum	Cintractia standleyana	JAG73	DQ846888	DQ846890
Melanotaeniaceae
Melanotaenium
M. cingens	Ustilago cingens	L.E.Kari191(M)	DQ875364	DQ875347
M. endogenum	Protomyces endogenus	CBS 481.91	DQ789979	DQ789981
M. euphorbiae	Tilletia euphorbiae	HUV17733	JN367314	JN367289
Ustilaginaceae
Anomalomyces
A. panici		BRIP46421	DQ459347	DQ459348
A. yakirrae		HUV 21918	KC184906	KC184907
Anthracocystis
A. anthracoideispora	Sporisorium anthracoideisporum	HUV18350	JN367315	JN367290
A. apludae	Sorosporium apludae	KVU967	JN367319	JN367294
A. apludae-aristatae	Sorosporium apludae-aristatae	MS287	AY740098	AY740045
A. cenchri	Ustilago cenchri	MP1974	AF453943	AY344972
A. cenchri-elymoidis	Sporisorium cenchri-elymoidis	BRIP 26491	HQ013122	HQ013094
A. chrysopogonis	Sporisorium chrysopogonis	MS135	AY740131	AY344973
A. destruens		Ust.exs.472 (M)	AY747077	AY344976
A. elionuri	Ustilago elionuri	MP2601 (LPB)	AY740157	AY740157
A. fascicularis		MS198	AY740088	AY740035
A. formosana	Ustilago formosana	Ust. Exs. 688 (M)	AY740134	AY344979
A. flocculosa1	Pseudozyma flocculosa1	CBS 167.88T	AJ235299	AF294690
Sporothrix flocculosa1
A. heteropogonicola	Sorosporium heteropogonicola	BRIP51822	HQ013135	HQ013101
A. hwangensis	Sporisorium hwangense	MS267	AY740104	AY740051
A. loudetiae-pedicellatae	Sporisorium loudetiae-pedicellatae	MS252	AY740106	AY740053
A. ovaria	Sorosporium ovarium	MP1871	AJ236137	AY740020
A. pampara comb. nov.	Ustilago pamparum	JCM 2007	KP322980	KP322980
A. polliniae	Sorosporium polliniae	MS32	AY740138	AY344987
A. provincialis	Sorosporium ellisii var. provinciale	Ust.exs.759 (M)	AY747076	AY344988
A. pseudanthistiriae	Sorosporium pseudanthistiriae	KVU969	JN367320	JN367295
A. themedae-arguentis	Sporisorium themedae-arguentis	Ust. Exs. 855	AY740140	AY344991
A. tumefaciens	Sorosporium tumefaciens	MS139	AY740128	AY344969
A. walkeri	Sporisorium walkeri	KVU975	JN367322	JN367297
Dirkmeia gen. nov.1
D. churashimaensis comb. nov.1	Pseudozyma churashimaensis1	OK96T	AB548955	AB548947
Kalmanozyma gen. nov.1
K. fusiformata comb. nov.1	Pseudozyma fusiformata1	CBS 6951T	AB089367	AB089366
K. brasiliensis comb. nov.1	Pseudozyma brasiliensis1	GHG001T	KF737866	KF737866
K. vetiver comb. nov.1	Pseudozyma vetiver1	DMKU-LV99T	AB809649	AB809652
Langdonia
L. aristidae	Ustilago aristidae	HUV19145	JN367317	JN367292
L. confusa	Sorosporium confusum	BRIP42670	HQ013132	HQ013095
L. jejuensis comb. nov.1	Pseudozyma jejuensis1	CBS 10454T	FN428865	EF079966
Macalpinomyces
M. eragrostiellae		Ust.Exs.960(M)	AY740089	AY740036
M. eriachnes	Sorosporium eriachnes	CBS 131454	JN367312	JN367287
M. loudetiae	Sorosporium loudetiae	MS250	AY740151	AY740151
M. mackinlayi		BRIP52549	HQ013131	GU014817
M. neglectus	Ustilago neglecta	RB2056 (TUB)	AY740109	AY740056
M. spermophorus		F565	AY740171	AY740171
M. trichopterygis		MS248	AY740092	AY740039
M. tristachyae		MS15	AY740164	AY740164
M. viridans		BRIP 49133	HQ013125	HQ013089
Melanopsichium
M. pennsylvanicum	Melanopsichium pennsylvanicum	HUV17548 (TUB)	AY740093	AY740040
Moesziomyces
M. antarcticus comb. nov.1	Candida antarctica1	CBS 5955	AJ235302	AB089358
Pseudozyma antarctica1	JCM 10317T	JN940521	JN942668
Trichosporon oryzae1
Vanrija antarctica1
M. aphidis comb. nov.1	Pseudozyma aphidis1	JCM 10318	JN940519	JN942666
CBS 517.83T	AB089363	AF294699
M. bullatus	Sorosporium bullatum	CBS 425.34	DQ831011	DQ831013
M. parantarcticus comb. nov.1	Pseudozyma parantarctica1	CBS 10005T	AB089357	AB089356
M. rugulosus comb. nov.1	Pseudozyma rugulosa1	CBS 170.88T	JN940523	JN942670
Sporisorium
S. aegypticum	Ustilago aegyptiaca	Ust.Exs.756(M)	AY740129	AY344970
S. andropogonis	Uredo andropogonis	MS283	AY740095	AY740042
S. arthraxonis	Ustilago arthraxonis	MS338	AY740099	AY740046
S. cordobense	Ustilago cordobensis	MS159	AY740155	AY740155
S. cruentum	Ustilago cruenta	MS14	AY740156	AY740156
S. culmiperdum	Ustilago culmiperda	MP2060	AF133580	AY344975
S. dimeriae-ornithopodae		Ust.exs. 472	AY740132	AY344977
S. erythraeense	Ustilago erythraeensis	Ust.Exs.849 (M)	AY740102	AY740049
S. exsertum	Cintractia exserta	KVU965	JN367318	JN367293
S. fastigiatum		MP1976	AY740133	AY344978
S. foveolati	Sphacelotheca foveolati	MS21	AY740103	AY740050
S. graminicola comb. nov.1	Pseudozyma graminicola1	LI20T	AB180728	AB180728
S. holwayi	Sphacelotheca holwayi	MP1271	AF453941	AY344980
S. lacrymae-jobi	Ustilago lachrymae-jobi	M56611	AY740105	AY740052
S. lepturi	Ustilago carbo var. lepturi	Ust.exs.966 (M)	AY740135	AY344981
S. manilense	Ustilago manilensis	Ust.Exs.854 (M)	AY740112	AY740059
S. modestum	Ustilago modesta	MS237	AY740107	AY740054
S. moniliferum	Ustilago monilifera	MS 98	AF453940	AY344984
S. nervosum		MS241	AY740110	AY740057
S. occidentale	Sphacelotheca occidentalis	Ust.exs.758 (M)	AY740137	AY344985
S. ophiuri	Ustilago ophiuri	HB20	AJ236136	AY740019
S. pseudechinolaenae		Ust.exs.853 (M)	AY740139	AY344989
S. puellare	Ustilago puellaris	MP2372	AY740111	AY740058
S. reilianum	Ustilago reiliana	Ust.exs. 527	AY740163	AY740163
S. scitamineum	Ustilago scitaminea	MP541	AY740147	AY740070
S. sorghi		MP2036a	AF009872	AY740021
S. trachypogonicola		MP2463 (HAJB)	AY740141	AY344992
S. trachypogonis-splumosi		MS281	AY740113	AY740060
S. veracruzianum	Sphacelotheca veracruziana	MP960	AY740114	AY344993
S. vermiculum		BRIP49748	HQ013134	HQ013114
S. wynaadense	Ustilago wynaadensis	BRIP27640	HQ013124	HQ013116
Stollia
S. bursa	Ustilago bursa	KVU844	JN367316	JN367291
S. ewartii	Ustilago ewartii	BRIP51818	HQ013127	HQ013087
Tranzscheliella
T. hypodytes	Caeoma hypodytes	MS342	DQ191256	DQ191250
T. williamsii	Sorosporium williamsii	CBS 131475	JN367338	JN367310
Triodiomyces
T. altilis	Ustilago altilis	BRIP52543	HQ013136	AY740166
T. crassus comb. nov.1	Pseudozyma crassa	DMST17136T	AB117962	AB117962
T. triodiae	Ustilago triodiae	HUV17662	AY740126	AY740074
Tubisorus
T. pachycarpus	Sorosporium pachycarpum	HUV 21891	JN871718	JN871717
Ustilago
U. abaconensis comb. nov.1	Pseudozyma abaconensis1	CBS 8380T	FJ008047	FJ008053
U. affinis		MP692	AF133581	AY344995
U. austro-africana		MS316	AY740115	AY740061
U. avenae	Uredo segetum var. avenae	DB559	AY740117	AY740063
U. bromivora	Ustilago carbo d bromivora	MS175	AY740118	AY740064
U. bullata		MP2363	AF453935	AY344998
U. bouriquetii		MS315	—	AY740167
U. calamagrostidis	Tilletia calamagrostidis	MS314	AY740119	AY740065
U. crameri		MS72	AY740143	AY344999
U. cynodontis	Ustilago carbo ß cynodontis	MS199	AY740168	AY740168
U. davisii		HUV19252	AY740169	AY740169
U. echinata		MS132	AY740144	AY345001
U. esculenta		Ust.exs. 540	AF453937	AY345002
U. filiformis	Lycoperdon filiforme	RB3011	AY740120	AY740066
U. hordei	Uredo segetum a hordei	Ust.exs. 784	AF453934	AY345003
U. hordei		CBS 131470	KF706429	KF706437
U. ixophori		MP2194 (USJ)	AY740121	AY740067
U. maydis	Mycosarcoma maydis	CBS 504.76	AF453938	AY854090
U. maydis		FB1	KP866233	KP866233
U. maydis	Pseudozyma prolifica1	CBS 319.87T	AJ235298	AF294700
U. nuda	Ustilago segetum var. nuda	HUV17782	JN367334	JN367307
U. pamirica		Ust.exs.789 (M)	AY740145	AY345005
U. shanxiensis comb. nov.1	Pseudozyma shanxiensis1	AS 2.2523T	DQ008955	DQ008956
U. schmidtiae		BRIP 51848	HQ013129	HQ013121
U. schroeteriana		Ust.exs.887 (M)	AY740146	AY345006
U. siamensis comb. nov.1	Pseudozyma siamensis1	DMST17137T	AB117963	AB117963
U. sparsa		KVU892	JN367335	JN367308
U. striiformis		HUV18286	DQ875375	AY740172
U. syntherismae	Caeoma syntherismae	Ust.Exs.998 (M)	AY740123	AY740071
U. tragana		MS320	AY740124	AY740072
U. trichophora	Caeoma trichophorum	MS339	AY740125	AY740073
U. tritici	Uredo segetum ß tritici	CBS 669.70	DQ094784	DQ846894
U. vetiveriae		HUV17954	JN367337	AY345011
U. xerochloae		Ust.exs.1000 (M)	AY740150	AY345012
Species remain to be reclassified
Pseudozyma alboarmeniaca pro tem.1		DMST17135T	AB117961	AB117961
P. hubeiensis pro tem.1		AS 2.2493T	DQ008953	DQ008954
P. pruni pro tem.1		CBS 10937T	EU379943	EU379942
P. thailandica pro tem.1		CBS 10006T	AB089355	AB089354
P. tsukubaensis pro tem.1		JCM 10324T	AB089373	AB089372
Websdaneaceae
Websdanea
W. lyginiae	Ustilago lyginiae	HUV 17900	AJ236159	DQ875357
Malasseziomycetes1
Malasseziales1
Malasseziaceae1
Malassezia1
M. caprae1		CBS 10434T	AY743616	AY743656
M. cuniculi1		CBS 11721T	GU733708	GU733709
M. dermatis1		CBS 9169T	AB070365	AY390284
M. equina1		CBS 9969T	AY743621	KF706439
M. furfur1	Microsporum furfur1	CBS 1878NT	AF063214	AY743634
M. globosa1		CBS 7966T	AF064025	AY387132
M. japonica1		CBS 9431T	EF140672	EF140669
M. nana1		CBS 9558	EF140673	EF140667
M. obtusa1		CBS 7876T	AB105197	AY387137
M. pachydermatis1	Pityrosporum pachydermatis1	CBS 1879T	AY743605	AB118941
M. restricta1		CBS 7877NT	AF064026	AY743636
M. slooffiae1		CBS 7956T	AJ249956	AY743633
M. sympodialis1		CBS 7222T	AF064024	AY743632
M. yamatoensis1		CBS 9725T	AB125263	AB125261
Moniliellomycetes1
Moniliellales1
Moniliellaceae1
Moniliella1
M. acetoabutens1		CBS 169.66T	AF335523	EU252153
M. byzovii1		TBY 2041.7	KC213817	KC213818
M. carnis1		KFP 246	JQ814873	—
M. dehoogii1		KFP 211	JQ814874	—
M. fonsecae1		ST-26	DQ400366	—
M. madida1	Trichosporonoides madida1	CBS 240.79T	AF335522	—
M. megachiliensis1	Trichosporonoides megachiliensis1	CBS 190.92T	EF137916	KF706433
M. mellis1	Zygosaccharomyces mellis1	CBS 350.33T	EU545185	—
M. nigrescens1	Trichosporonoides nigrescens1	CBS 269.81T	AF335527	KF706436
M. oedocephali1	Trichosporonoides oedocephalis1	CBS 649.66T	AF335521	KF706435
M. pollinis1	Moniliella tomentosa var. pollinis1	CBS 461.67T	AF335525	KF706434
M. spathulata1	Trichosporonoides spathulata1	CBS 241.79T	AF335526	KF706432
M. suaveolens1	Sachsia suaveolens1	CBS 126.42T	AF335520	KF706431

