Logo of persooniaLink to Publisher's site
Persoonia. 2014 Dec; 33: 41–47.
Published online 2014 May 23. doi: 10.3767/003158514X682313
PMCID: PMC4312936
PMID: 25737592

Moniliellomycetes and Malasseziomycetes, two new classes in Ustilaginomycotina

Q.-M. Wang, 1 B. Theelen, 2 M. Groenewald, 2 F.-Y. Bai, 1 , 2 and T. Boekhout 1 , 2 , 3 , 4
Author information Article notes Copyright and License information Disclaimer

Abstract

Ustilaginomycotina (Basidiomycota, Fungi) has been reclassified recently based on multiple gene sequence analyses. However, the phylogenetic placement of two yeast-like genera Malassezia and Moniliella in the subphylum remains unclear. Phylogenetic analyses using different algorithms based on the sequences of six genes, including the small subunit (18S) ribosomal DNA (rDNA), the large subunit (26S) rDNA D1/D2 domains, the internal transcribed spacer regions (ITS 1 and 2) including 5.8S rDNA, the two subunits of RNA polymerase II (RPB1 and RPB2) and the translation elongation factor 1-α (EF1-α), were performed to address their phylogenetic positions. Our analyses indicated that Malassezia and Moniliella represented two deeply rooted lineages within Ustilaginomycotina and have a sister relationship to both Ustilaginomycetes and Exobasidiomycetes. Those clades are described here as new classes, namely Moniliellomycetes with order Moniliellales, family Moniliellaceae, and genus Moniliella; and Malasseziomycetes with order Malasseziales, family Malasseziaceae, and genus Malassezia. Phenotypic differences support this classification suggesting widely different life styles among the mainly plant pathogenic Ustilaginomycotina.

Keywords: fungi, molecular phylogeny, smuts, taxonomy, yeasts

INTRODUCTION

Basidiomycota (Dikarya, Fungi) contains three main phylogenetic domains, namely the subphyla Agaricomycotina, Pucciniomycotina and Ustilaginomycotina(Hibbett et al. 2007). Within Ustilaginomycotina three classes have been proposed, namely Ustilaginomycetes, Exobasidiomycetes and Entorrhizomycetes (Begerow et al. 1997, 2006, Bauer et al. 2001, 2006). Other researchers, however, questioned the status of Entorrhizomycetes and considered them incertae sedis among Basidiomycota (Matheny et al. 2006, Hibbett et al. 2007).

Ustilaginomycotina comprises plant pathogenic fungi (smuts), which are mostly dimorphic and present a yeast stage during the live cycle, and asexual fungi which are known only as yeasts or yeast-like species, e.g. Acaromyces spp., Pseudozyma spp., Meira spp., Tilletiopsis spp. and Malassezia spp. (Boekhout 1991, 1995, Boekhout et al. 1995, 2003, 2011, Begerow et al. 2000, 2006, Fell et al. 2000). Pseudozyma spp. belong to Ustilaginomycetes and the genera Acaromyces, Meira and Tilletiopsis to Exobasidiomycetes (Begerow et al. 2006, Hibbett et al. 2007, Boekhout et al. 2011). The taxonomic position of Malassezia spp., that is an important inhabitant of the human and animal skin microbiota (Guého-Kellermann et al. 2010, Sugita et al. 2010, Gaitanis et al. 2012, Findley et al. 2013), is not settled. It has been proposed that the genus belongs to Ustilaginomycotina (Begerow et al. 2000, Xu et al. 2007), but its final affiliation within this group remained problematic. The genus was treated to represent a distinct order Malasseziales in the Exobasidiomycetes based on molecular phylogenetic analyses of the nuclear ribosomal RNA genes alone or in combination with protein genes (Begerow et al. 2000, 2006, Bauer et al. 2001, Weiß et al. 2004). However, Matheny et al. (2006) suggested that the Malasseziales might be affiliated with Ustilaginomycetes. Therefore, Hibbett et al. (2007) excluded Malasseziales from Exobasidiomycetes and treated it as incertae sedis in Ustilaginomycotina.

The yeast-like genus Moniliella was described by Stolk & Dakin (1966). In the following year the genus Trichosporonoides was introduced by Haskins & Spencer (1967). Both have a basidiomycetous affinity because they can hydrolyse urea, show a positive Diazonium Blue B (DBB) staining and have multi-lamellar cell walls. The septal pores of the species studied so far (M. oedocephala, M. spathulata, M. suaveolens) show a diversity of septa. Moniliella suaveolens has typical dolipores with an arch of endoplasmic reticulum, M. spathulata has a micropore-like structure and M. oedocephala has both (Haskins 1975, Martínez 1979). Boekhout (1998) and de Hoog & Smith (1998a, b) indicated that Trichosporonoides was probably synonymous with Moniliella. Later Rosa et al. (2008) confirmed that both genera were indeed congeneric based on 26S rRNA D1/D2 domain sequence analysis and, consequently, transferred all species into the genus Moniliella. These authors were, however, not sure about the phylogenetic relationships with either Ustilaginomycotina or Agaricomycotina.

In order to clarify the phylogenetic affiliations of Malassezia and Moniliella, we performed phylogenetic analyses based on the six genes that were used to address the higher-level phylogeny of the Fungi (James et al. 2006, Hibbett et al. 2007). Our results demonstrated that Malassezia and Moniliella belong to Ustilaginomycotina where they form deep and well-supported lineages with a sister relationship to both Ustilaginomycetes and Exobasidiomycetes. We therefore propose two new classes, Malasseziomycetes and Moniliellomycetes for these lineages, with additional support from phenotypic characters.

MATERIALS AND METHODS

Taxon sampling

Almost all the recognised Malassezia and Moniliella species were employed (Table 1). Reference species representing Pucciniomycotina, Agaricomycotina and currently recognised classes of Ustilaginomycotina were selected based on sequence availability for the six genes used in the AFTOL1 project (http://aftol.org/data.php) (Table 1). Sequence data generated in this study or data retrieved from GenBank were mostly from type strains of the taxa compared.

Table 1

Taxa sampled and sequence accession numbers employed (those in bold are determined in this study).