¹Yeast species.

PCR and DNA sequencing

Genomic DNA was extracted from cultures grown on yeast extract peptone dextrose (YPD) plates using the method described by Bolano et al. (2001). Seven loci were selected, including four protein-coding genes, namely the two RNA polymerase II subunits (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial cytochrome b (CYTB); and three rRNA gene regions, namely the small subunit nuclear ribosomal RNA (SSU or 18S rRNA), the D1/D2 domains of the large subunit (LSU or 26S rRNA) and the ITS 1+2 regions (including 5.8S rRNA). PCR and sequencing of the three rRNA gene regions and three protein genes, RPB1, RPB2 and TEF1, were performed as described in Wang et al. (2014). PCR and sequencing of the CYTB gene were performed according to Wang & Bai (2008). Cycle sequencing was performed using the ABI BigDye cycle sequencing kit (Applied Biosystems, Foster, California). Electrophoresis was done using an ABI PRISM 3730 DNA sequencer.

Molecular phylogenetic analyses

Five data sets consisting of the D1/D2 domains of the LSU rRNA gene, the combined ITS (including 5.8S rRNA gene) and D1/D2 domains of the LSU rRNA gene, the combined three rRNA regions, the combined four protein coding genes, and the combined seven genes, respectively, were constructed. Introns were deleted from all sequences before the alignment performed. Sequences of those data sets were aligned with the MAFFT program (Standley 2013). The alignments of different genes were concatenated in the respective analyses. The alignment data sets were firstly analysed with Modeltest version 3.04 (Posada & Crandall 1998) using the Akaike information criterion (AIC) to find the most appropriate model of DNA substitution. A general time-reversible model of DNA substitution additionally assuming a percentage of invariable sites and Γ-distributed substitution rates at the remaining sites (GTR + I + G) was selected for further analyses. Maximum likelihood (ML) analysis was conducted in RAxML-HPC2 7.2.8 (Stamatakis 2006) using 1 000 bootstrap replicates analysis. Maximum parsimony (MP) analysis was conducted using PAUP* 4.0b10 (Swofford 2002) and the support of the branching topologies was derived from 1 000 replicates with 10 random additions. Bayesian inference (BI) analysis was conducted in MrBayes 3.2 (Ronquist et al. 2012) with parameters set to 5 000 000 generations, two runs and four chains. The chains were heated to 0.25 and a stop value of 0.01 was used. Sequences from several species of Puccinionycotina were used as outgroups in the seven genes-based phylogenetic reconstructions.