Species Strain D1D2ITSSSURPB1RPB2EF1-α
Ustilaginomycetes
     Cintractia limitataHAJB 10488DQ645506DQ645508DQ645507DQ645510DQ645509DQ645511
     Melanotaenium endogenumAFTOL ID1918DQ789979DQ789981DQ789980–––
     Melanotaenium euphorbiaevoucher HUV17733JN367314JN367289JN367342––JN367365
     Rhodotorula acheniorumAS 2.3198TAF190001AB038128AJ496256KF706499KF706522KF706474
     Schizonella melanogrammaCBS 174.42DQ832210DQ832212DQ832211DQ832214DQ832213DQ832215
     Sporisorium reilianumCBS 131460KF706430KF706438KF706441–KF706511KF706472
     Urocystis colchiciAFTOL-ID1647DQ838576DQ839596DQ839595–DQ839597DQ839598
     Urocystis eranthidisvoucher hmk292JN367324JN367299JN367352JN367428–JN367375
     Ustanciosporium gigantosporumHRK 023JN367325JN367300JN367353JN367429–JN367376
     Ustilago hordeiCBS 131470KF706429KF706437KF706442KF706498KF706521KF706473
     Ustilago maydisCBS 504.76/MS 115AF453938AY854090X62396XM401478AY485636AY885160
     Ustilago triticiCBS 669.70DQ094784DQ846894DQ846895DQ846897DQ846896DQ846898
Exobasidiomycetes
     Exobasidium gracileDSM 4460DQ663699DQ663700DQ785786DQ663702DQ663701DQ663703
     Exobasidium rhododendriCBS 101457DQ667151DQ667153DQ667152DQ667155DQ667154DQ667156
     Jaminaea angkoriensisC5bEU587489EU604147EU604148–––
     Microstroma juglandisCBS 287.63AF009867DQ789988DQ789987DQ789990DQ789989DQ789991
     Quambalaria cyanescensCBS 876.73DQ317616DQ317623KF706440–KF706531KF706485
     Rhamphospora nymphaeaeCBS 72.38DQ831032DQ831034DQ831033–DQ831035DQ831036
     Tilletiaria anomalaCBS 436.72AJ235284DQ234558AY803752DQ234571AY803750DQ835991
CBS 607.83TAJ235282AB025704KF706451–KF706530KF706483
     Tilletiopsis washingtonensisCBS 544.50TAJ235278DQ835994AJ271382–DQ835995DQ835996
Malasseziomycetes
     Malassezia capraeCBS10434TAY743616AY743656KF706456KF706495KF706513KF706467
     Malassezia dermatisCBS 9169TAB070365AY390284KF706452KF706490KF706532KF706461
     Malassezia equinaCBS 9969TAY743621KF706439KF706454KF706492KF706515KF706463
     Malassezia furfurCBS 1878TAF063214AY743634KF706457KF706497KF706516KF706469
     Malassezia globosaCBS 7966TAF064025AY387132–KF706493KF706518KF706465
     Malassezia japonicaCBS 9431TEF140672EF140669KF706458–KF706514KF706464
     Malassezia nanaCBS 9558TEF140673EF140667KF706453KF706491KF706510KF706462
     Malassezia obtusaCBS 7876TAB105197AY387137KF706455–KF706519KF706470
     Malassezia pachydermatisCBS 1879TAY743605AB118941DQ457640DQ785792DQ408140DQ028594
     Malassezia restrictaCBS 7877TAF064026AY743636EU192367KF706496KF706520KF706471
     Malassezia slooffiaeCBS 7956TAJ249956AY743633KF706459–––
     Malassezia sympodialisCBS 7222TAF064024AY743632KF706460–––
     Malassezia yamatoensisCBS 9725TAB125263AB125261–KF706494KF706512KF706466
Moniliellomycetes
     Moniliella acetoabutensCBS 169.66TAF335523EU252153KF706443KF706500KF706523KF706476
     Moniliella madidaCBS 240.79TAF335522–KF706447KF706502KF706525KF706478
     Moniliella megachiliensisCBS 190.92TEF137916KF706433KF706448KF706501KF706524KF706477
     Moniliella mellisCBS 350.33TEU545185–KF706446–KF706528KF706481
     Moniliella nigrescensCBS 269.81TAF335527KF706436–KF706504KF706527KF706480
     Moniliella oedocephalisCBS 649.66TAF335521KF706435KF706449––KF706484
     Moniliella pollinisCBS 461.67TAF335525KF706434KF706450KF706505KF706529KF706482
     Moniliella spathulataCBS 241.79TAF335526KF706432KF706444KF706503KF706526KF706479
     Moniliella suaveolensCBS 126.42TAF335520KF706431KF706445––KF706475
Pucciniomycotina
     Bensingtonia ciliataAS 2.1945TAF189887AF444563D38233KF706509KF706536KF706486
     Chrysomyxa arctostaphyliCFB22246AY700192DQ200930AY657009–DQ408138DQ435789
     Endocronartium harknessiiCFB22250AY700193DQ206982AY665785–DQ234551DQ234567
     Erythrobasidium hasegawianumAS 2.1923TAF189899AF444522D12803KF706506KF706534KF706488
     Naohidea sebaceaCBS 8477DQ831020DQ911616–KF706508KF706535KF706487
     Platygloea disciformisIFO32431AY629314DQ234556DQ234563–DQ234554DQ056288
     Puccinia graminisCRL75-36-700-3/ECSAF522177AF468044AY125409XM_003334476XM_003321826XM_003333024
     Sporidiobolus salmonicolorCBS 490TAF070439AY015434AB021697KF706507KF706533KF706489
Agaricomycotina
     Auriculibuller fuscusCBS 9648TAF444763AF444669KF036604KF036314KF036727KF036999
     Bulleromyces albusCBS 501TAF075500AF444368X60179KF036334KF036745KF037016
     Boletellus projectellusMB03-118AY684158AY789082AY662660AY788850AY787218AY879116
     Dacryopinax spathulariaGEL 5052AY701525AY854070AY771603AY857981AY786054AY881020
     Filobasidiella depauperataCBS 7841TAF487884EF211248AJ568017KF036417KF036885KF037150
Wallemia clade
     Wallemia ichthyophagaEXF994/EXF1059DQ847516AY302523AY741382DQ847522DQ847519DQ847525
     Wallemia muriaeMZKI-B952/EXF1054DQ847517AY302534AY741381DQ847523DQ847520DQ847526
     Wallemia sebiEXF483DQ847518AY328917AY741379DQ847524DQ847521DQ847527
Ascomycota
     Aleuria aurantiaOSC 100018AY544654DQ491495NG013139DQ471120DQ247785DQ466085
     Aspergillus nidulansNRRL 2395/FGSC4EF652445AY373888U77377XM_653321XM_677297XM_656730
     Neurospora crassaNRRL 13141/ICMP 6360AY681158AY681193AY046271XM_959004AF107789AF402094
     Schizosaccharomyces pombe972H-CU329672CU329672CU329672D13337X56564NC_003421