Results and discussion

Based on the sequences determined in this study and those retrieved from GenBank (http://www.ncbi.nlm.nih.gov/genbank) two datasets comprising concatenated sequences of the seven genes and of the four protein-coding genes solely were constructed for the analysis of the phylogeny of yeast and representative teleomorphic taxa and to visually examine the topological concordance of the trees generated using different algorithms. In order to further examine the fine phylogenetic relationships of yeast species with teleomorphic taxa, a dataset consisting of the combined ITS (including 5.8S rRNA gene) and LSU rRNA gene sequences and a dataset consisting of only LSU rRNA gene sequences were constructed and analysed.

The analysis of the combined seven genes, the combined ITS and LSU rRNA genes and the four protein genes (Fig. 1, Fig. 2, Fig. 3) confirmed that Malasseziomycetes and Moniliellomycetes containing only yeast species are monophyletic deep lineages as shown in Wang et al. (2014). Ustilaginomycetes is also monophyletic, whereas Exobasidiomycetes is polyphyletic (Fig. 1, Fig. 2, Fig. 3). The phylogenies of the latter two classes containing a mixture of yeast species and teleomorphic taxa are discussed below in detail.

Fig. 1.

Phylogenetic tree constructed using maximum likelihood analysis from combined sequences of the SSU rRNA gene, LSU rRNA D1/D2 domains, ITS1+2 regions (including 5.8S rRNA gene), RPB1, RPB2, TEF1 and CYTB depicting the phylogenetic placements of yeast genera within Ustilaginomycotina. Branch lengths are scaled in terms of expected numbers of nucleotide substitutions per site. Bayesian posterior probabilities (PP) and bootstrap percentages (BP) from 1 000 replicates of maximum likelihood and maximum parsimony analyses are shown respectively from left to right on the deep and major branches resolved. Taxa in bold are yeast and yeast-like fungi. Note: nm, not monophyletic; ns, not supported (PP < 0.9 or BP < 50 %).

Fig. 2.

Phylogenetic tree constructed using maximum likelihood analysis from the combined sequences of the LSU rRNA D1/D2 domains and ITS1+2 regions (including 5.8S rRNA gene) depicting the phylogenetic relationships of yeast taxa with teleomorphic taxa within Ustilaginomycotina. Branch lengths are scaled in terms of expected numbers of nucleotide substitutions per site. Bayesian posterior probabilities (PP) and bootstrap percentages (BP) from 1 000 replicates of maximum likelihood and maximum parsimony analyses are shown respectively from left to right on the deep and major branches resolved. A. The outline of the tree showing the phylogenetic relationships of the genera or clades within Ustilaginomycotina. B. A part of the tree showing the phylogenetic relationships of a part of taxa within the Ustilaginales. C. A part of the tree showing the phylogenetic relationships of another part the taxa within the Ustilaginales and the taxa in the Urocystales. D. A part of the tree showing the phylogenetic relationships of the taxa within Exobasidiomycetes. Taxa in bold are yeast and yeast-like fungi. Notes: nm, not monophyletic; ns, not supported (PP < 0.9 or BP < 50 %).

Fig. 3.

Phylogenetic tree constructed from maximum likelihood analysis based on the combined sequences of protein-coding genes including RPB1, RPB2, TEF1 and CYTB, showing the phylogenetic relationships of yeast genera within Ustilaginomycotina. Branch lengths are scaled in terms of expected numbers of nucleotide substitutions per site. Bayesian posterior probabilities (PP) and bootstrap percentages (BP) from 1 000 replicates of maximum likelihood and maximum parsimony analyses are shown respectively from left to right on the deep and major branches resolved. Taxa in bold are yeast and yeast-like fungi. Note: nm, not monophyletic; ns, not supported (PP < 0.9 or BP < 50 %).

Ustilaginomycetes

Two orders Ustilaginales and Urocystales were recognised in this class (Boekhout et al., 2011, Begerow et al., 2014). They were resolved as monophyletic groups in the trees constructed from all the datasets analysed in this study with strong bootstrap (BP) and posterior probability (PP) support values (Fig. 1, Fig. 2, Fig. 3). The yeasts classified in the anamorphic genera Farysizyma and Pseudozyma (Inácio et al., 2008, Boekhout et al., 2011) were located within Ustilaginales and those in the genus Fereydounia occurred within Urocystidales as shown in Nasr et al. (2014). In the tree based on the ITS and LSU dataset Fereydounia occurred in a separated lineage distinct from the other genera in the Urocystidales (Fig. 2C), which is in agreement with Nasr et al. (2014). The Farysizyma species formed a monophyletic clade in the trees drawn from the seven gene and the four protein gene datasets (Fig. 1, Fig. 3) and clustered together with Farysia chardoniana in the tree based on the ITS and LSU dataset (Fig. 2C) as shown in Inácio et al. (2008). This clade was closely related with Schizonella and Stegocintractia species (Fig. 1, Fig. 2, Fig. 3) within Anthracoideaceae (Begerow et al. 2014). The genus Farysia, with the type species of F. javanica, proposed by Raciborski (1909) contained 21 species that are parasites on Cyperaceae (Begerow et al. 2014). The morphological characters are unique and at present there are no hints for a polyphyletic nature of Farysia. Therefore, we consider Farysizyma species representing anamorphic stages of the genus Farysia.

The Pseudozyma species were located mainly in various clades together with teleomorphic species from the so called Ustilago-Sporisorium-Macalpinomyces complex (McTaggart et al., 2012a, McTaggart et al., 2012b) in the trees made from the seven gene and the four protein gene datasets (Fig. 1, Fig. 3), being in agreement with previous studies based on rRNA gene sequence analysis (Boekhout et al. 2011). The three teleomorphic genera were also found to be polyphyletic (Stoll et al., 2003, Stoll et al., 2005). McTaggart et al. (2012a) recently reconstructed the phylogeny of the complex using four nuclear loci including ITS, LSU rRNA gene, GAPDH and TEF1 and defined eight groups, Clade 1 to Clade 8. Each of the clades was also characterised by host specificity and soral synapomorphies (McTaggart et al. 2012a). Consequently, the authors re-classified the complex by emending the genera Sporisorium (Clade 1) and Anthracocystis (Clade 4), and proposed three new genera, Langdonia (Clade 8), Stollia (Clade 3) and Triodiomyces (Clade 5) to reflect morphological synapomorphies (McTaggart et al. 2012b).

The fine phylogenetic relationships of the Pseudozyma species with the teleomorphic taxa in the Ustilaginales are shown in the tree constructed from the ITS and LSU dataset which contained the species employed in McTaggart et al., 2012a, McTaggart et al., 2012b and other smut fungi (Fig. 2). Sporisorium (Clade 1), Stollia (Clade 3), Anthrococystis (Clade 4), Triodiomyces (Clade 5), Langdonia (Clade 8) and Clade 7 were resolved as well supported monophyletic clades here, being in agreement with McTaggart et al., 2012a, McTaggart et al., 2012b. However, Clade 2 and Clade 6 as defined by McTaggart et al. (2012a) were shown to be polyphyletic in this study (Fig. 2A). Species from Clade 2 were located in two different subgroups and those from Clade 6 in three subgroups (Fig. 2A). The phylogenetic relationships among these subgroups were not resolved due to the lack of support. The statistical support values for Clade 2 and Clade 6 were weak in the previous study (McTaggart et al. 2012a). Clade 2 lacked Bayesian PP support and Clade 6 with three sub-clades lacked both ML BP and Bayesian PP support. The Ustilago davisii and Ustilago esculenta sub-clades defined by McTaggart et al. (2012a) in Clade 6 also lacked statistical support.

As shown in previous studies based on rRNA gene sequence analyses (Fell et al., 2000, Boekhout et al., 2011), the type species of the genus Pseudozyma, P. prolifica, clustered together with Ustilago maydis in the trees reconstructed from the seven gene, the four protein gene and the two rRNA genes datasets (Fig. 1, Fig. 2, Fig. 3). The type strain of P. prolifica shared identical ITS and LSU rRNA gene sequences with Ustilago maydis CBS 504.76, suggesting that P. prolifica represents the saprobic asexual stage of Ustilago maydis and should be treated as a synonym of the latter according to the new nomenclature for fungi (McNeill et al. 2012). As a consequence, the genus name Pseudozyma is not available any more.

Four Pseudozyma species, namely P. antarctica, P. aphidis, P. parantarctica and P. rugulosa, clustered together with Moesziomyces bullatus, the sole described species of this teleomorphic genus (Begerow et al. 2014) with strong BP and PP support values in the tree constructed from the ITS and LSU dataset (Fig. 2C). The close affinity of the four Pseudozyma species with Moesziomyces bullatus was also resolved and strongly supported in the trees made from the seven genes and the four protein genes datasets (Fig. 1, Fig. 3). Another teleomorphic species, Macalpinomyces eriachnes, occurred as a basal branch to the Moesziomyces clade (Fig. 1, Fig. 3). The close phylogenetic relationship of the four Pseudozyma species with the monotypic genus Moesziomyces suggests that the former represent anamorphic and culturable stages of Moesziomyces species and can be transferred to the genus Moesziomyces.

Pseudozyma graminicola clustered in the recently emended genus Sporisorium (McTaggart et al. 2012b). The closest relative of this species was S. holwayii (Fig. 2B). P. graminicola differed from S. holwayii by 47 (7 %) and 6 (1 %) mismatches in the ITS and LSU rRNA gene regions, respectively, suggesting that the former represents a distinct species in the genus Sporisorium and a new combination is proposed.

The close relationship between Pseudozyma flocculosa and Anthracocystis apludae was shown in the seven genes and the four protein genes based trees (Fig. 1, Fig. 3). The affinity of P. flocculosa with Anthracocystis was confirmed by the phylogenetic analysis based on the ITS and LSU dataset (Fig. 2B). This species has been recently transferred into the genus Anthracocystis by Piątek et al. (2015).

Pseudozyma crassa occurred in the Triodiomyces clade with 75–89 % BP and 1.0 PP support values (Fig. 2C). P. crassa was most closely related to T. altilis with 3 and 92 mismatches in the LSU rRNA gene and ITS region, respectively. The result suggests that P. crassa belongs to the genus Triodiomyces. Pseudozyma jejuensis was located in the Langdonia clade with 56–58 % BP and 0.99 PP support values (Fig. 2B), indicating that this species can be transferred to the genus Langdonia.

Pseudozyma abaconensis, P. shanxiensis and P. siamensis occurred in the Ustilago sensu stricto sub-clade (Clade 6) containing U. hordei, the type species of Ustilago (McTaggart et al. 2012a), with strong BP (90–95 %) and PP (1.0) support values (Fig. 2B). P. siamensis branched first in the Ustilago sensu stricto sub-clade while the phylogenetic positions of P. abaconensis and P. shanxiensis within this sub-clade were not resolved. The Ustilago sensu stricto sub-clade was also resolved as a strongly supported monophyletic group by McTaggart et al. (2012a). Due to the presence of U. hordei, the generic type, the genus name Ustilago will be used for this sub-clade. Therefore, it is reasonable to transfer these three Pseudozyma species to the genus Ustilago.

Three Pseudozyma species, including P. brasiliensis, P. fusiformata and P. vetiver, clustered together in an independent clade with 79–87 % BP and 1.0 PP support values (Fig. 2B). The phylogenetic relationship of this clade with other clades in the Ustilaginales were not resolved based on the phylogenetical analysis of the ITS and LSU datasets, being in agreement with Chamnanpa et al. (2013) and Oliveira et al. (2014). The result suggests that this clade represents a distinct genus. Pseudozyma churashimaensis occurred in an isolated deep branch within Ustilaginaceae in the tree drawn from the ITS and LSU dataset (Fig. 2C). The affinity of this species to any teleomorphic taxa was not resolved, suggesting that this species represents another genus.

Three Pseudozyma species, including P. alboarmeniaca, P. thailandica and P. tsukubaensis clustered in Clade 7 recognised by McTaggart et al. (2012a) with 73 % ML BP and 1.0 PP support values (Fig. 2C). This clade containing mixed smut species from the genera Macalpinomyces, Sporisorium and Ustilago, was also resolved by Stoll et al., 2003, Stoll et al., 2005. P. thailandica was most closely related to Macalpinomyces viridians; P. tsukubaensis had identical LSU rRNA gene sequences with Ma. spermophorus; and P. alboarmeniaca showed close affinity to Ustilago austro-africana, Ma. spermophorus and P. tsukubaensis. Because of the taxonomic confusion between the teleomorphic genera, the taxonomic treatment of these three Pseudozyma species should be made together with the taxonomic revision of the teleomorphic species in this clade.

Pseudozyma pruni clustered together with the teleomorphic species Anomalomyces yakirrae, Anomalomyces panici and Sporisorium trachypogonis-plumosi without significant support (Fig. 2B). P. pruni was proposed as a close relative of P. fusiformata by Liou et al. (2009). The former exhibited a close affinity to A. yakirrae in previous studies based on sequence analysis of the ITS and LSU rRNA gene regions (Chamnanpa et al., 2013, Oliveira et al., 2014). A. panici, the type species of the genus Anomalomyces, was located in an isolated branch in the Ustilaginales in McTaggart et al. (2012a). A. yakirrae was proposed as the second member in Anomalomyces by Shivas et al. (2013) because it was located in the same clade with A. panici in the ITS and LSU rRNA gene based tree. A. yakirrae and A. panici also shared some morphological characters and occurred on closely related hosts. However, the close relationship between A. yakirrae and A. panici was not confidently resolved in this study and was only weakly supported by previous molecular data compared in Shivas et al. (2013). Thus, a more robust phylogenetic analysis using more genes will be required for a taxonomic treatment of P. pruni and related teleomorphic species.

In the tree based on the seven genes dataset (Fig. 1), the position of Pseudozyma hubeiensis remained uncertain probably because of the limited sampling of teleomorphic taxa. In the ITS and LSU dataset based tree, this species was located in Clade 2 (McTaggart et al. 2012a) together with Ustilago maydis, Ustilago bouriquetii, Tubisorus pachycarpus, Ustilago vetiveriae and Macalpinomyces mackinlayi, but the phylogeny lacked statistical support (Fig. 2B). Thus, the taxonomic position of P. hubeiensis remains to be determined.

Exobasidiomycetes

Eight orders were previously proposed in this class (Begerow et al., 2006, Begerow et al., 2014, Boekhout et al., 2011). After the proposal of class Malasseziomycetes to accommodate the Malasseziales (Wang et al. 2014), Exobasidiomycetes currently contains four orders, Entylomatales, Exobasidiales, Georgefischeriales and Microstromatales, that have species with a yeast state and three orders, Ceraceosorales, Doassansiales and Tilletiales, that do not have any known yeast species (Boekhout et al. 2011). Begerow et al. (2006) proposed the order Ceraceosorales for Ceraceosorus bombacis which appeared to be closely related to a yeast-like species Tilletiopsis albescens. However, in the tree drawn form the LSU dataset in this study, T. albescens is not closely related to C. bombacis (Fig. 4). The phylogenetic position of C. bombacis and its relationship with T. albescens remain controversial (Hibbett et al., 2007, Boekhout et al., 2011, Begerow et al., 2014).

Fig. 4.

Phylogenetic tree constructed from maximum likelihood analysis based on the D1/D2 domains of the LSU rRNA, showing the relationships of taxa within the Exobasidiomycetes. Bootstrap percentages over 50 % from 1 000 replicates are shown. Taxa in bold are yeast and yeast-like fungi.