PCR and DNA sequencing

Genomic DNA was extracted from the living cultures grown on the Yeast Extract Peptone Dextrose (YPD) plate using the method as described by Bolano et al. (2001). A set of six genes were selected, including three protein-coding genes, namely RPB1 (the largest subunit of RNA polymerase II), RPB2 (the second largest subunit of RNA polymerase II) and EF1-α (translation elongation factor 1-α), and three rRNA genes namely small subunit (SSU or 18S) ribosomal DNA (rDNA) D1/D2 domains of the large subunit (LSU or 26S) rDNA, and the ITS 1+2 regions (including 5.8S rDNA) of the rDNA. PCR and sequencing of the rRNA genes were performed using the methods described previously (Fell et al. 2000, Scorzetti et al. 2002, Wang et al. 2003). PCR and sequencing primers for RPB1, RPB2 and EF1-α are listed in Table 2. PCR parameters for amplifying RPB1 and RPB2 were as follows: an initial denaturation step at 94 °C for 4 min; 36 cycles of denaturation at 94 °C for 1 min, annealing at 50–52 °C for 1 min and extension at 72 °C for 1 min; and a final extension step of 8 min at 72 °C. Amplification of the EF1-α gene used a touchdown PCR: an initial denaturation at 94 °C for 4 min; an annealing temperature of 62 °C in the first cycle, successively reducing the Tm by 1 °C per cycle over the next nine cycles to reach a final Tm of 52 °C, which is used in the remaining 30 cycles and extension at 72 °C for 1 min; and a final extension step of 8 min at 72 °C. Cycle sequencing was performed using the ABI BigDye cycle sequencing kit (QIAGEN, Valencia, California). Electrophoresis was done on an ABI PRISM 3710 or 3730 DNA sequencer.

Table 2

PCR and sequence primers used.