In the trees constructed from the seven genes, the four protein coding genes and the two rRNA genes, each of the four yeast containing orders, Entylomatales, Exobasidiales, Georgefischeriales and Microstromatales, was resolved as a strongly supported monophyletic clade. The three orders without yeast species were also resolved as separate clades in these analyses (Fig. 1, Fig. 2, Fig. 3, Fig. 4). However, these orders assigned to Exobasidiomycetes did not form a monophyletic lineage. In the trees drawn from the seven genes and the four protein coding genes, the Georgefischeriales occurred as a sister lineage to Moniliellomycetes with strong support (Fig. 1, Fig. 3). The orders Entylomatales, Exobasidiales and Doassansiales formed a monophyletic lineage together but with weak BP support; while Microstromatales and Tilletiales formed distinct lineages with paraphyletic relationships to the other orders in Exobasidiomycetes (Fig. 1, Fig. 3). The results confirmed that Exobasidiomycetes is not monophyletic, but might support the originally described superorder Exobasidianae including the three orders Entylomatales, Doassansiales and Exobasidiales based on morphological similarities of the interaction apparatus as suggested by Bauer et al. (1997).

Seven genera of yeasts or yeast-like fungi, namely Acaromyces, Jaminaea, Meira, Rhodotorula (pro parte), Sympodiomycopsis, Tilletiaria and Tilletiopsis are currently included in the Exobasidiomycetes. Since the protein coding gene and even the SSU and ITS rRNA gene sequences of many teleomorphic taxa of Exobasidiomycetes are not available at present, a supplementary dataset containing only LSU rRNA gene sequences was used for analysing the phylogenetic relationships of yeast species with teleomorphic species in the Exobasidiomycetes.

In the trees drawn from the seven genes, the four protein genes and the ITS dataset, Acaromyces ingoldii and three Meira species were located together with three Exobasidium species in the Exobasidiales with strong support (Fig. 1, Fig. 2, Fig. 3), being in agreement with Boekhout et al. (2011). However, in the tree made from the LSU dataset containing more teleomorphic species, the taxa of Exobasidiales as defined by Begerow et al. (2014) were separated into two clades (Fig. 4). Ac. ingoldii occurred in a well supported clade together with species of the teleomorphic genera Clinoconidium, Coniodictyum, Drepanoconis and Laurobasidium. Ac. ingoldii was closely related with Laurobasidium lauri and shared an identical LSU rRNA gene sequence with a GenBank entry (AB177562) labelled as ‘Laurobasidium hachijoense’ (Exobasidium hachijoense). The name Laurobasidium hachijoense has not been validly published and L. lauri is presently the solely published species in the genus Laurobasidium (Begerow et al. 2014). It is not sure whether Ac. ingoldii represents an anamorphic species of Laurobasidium because the ML BP support for a close affinity of Ac. ingoldii and L. lauri remained weak (62 %) (Fig. 4). Besides, the sequence difference between Ac. ingoldii and L. lauri appeared greater than that between the two teleomorphic species Clinoconidium bullatum and Drepanoconis larviformis presently classified into different genera. Therefore, the genus Acaromyces will be maintained at present. In the LSU rRNA gene-based tree, the Meira species were located in another clade together with teleomorphic species from Exobasidium and other genera of the Exobasidiales, including Dicellomyces, Graphiola and Kordyana (Fig. 4). In this clade, the four Meira species formed a distinct sub-clade with 100 % ML BP value, supporting the recognition of this genus.

The Jaminaea and Sympodiomycopsis species and three Rhodotorula species clustered in the Microstromatales together with teleomorphic species of Microstroma, Quambalaria and Volvocisporium (Fig. 1, Fig. 2, Fig. 4). The two Jaminaea species formed a first branched clade in the Microstromatales in the seven genes and the four protein genes based trees (Fig. 1, Fig. 3). A close relationship of the Jaminaea species with Microstroma albiziae was shown in the trees drawn from the combined seven gene sequences (Fig. 1) and the LSU rRNA gene sequences alone (Fig. 4), but not supported in the combination of ITS and LSU datasets (Fig. 2D). The genus Microstroma is polyphyletic as shown previously (Begerow et al., 2006, Begerow et al., 2014, Boekhout et al., 2011) and in the present study. M. albiziae is not the type species of the genus, and, therefore, the genus Jaminaea should be remained. However, the affiliation to Jaminea or Sympodiomycopsis lacks fundamental support and further data are needed before a new combination can be proposed. Begerow et al. (2014) assigned Jaminea to the family Quambalariaceae, but the close relationship of this genus with the teleomorphic species Quambalaria cyanescens was not shown in any of the trees constructed in this study. Therefore and due to the lack of other Quambalaria species in our dataset, it is preferred to treat Jaminaea as ‘incertae sedis’ within Microstromatales as Sipiczki & Kajdacsi (2009) suggested before.

The affiliation of Sympodiomycopsis species within the Microstromatales was confirmed in this study, but the relationship of this genus with the other members of the order was not resolved (Fig. 1, Fig. 2, Fig. 3, Fig. 4), being in agreement with Begerow et al. (2014) who treated the genus as ‘incertae sedis’ in the Microstromatales.

Among the three Rhodotorula species belonging to the Microstromatales, R. bacarum had almost identical ITS and LSU rRNA gene sequences with Microstroma album, the type species of the genus Microstroma (Fig. 2, Fig. 4). As commented by Sampaio (2011), R. bacarum should be regarded as representing the asexual stage of M. album and thus should be treated as a synonym of the latter. The other two Rhodotorula species, R. hinnulea and R. phylloplana, exhibited a close relationship with Microstroma juglandis in all the trees constructed in this study (Fig. 1, Fig. 2, Fig. 3, Fig. 4). R. hinnulea was considered a synonym of R. phylloplana in Sampaio (2011) because of identical ITS and LSU rRNA gene sequences. In this study we showed that the type strains of the two species also shared similar protein gene sequences (Fig. 3), supporting their assumed conspecificity (Fig. 2D). In the LSU rRNA gene based tree, R. phylloplana was located together with M. juglandis (Fig. 4). In the seven genes and the four protein genes based trees, the close affinity of R. phylloplana and M. juglandis with R. bacarum (the anamorph of M. album) was resolved (Fig. 1, Fig. 3). The result suggests that R. phylloplana represents an anamorphic species in the genus Microstroma.

In agreement with previous studies (Fell et al. 2000) the genus Tilletiopsis was shown to be polyphyletic in this study. Three Tilletiopsis species, including the type species of the genus, T. washingtonensis, formed a well supported (100 % BP and 1.0 PP) clade in the Entylomales in all the trees constructed using different datasets (Fig. 1, Fig. 2, Fig. 3, Fig. 4). This clade was resolved as a sister group of the genus Entyloma. The result suggests that this clade represents a distinct genus which should keep the name Tilletiopsis.

Six Tilletiopsis species belonged to the Georgefischeriales (Fig. 4). As shown in Boekhout et al. (2011), T. derxii, T. flava, T. fulvescens and T. oryzicola formed a clade together with two teleomorphic species Tilletiaria anomala and Phragmotaenium indicum in the tree constructed from the LSU rRNA gene sequences (Fig. 4). The latter two teleomorphic species differ remarkably in the morphology of teliospores (Bauer et al. 2001b) and the genetic distance between them is similar with those between other genera, suggesting they represent two different genera. Tilletiaria anomala formed a basal position in this clade. The four Tilletiopsis species were resolved to be more closely related to Phragmotaenium indicum with 90 % ML BP support, suggesting that they belong to the genus Phragmotaenium.

The other two Tilletiopsis species in the Georgefischeriales, T. minor and T. penniseti, formed another clade with a teleomorphic species Gjaerumia ossifragi, the type of the genus, as a basal branch with 61 % ML BP support (Fig. 4). Bauer et al. (2005) also showed that G. ossifragi formed a statistically supported cluster with T. minor, T. penniseti, and two undescribed Tilletiopsis species based on the Bayesian inference analysis of the LSU rRNA genes. The results support transferring T. minor and T. penniseti into Gjaerumia.

Two Tilletiopsis species, T. albescens and T. pallescens, could not be assigned to any recognised orders in the Exobasidiomycetes. In the ML trees constructed from the seven gene and four protein gene datasets, they clustered together in a deep lineage with 93 % and 94 % BP support, but their phylogenetic relationship with other lineages of Exobasidiomycetes was not resolved. The MP and BI analyses of the two datasets did not support a close relationship between the two Tilletiopsis species (Fig. 1, Fig. 3). In the trees generated from the other datasets, these two species formed independent deep branches with uncertain phylogenetic positions (Fig. 2, Fig. 4). These two Tilletiopsis species were also treated as ‘incertae sedis’ in the Exobasidiomycetes by Begerow et al., 2006, Begerow et al., 2014 and Hibbett et al. (2007). Our results suggested that T. albescens and T. pallescens represent two separate genera belonging to two different orders.

Taxonomy

The phylogenetic analyses described above confirm that the class Exobasidiomycetes is polyphyletic. However, it is immature to redefine this class at present because molecular data, especially protein gene sequences from the majority of the teleomorphic taxa in this class, that will offer a more robust phylogenetic analysis integrating the yeasts, are not available. It is, however, needed to make taxonomic revisions for yeast taxa at the genus level based on the phylogenetic data presented here. Fereydounia, Jaminaea, Meira, Sympodiomycopsis and Tilletiaria together with Malassezia and Moniliella as shown in Wang et al. (2014) and Nasr et al. (2014) are monophyletic genera. In order to avoid possible name changes in the future, Acaromyces will be remained at present before a taxonomic revision can be made that need to include more teleomorphic genera.

We propose to transfer the Farysizyma species to the genus Farysia and Rhodotorula phylloplana to Microstroma. For the Pseudozyma species, it is clear that P. prolifica, the type species of the genus, is a synonym of Ustilago maydis. We propose to transfer 1) P. abaconensis, P. shanxiensis and P. siamensis to the genus Ustilago; 2) P. antarctica, P. aphidis, P. parantarctica and P. rugulosa to Moesziomyces; 3) P. crassa to Triodiomyces; 4) P. graminicola to Sporisorium; and 5) P. jejuensis to Langdonia. P. brasiliensis, P. fusiformata, and P. vetiver represent a new genus for which we propose Kalmanozyma gen. nov. Pseudozyma churashimaensis represents another new genus for which Dirkmeia gen. nov. is proposed. The taxonomic treatment for the remaining Pseudozyma species, including P. alboarmeniaca, P. thailandica, P. tsukubaensis, P. hubeiensis and P. pruni remains to be determined. These species are embedded in groups with lots of teleomorphic species, where only very few specimens have been sequenced so far, thus we expect, that they probably have already a synonym, which we just did not identify so far. Because the genus name Pseudozyma is not available any more, we suggest to use ‘pro tempore’ or ‘pro tem.’ in abbreviation to indicate that these species names are temporarily remained.

We propose to emend the genus Tilletiopsis in the order Entylomatales by retaining the genus name for the monophyletic clade represented by the type species T. washingtonensis. For the taxonomic treatments of the remaining Tilletiopsis species, we propose to transfer T. derxii, T. flava, T. fulvescens and T. oryzicola to the genus Phragmotaenium; and T. minor and T. penniseti to Gjaerumia. Two new generic names, Robbauera gen. nov. and Golubevia gen. nov., are proposed for T. albescens and T. pallescens, respectively. Two new orders are also proposed for them to accommodate the sisterhood of these two new genera with other orders of Exobasidiomycetes.

Golubeviales Q.M. Wang, F.Y. Bai, Begerow & Boekhout ord. nov. MycoBank MB812083.

Member of Exobasidiomycetes. The diagnosis of the order Golubeviales is based on the description of the genus Golubevia. The nomenclature of the order is based on the genus Golubevia.

Type family: Golubeviaceae Q.M. Wang, F.Y. Bai, Begerow & Boekhout

Golubeviaceae Q.M. Wang, F.Y. Bai, Begerow, & Boekhout fam. nov. MycoBank MB812692.

Member of Golubeviales (Exobasidiomycetes).The diagnosis of the family Golubeviaceae is based on the description of the genus Golubevia. The nomenclature of the family is based on the genus Golubevia.

Type genus: Golubevia Q.M. Wang, F.Y. Bai, Begerow & Boekhout

Golubevia Q.M. Wang, F.Y. Bai, Begerow & Boekhout gen. nov. MycoBank MB812694.

Etymology: The genus is named in honour of W.I. Golubev for his pioneering contributions to the taxonomic of basidiomycetous yeasts.

This genus is proposed for the single species clade formed by Tilletiopsis pallescens as resolved by multiple gene sequence analyses. It occurred as a sister lineage of the other orders within Exobasidiomycetes (Fig. 1, Fig. 2, Fig. 3, Fig. 4).

Sexual reproduction unknown, but chlamydospore-like structures germinating with a holobasidium-like structure that forms ballistospores on the apex, have been observed (Begerow et al. 2000). Colonies pale yellowish-brown or cream and have an eroded margin. Budding cells present. Hyphae regularly branched, narrow and cylindrical, and with retraction septa, but lack clamp connections. Chlamydospores may occur terminally or intercalarily. Ballistoconidia present. Xylose absent, but glucose, galactose and mannose present in whole-cell hydrolysates. The major ubiquinone Q-10. Starch-like compounds are not produced.

Type species: Golubevia pallescens (Gokhale) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812695.

Robbauerales Boekhout, Begerow, Q.M. Wang & F.Y. Bai ord. nov. MycoBank MB812696.

Member of Exobasidiomycetes. The diagnosis of the order Robbauerales is based on the description of the genus Robbauera. The nomenclature of the order is based on the genus Robbauera.

Type family: Robbaueraceae Boekhout, Begerow, Q.M. Wang & F.Y. Bai

Robbaueraceae Boekhout, Begerow, Q.M. Wang & F.Y. Bai fam. nov. MycoBank MB812697.

Member of Robbauerales (Exobasidiomycetes). The diagnosis of the family Robbaueraceae is based on the description of the genus Robbauera. The nomenclature of the family is based on the genus Robbauera.

Type genus: Robbauera Boekhout, Begerow, Q.M. Wang & F.Y. Bai

Robbauera Boekhout, Begerow, Q.M. Wang & F.Y. Bai gen. nov. MycoBank MB812698.

Etymology: The genus is named in honour of Robert Bauer for his contributions to the taxonomy and ultrastructure of smuts.

This genus is proposed for the single species clade formed by Tilletiopsis albescens as resolved by multiple gene sequence analyses. It occurred as a sister lineage of the other orders within Exobasidiomycetes (Fig. 1, Fig. 2, Fig. 3, Fig. 4).

Sexual reproduction unknown. Colonies are whitish-cream and with an eroded margin. Hyphae regularly branched, narrow, with retraction septa, but lack clamp connections. Chlamydospores may be present. Ballistoconidia present. Xylose absent, but glucose, galactose and mannose present in whole-cell hydrolysates. The major ubiquinone Q-10. Starch-like compounds not produced.

Type species: Robbauera albescens (Gokhale) Boekhout, Begerow, Q.M. Wang & F.Y. Bai comb. nov. MycoBank MB812699.

Basionym: Tilletiopsis albescens Gokhale, Nova Hedwigia 23: 803. 1972.

Dirkmeia F.Y. Bai, Q.M. Wang, Begerow & Boekhout gen. nov. MycoBank MB812700.

Etymology: the genus is named in honour of Dirk van der Mei who was a former director of CBS Fungal Biodiversity Centre (CBS-KNAW).

Member of Ustilaginaceae (Ustilaginales, Ustilaginomycetes). This genus is proposed to accommodate Pseudozyma churashimaensis which belongs to an isolated branch in the Ustilaginaceae based on the combined ITS and LSU rRNA gene sequence analysis (Fig. 2C).

Sexual reproduction unknown. Colonies cream-coloured, shiny, smooth, and with an eroded margin. Budding cells present. Ballistoconidia absent. Cell carbohydrates not determined. The major ubiquinone unknown. Starch-like compounds not produced.