Locus Primers (5’-3’)
RPB1RPB1-Af: GAR TGY CCD GGD CAY TTY GG
RPB1-Cr: CCN GCD ATN TCR TTR TCC ATR TA
RPB2fRPB2-5F: GAY GAY MGW GAT CAY TTY GG
fRPB2-7cR: CCC ATR GCT TGY TTR CCC AT
bRPB2-6F: TGG GGY ATG GTN TGY CCY GC
gRPB2-6R: GCA GGR CAR ACC AWM CCC CA
EF1-αEF1-983F: GCY CCY GGH CAY CGT GAY TTY AT
EF1-2218R: AT GAC ACC RAC RGC RAC RGT YTG
EF1-1577F: CAR GAY GN TAC AAG ATY GGT GG
EF1-1567R: AC HGT RCC RAT ACC ACC RAT CTT

Molecular phylogenetic analyses

Sequences were aligned with the Clustal X program (Thompson et al. 1997). The alignment datasets were firstly analysed with Modeltest v. 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) analyses were conducted in MEGA v. 5 (Tamura et al. 2011). Maximum parsimony (MP) analysis was conducted in PAUP v. 4.0b10 (Swofford 2002) where the support of the branching topologies was derived from 1 000 replicates with 10 random additions. Three to four ascomycetous species were used as outgroups. Bayesian posterior probability analyses were conducted in MrBayes v. 3.2 (Ronquist et al. 2012) with parameters set to 1 000 000 generations, four runs and four chains. The chains were heated to 0.25 and a stop value of 0.01 was used. The alignment matrix was deposited in TreeBASE (www.treebase.org) with submission ID 14907.

RESULTS

A total of 108 new sequences were generated from 31 species in this study (Table 1). New sequences and those retrieved from GenBank generated from the same species were concatenated in different combinations to form three separate datasets as follows: 1) a rRNA gene dataset formed by SSU, LSU D1/D2 and ITS (including 5.8S rDNA); 2) a protein gene dataset consisted of RPB1, RPB2 and EF1-α; and 3) a six-gene dataset formed by the combination of the former two datasets as used in James et al. (2006). All the datasets were subjected to ML, MP and Bayesian analyses respectively and the topologies of the trees obtained were visually examined for phylogenetic concordance.

In the majority of the trees, four distinct monophyletic clades, namely Exobasidiomycetes, Malassezia, Moniliella and Ustilaginomycetes, were consistently resolved within Ustilaginomycotina (Table 3, Fig. 1, ​,2).2). The Malassezia, Moniliella and Ustilaginomycetes clades each received 1.0 post probability and 99–100 % bootstrap support in the trees constructed using different algorithms based on the six-gene dataset. These three clades were also clearly resolved and strongly supported (1.0 post probability and 92–100 % bootstrap values) in the trees drawn from the rRNA gene and the protein gene datasets, except for the Ustilaginomycetes clade which received weak (51–65 %) bootstrap support in the ML and MP trees drawn from the rRNA gene dataset (Table 3, Fig. 2). The Exobasidiomycetes was resolved as a monophyletic clade in the trees constructed from the rRNA gene and the six-gene datasets, but only received strong support in the Bayesian and ML trees drawn from the rRNA gene dataset. This clade was shown to be non-monophyletic in all the trees drawn from the protein gene dataset (Table 3, Fig. 1, ​,2).2). In the Bayesian and ML trees (Fig. 2d, e), Tilletiopsis fulvescens and Tilletiaria anomala formed a separate branch, while the remaining taxa of the Exobasidiomycetes formed an unsupported (0.6 post probability) group in the Bayesian tree (Fig. 2d) and two separate groups in the ML tree (Fig. 2e). In the MP tree (Fig. 2f), two Exobasidium species formed a separate branch from the other Exobasidiomycetes taxa, which in turn formed an unsupported group.

Table 3

Statistical support values for the major clades resolved in Ustilaginomycotina.

CladeThree rRNA genes
Three protein genes
Combined six genes
PPMLBPMPBPPPMLBPMPBPPPMLBPMPBP
Exobasidiomycetes1.076< 50nmnmnm1.051< 50
Malassezia1.01001001.01001001.0100100
Moniliella1.01001001.01001001.0100100
Ustilaginomycetes1.051651.092981.09999

MLBP = bootstrap percentage from maximum likelihood analysis.

MPBP = bootstrap percentage from maximum parsimony analysis.