Type species: Dirkmeia churashimaensis (T. Morita, Y. Ogura, M. Takash., N. Hirose, Fukuoka, Imura, Y. Kondo & Kitamoto) F.Y. Bai, Q.M. Wang, Begerow & Boekhout comb. nov. MycoBank MB812727.

Basionym: Pseudozyma churashimaensis T. Morita, Y. Ogura, M. Takash., N. Hirose, Fukuoka, Imura, Y. Kondo & Kitamoto, J. Biosci. Bioeng. 112: 142. 2011.

Kalmanozyma Q.M. Wang, F.Y. Bai, Begerow & Boekhout gen. nov. MycoBank MB812702.

Etymology: The genus is named in honour of Kálmán Vánky for his contributions to the taxonomy of smuts.

Member of Ustilaginaceae (Ustilaginales, Ustilaginomycetes). This genus is proposed to accommodate Pseudozyma fusiformata, Pseudozyma brasiliensis and Pseudozyma vetiver that form a distinct clade in the Ustilaginaceae based on the phylogenetic analysis of the ITS and LSU rRNA gene sequences (Fig. 2B).

Sexual reproduction unknown. Colonies whitish, cream to light salmon, shiny, smooth, and with an eroded margin. Budding cells present. Ballistoconidia absent. Pseudomycelium and true mycelium may be formed. Cell carbohydrates not determined. The major ubiquinone Q-10. Starch-like compounds not produced.

Type species: Kalmanozyma fusiformata (Buhagiar) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812703.

Basionym: Candida fusiformata Buhagiar, J. Gen. Microbiol. 110: 95. 1979.

≡ Pseudozyma fusiformata (Buhagiar) Boekhout, J. Gen. Appl. Microbiol. 41: 363. 1995.

New combinations in Kalmanozyma

Kalmanozyma brasiliensis (J.V.C. Oliveira, T.A. Borges, R.A.C. Santos, L.F.D. Freitas, C.A. Rosa, G.H. Goldman & D.M. Riaño-Pachón) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812704.

Basionym: Pseudozyma brasiliensis J.V.C. Oliveira, T.A. Borges, R.A.C. Santos, L.F.D. Freitas, C.A. Rosa, G.H. Goldman & D.M. Riaño-Pachón, Int. J. Syst. Evol. Microbiol. 64: 2159. 2013.

Kalmanozyma vetiver (Chamnanpa & Limtong) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812735.

Basionym: Pseudozyma vetiver Chamnanpa & Limtong, Antonie van Leeuwenhoek 104: 637. 2013.

Tilletiopsis Derx, Bulletin du Jardin Botanique de Buitenzorg 17: 471. 1948. emend. Begerow, Q.M. Wang, F.Y. Bai & Boekhout.

Member of Entylomatales (Exobasidiomycetes). This genus is emended to include only the species in the clade represented by T. washingtonensis, T. lilacina and T. cremea.

Sexual reproduction unknown. Colonies cream coloured and with an entire or eroded margin. Budding cells present. Hyphae narrow, with retraction septa, but lack clamp connections. Chlamydospores may be present. Ballistoconidia present. Xylose in cell wall hydrolysate absent. The major ubiquinone Q-10. Starch-like compounds not produced.

Type species: Tilletiopsis washingtonensis Nyland, Mycologia 42: 488. 1950.

Anthracocystis Bref., Unters. Gesammtgeb. Mykol. (Leipzig) 15: 53. 1912.

Type species: Anthracocystis destruens Bref.

New combination in Anthracocystis

Anthracocystis pampara (Speg.) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812705.

Basionym: Ustilago pamparum Speg., Boln Acad. nac. Cienc. Córdoba 11: 28. 1887.

≡ Sphacelotheca pamparum (Speg.) G.P. Clinton, J. Mycol. 8: 140. 1902.

Farysia Racib., Bull. int. Acad. Sci. Lett. Cracovie, Cl. sci. math. nat. Sér. B, sci. nat. 3: 354. 1909. emend. Q.M. Wang, F.Y. Bai, Begerow & Boekhout.

= Elateromyces Bubák, Arch. Přírodov. Výzk. Čech. 15: 32. 1912.

= Farysizyma A. Fonseca, FEMS Yeast Res. 8: 505. 2008.

Type species: Farysia butleri (H. & P. Sydow) H. & P. Sydow.

This genus was originally described for teleomorphic smut fungi occurring on Cyperaceae plants and was redefined Vánky, 2002, Vánky, 2012. Here it is emended to include free-living yeast species with unknown sexual states as shown by molecular phylogenetic analysis (Fig. 2C).

New combinations in Farysia

Farysia itapuensis (Landell & Valente) Begerow, Q.M. Wang, F.Y. Bai & Boekhout comb. nov. MycoBank MB812706.

Basionym: Farysizyma itapuensis Landell & Valente, FEMS Yeast Res. 8: 506. 2008.

Farysia taiwaniana (P.-H. Wang, Y.-T. Wang & S.-H. Yang) Begerow, Q.M. Wang, F.Y. Bai & Boekhout comb. nov. MycoBank MB812707.

Basionym: Farysizyma taiwaniana P.-H. Wang, Y.-T. Wang & S.-H. Yang, FEMS Yeast Res. 8: 506. 2008.

Farysia setubalensis (Fonseca & Inácio) Begerow, Q.M. Wang, F.Y. Bai & Boekhout comb. nov. MycoBank MB812708.

Basionym: Farysizyma setubalensis Fonseca & Inácio., FEMS Yeast Res. 8: 507. 2008.

Farysia acheniorum (Buhagiar & Barnett) Begerow, Q.M. Wang, F.Y. Bai & Boekhout comb. nov. MycoBank MB812709.

Basionym: Sterigmatomyces acheniorum Buhagiar & Barnett., J. Gen. Microbiol. 77: 78. 1973.

≡ Farysizyma acheniorum (Buhagiar & Barnett) Fonseca, FEMS Yeast Res. 8: 499. 2008.

≡ Rhodotorula acheniorum (Buhagiar & Barnett) Rodrigues de Miranda, Stud. Mycol. 14: 28. 1977.

Gjaerumia R. Bauer, M. Lutz & Oberw., Mycol. Res. 109: 1257. 2005. emend. Q.M. Wang, F.Y. Bai, Begerow & Boekhout.

Type species: Gjaerumia ossifragi (Rostr.) R. Bauer, M. Lutz & Oberw.

This genus was originally proposed for teleomorphic smut fungi occurring on Asparagaceae, Melanthiaceae and Xanthorrhoeaceae (Bauer et al. 2005) and is emended to include free-living yeast species with unknown sexual states as shown by molecular phylogenetic analysis (Fig. 4).

New combinations in Gjaerumia

Gjaerumia minor (Nyland) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812710.

Basionym: Tilletiopsis minor Nyland, Mycologia 42: 489. 1950.

Gjaerumia penniseti (Takashima & Nakase) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812711.

Basionym: Tilletiopsis penniseti Takashima & Nakase, Antonie van Leeuwenhoek 80: 43. 2001.

Langdonia McTaggart & R.G. Shivas, Persoonia, 29: 130. 2012. emend. Q.M. Wang, F.Y. Bai, Begerow & Boekhout.

Type species: Langdonia fraseriana (Syd.) McTaggart & R.G. Shivas.

This genus was originally proposed for teleomorphic smut fungi occurring on Poaceae (McTaggart et al. 2012b) and is emendied to include free-living yeast species with unknown sexual states as showed by molecular phylogenetic analysis (Fig. 2B).

New combination in Langdonia

Langdonia jejuensis (Seo, Um, Min, Rhee, Cho, Kim & Lee) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812712.

Basionym: Pseudozyma jejuensis H.S. Seo, H.J. Um, J. Min, S.K. Rhee, T.J. Cho, Y. H. Kim & J. Lee, FEMS Yeast Res. 7: 1039. 2007.

Microstroma Niessl, Öst. bot. Z. 11: 250. 1861. emend. Q.M. Wang, F.Y. Bai, Begerow & Boekhout.

Type species: Microstroma album (Desm.) Sacc.