PP = posterior probability from Bayesian analysis.

Nm = not monophyletic.

An external file that holds a picture, illustration, etc. Object name is per-33-041-g001.jpg

Phylogenetic tree constructed using Bayesian analysis of the combined sequences of 18S rDNA, 26S rDNA D1/D2 domains, ITS regions (including 5.8S rDNA), RPB1, RPB2 and EF1-α depicting the phylogenetic placements of genera Moniliella and Malassezia within the Ustilaginomycotina. Branch lengths are scaled in terms of expected numbers of nucleotide substitutions per site. Bayesian posterior probabilities and bootstrap percentages 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.

An external file that holds a picture, illustration, etc. Object name is per-33-041-g002.jpg

Phylogenetic trees based on datasets of rRNA genes including 18S, D1/D2 domains of 26S and ITS-5.8S (a, b and c); protein genes including RPB1, RPB2 and EF1-α (d, e and f) and the combined six genes (g, h and i) using Bayesian (a, d and g), maximum likelihood (b, e and h) and maximum parsimony (c, f and i) analyses, showing the major clades resolved within the Ustilaginomycotina. Bayesian posterior probabilities above 0.7 or bootstrap percentages over 50 % from 1 000 replicates are shown.

The phylogenetic relationships among the Exobasidiomycetes, Malassezia, Moniliella and Ustilaginomycetes clades were clearly resolved by Bayesian analysis of the six-gene dataset, showing that the Exobasidiomycetes clade was located basal to the other three clades; Malassezia and Moniliella were sister clades and Ustilaginomycetes was basal to them. Their relationships were all strongly supported by 1.0 post probability (Fig. 1, ​,2g).2g). However, the relationships among the four clades within Ustilaginomycotina were largely unresolved in the other trees (Fig. 2).

DISCUSSION

Basidiomycetous species in the subphylum Ustilaginomycotina are usually dimorphic, producing a saprobic haploid yeast phase and a parasitic dikaryotic hyphal phase. A considerable number of cultivable ustilaginomycetous fungi are only known by asexual yeasts and yeast-like microbes and are classified mainly based on physiological, biochemical and molecular criteria commonly used for yeasts, forming a taxonomic system hitherto independent from that of filamentous fungi (Boekhout 1991, Boekhout et al. 2011). Molecular methods recently showed the affiliation of these yeasts with various filamentous smuts and merged the two groups into a unified taxonomic system (Bauer et al. 2001, Begerow et al. 2000, 2006, Weiß et al. 2004, Matheny et al. 2006, Boekhout et al. 2011). However, the fine phylogenetic positions of the yeast and yeast-like groups have been a matter of debate. Here we show that the Malassezia and Moniliella clades present two deeply rooted lineages within the smut fungi (Ustilaginomycotina, Basidiomycota, Fungi). They also possess unique phenotypic (morphological, ultrastructural, physiological and biochemical) characters distinct from those of Ustilaginomycetes and Exobasidiomycetes.

The genus Moniliella was originally classified in the order Moniliales of fungi imperfecti (Stolk & Dakin 1966). A sexual morph has not been observed (de Hoog 1979a) and all members of the genus have greyish to olivaceous black colonies, yeast-like growth, hyphae that disarticulate in arthroconidia (Martinez et al. 1979, de Hoog 1979b), and CoQ-9 as the major ubiquinone (de Hoog et al. 2011). All species, except M. fonsecae, can ferment glucose and some species also galactose, sucrose and/or raffinose (Martínez et al. 1979, de Hoog et al. 2011), which among Basidiomycota is a rare trait. Some species are considered xerophilic (Hocking & Pitt 1981, de Hoog et al. 2011) and most are known from industrial settings, food stuffs, fats, oils and acids or substrates with low water activity or were isolated from flowers in tropical forest ecosystems (de Hoog et al. 2011). Thus their origin and ecology also differs from the vast majority of Ustilaginomycotina that typically are plant pathogens (Begerow et al. 2006). Glucose, galactose and mannose (low) were found to be present in the cell walls of Moniliella species, whereas xylose and fucose were absent (Weijman 1979), which led this author to conclude that the genus may not be related to the Agaricomycotina. Ustilaginomycotina, as analysed thus far, have glucose as the dominant cell wall sugar, with some galactose and mannose, but without xylose (Dörfler 1990, Boekhout et al. 1992, Bauer et al. 1997, 2001, Prillinger et al. 2011, van der Klei et al. 2011), thus agreeing with the cell wall composition as known from Moniliella species.