This genus was originally proposed for teleomorphic smut fungi occurring on Juglandaceae, Fabaceae and Fagaceaeas (Begerow et al. 2014) as defined by Pires (1928) and is emended to include free-living yeast species with unknown sexual states as shown by molecular phylogenetic analysis (Fig. 2D).

New combinations in Microstroma

Microstroma phylloplanum (R.G. Shivas & Rodr. Mir.) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812713.

Basionym: Cryptococcus phylloplanus R.G. Shivas & Rodr. Mir., Antonie van Leeuwenhoek 49: 153. 1983.

≡ Rhodotorula phylloplana (R.G. Shivas & Rodr. Mir.) Rodr. Mir. & Weijman, Antonie van Leeuwenhoek 54: 549. 1988.

≡ Cryptococcus hinnuleus R.G. Shivas & Rodr. Mir., Antonie van Leeuwenhoek 49: 155. 1983.

= Rhodotorula hinnulea (R.G. Shivas & Rodr. Mir.) Rodr. Mir. & Weijman, Antonie van Leeuwenhoek 54: 549. 1988.

Moesziomyces Vánky, Bot. Notiser 130: 133. 1977. emend. Q.M. Wang, Begerow, F.Y. Bai & Boekhout.

Type species: Moesziomyces bullatus (J. Schröt.) Vánky

This genus was originally proposed for a teleomorphic smut fungus occurring on Poaceae as defined by Vánky, 2002, Vánky, 2012 and is emended to include free-living yeast species with unknown sexual states as showed by molecular phylogenetic analysis (Fig. 2C).

New combinations in Moesziomyces

Moesziomyces antarcticus (Goto, Sugiyama & Iizuka) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812714.

Basionym: Sporobolomyces antarcticus Goto, Sugiyama & Iizuka, Mycologia 61: 759. 1969.

≡ Pseudozyma antarctica (Goto, Sugiyama & Iizuka) Boekhout, J. Gen. Appl. Microbiol. 41: 364. 1995.

≡ Candida antarctica (Goto, Sugiyama & Iizuka) Kurtzman, M.J. Smiley, C.J. Johnson & M.J. Hoffman, Yeasts: Characteristics and Identification (Cambridge): 86. 1983.

≡ Vanrija antarctica (Goto, Sugiyama & Iizuka) R.T. Moore, Bibl. Mycol. 108: 167. 1987.

= Trichosporon oryzae H. Ito, Iizuka & T. Sato, Agric. Biol. Chem. 38: 1599. 1974.

Moesziomyces aphidis (Henninger & Windisch) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812715.

Basionym: Sterigmatomyces aphidis Henninger & Windisch, Arch. Mikrobiol. 105: 50. 1975.

≡ Pseudozyma aphidis (Henninger & Windisch) Boekhout, J. Gen. Appl. Microbiol. 41: 364. 1995.

Moesziomyces rugulosus (Traquair, L.A. Shaw & Jarvis) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812716.

Basionym: Sporothrix rugulosa Traquair, L.A. Shaw & Jarvis, Can. J. Bot. 66: 929. 1988.

≡ Pseudozyma rugulosa (Traquair, L.A. Shaw & Jarvis) Boekhout & Traquair, J. Gen. Appl. Microbiol. 41: 364. 1995.

≡ Stephanoascus rugulosus Traquair, L.A. Shaw & Jarvis, Can. J. Bot. 66: 929. 1988.

Moesziomyces parantarcticus (Sugita, Takashima, Mekha & Poonwan) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812717.

Basionym: Pseudozyma parantarctica Sugita, Takashima, Mekha & Poonwan, Microbiol. Immun. 47: 186. 2003.

Phragmotaenium R. Bauer, Begerow, A. Nagler & Oberw., Mycol. Res. 105: 423. 2001. emend. Q.M. Wang, Begerow, F.Y. Bai & Boekhout.

Type species: Phragmotaenium indicum (Vánky, M.S. Patil & N.D. Sharma) R. Bauer, Begerow, A. Nagler & Oberw.

This genus was originally proposed for a teleomorphic smut species occurring on Poaceae (Bauer et al. 2001b) and is emended to include free-living yeast species with unknown sexual states as shown by molecular phylogenetic analysis (Fig. 4).

New combinations in Phragmotaenium

Phragmotaenium flavum (Tubaki) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812726.

Basionym: Tilletiopsis minor Nyland var. flava Tubaki, Nagaoa 1: 28. 1952.

≡ Tilletiopsis flava (Tubaki) Boekhout, Stud. Mycol. 33: 151. 1991.

Phragmotaenium derxii (Takashima & Nakase) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812718.

Basionym: Tilletiopsis derxii Takashima & Nakase, Antonie van Leeuwenhoek 80: 43. 2001.

Phragmotaenium oryzicola (Takashima & Nakase) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812719.

Basionym: Tilletiopsis oryzicola Takashima & Nakase, Antonie van Leeuwenhoek 80: 43. 2001.

Phragmotaenium fulvescens (Gokhale) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812720.

Basionym: Tilletiopsis fulvescens Gokhale, Nova Hedwigia 23: 805. 1972.

Sporisorium Ehrenb. ex Link, in Willdenow, Sp. pl., Edn 4 6: 86. 1825. emend. Q.M. Wang, F.Y. Bai, Begerow & Boekhout.

Type species: Sporisorium sorghi Ehrenb. ex Link

This genus was originally proposed for teleomorphic smut fungi occurring on Poaceae. It was emended by McTaggart et al. (2012b) to include only the Sporisorium sensu stricto clade. Here it is emended further to include free-living yeast species with unknown sexual states as shown by molecular phylogenetic analysis (Fig. 2B).

New combination in Sporisorium

Sporisorium graminicola (W. Golubev, Sugita & N. Golubev) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812721.

Basionym: Pseudozyma graminicola W. Golubev, Sugita & N. Golubev, Mycoscience 48: 30. 2007.

Triodiomyces McTaggart & R.G. Shivas, Persoonia 29: 131. 2012. emend. Q.M. Wang, F.Y. Bai, Begerow & Boekhout.

Type species: Triodiomyces altilis (Syd.) McTaggart & R.G. Shivas

This genus was originally proposed to accommodate a group of teleomorphic smut fungi occurring on grasses of the genus Triodia (McTaggart et al. 2012b) and is emended to include free-living yeast species with unknown sexual states as shown by molecular phylogenetic analysis (Fig. 2C).

New combination in Triodiomyces

Triodiomyces crassus (Mekha, Takashima & Sugita) Q.M. Wang, F.Y. Bai, Begerow & Boekhout comb. nov. MycoBank MB812722.

Basionym: Pseudozyma crassa Mekha, Takashima & Sugita, Microbiol. Immunol. 58: 9. 2014.

New combinations in Ustilago (Pers.) Roussel, Fl. Calvados, Edn 2: 47. 1806.

Type species: Ustilago hordei (Pers.) Lagerh.

The genus Ustilago is polyphyletic and remains to be redefined (McTaggart et al. 2012a, b). It is immature to emend this genus at present but it is reasonable to transfer the three Pseudozyma species to this genus because they are located in the monophyletic Ustilago sensu stricto clade containing the type species of the genus (Fig. 2B). Thus the genus Ustilago also contains anamorphic fungi.

Ustilago abaconensis (Statzell, Scorzetti & Fell) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812723.

Basionym: Pseudozyma abaconensis Statzell, Scorzetti & Fell, Int. J. Syst. Evol. Microbiol. 60: 1983. 2010.

Ustilago shanxiensis (F.Y. Bai & Q.M. Wang) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812724.

Basionym: Pseudozyma shanxiensis F.Y. Bai & Q.M. Wang, Int. J. Syst. Evol. Microbiol. 56: 292. 2006.

Ustilago siamensis (Sugita, Takashima, Poonwan & Mekha) Q.M. Wang, Begerow, F.Y. Bai & Boekhout comb. nov. MycoBank MB812725.

Basionym: Pseudozyma siamensis Sugita, Takashima, Poonwan & Mekha, Microbiol. Immun. 58: 9. 2014.