The septal ultrastructure of the Moniliella species as investigated so far revealed a rather complex pattern with dolipores in M. suaveolens, micro-pore-like structures in M. spathulata and both types occurring in M. oedocephala. The dolipores resemble those of Agaricomycetes but with an arch of endoplasmic reticulum instead of parenthesomes (Haskins 1975, Martinez 1979, Bauer et al. 2006, van Driel et al. 2009). These differences in pore structures may be growth stage dependent, and differ between yeast-like, hyphal and arthroconidial stages, but they may also be caused by the fixation protocols used. The dolipore structure is quite different from the simple pore with membrane caps observed in the Ustilaginomycotina and the simple pore without membrane apparatus typical for the Pucciniomycotina (Boekhout et al. 1992, Bauer et al. 1997, 2001, 2006, van der Klei et al. 2011). The biochemical and ultrastructural characters made the taxonomic and phylogenetic positions of Moniliella elusive for a long time. However, our results clearly show that the Moniliella species belong to the Ustilaginomycotina with strong support (Fig. 1, ​,22).

Our analyses showed that the species of Malassezia formed a highly supported deep lineage in the Ustilaginomycotina that we rank at the class level. This is further sustained by the unique monopolar budding, the thick helicoidal cell wall, the lipid dependency of most Malassezia species and the lipophily of M. pachydermatis (Guého-Kellermann et al. 2011). Malassezia species occur commonly on human and animal skin, but metagenomic data also revealed the presence of the species in some unexpected habits, such as forest soil, nematodes or corals (Guého-Kellermann et al. 2010, Gaitanis et al. 2012). The genome comparison between Ustilago maydis and M. globosa revealed some major differences in the enzyme armamentarium used by human inhabiting Malassezia yeasts that differs from that of the plant pathogen U. maydis (Xu et al. 2007, Sun et al. 2013).

Our analyses of the three rRNA genes and the combined six genes indicated that Exobasidiomycetes seem to be monophyletic when the Malassezia clade is excluded, but it remains polyphyletic in the analysis of the three protein-coding genes. Begerow et al. (1997, 2000) and Bauer et al. (2001) showed that the Exobasidiomycetes were weakly supported or with 56–85 % bootstrap support values based on the LSU rDNA analysis. Begerow et al. (2006) indicated that Exobasidiomycetes were paraphyletic using a combined analysis of SSU, D1/D2, ITS, atp6 and β-tubulin sequences, but this lineage was found to be monophyletic when the SSU data were excluded, but with weak bootstrap support. Matheny et al. (2006) indicated that the taxa within Exobasidiomycetes except the Malassezia clustered together with or without statistical support based on the different gene combination datasets. Thus, for a better understanding of the phylogeny of Exobasidiomycetes further analyses using more molecular data or genomic data are needed.

In addition to the Clustal X, we also used the MAFFT program (Katoh & Standley 2013) to align the sequences and the Gblocks program (Talavera & Castresana 2007) to remove ambiguously aligned blocks from the alignments. The alignments produced by the MAFFT and those treated by the Gblocks were all subjected to Bayesian, ML and MP analyses. The consensus was that the Malassezia, Moniliella and Ustilaginomycetes taxa were respectively resolved as strongly supported monophyletic clades in all the trees obtained, while the Exobasidiomycetes was monophyletic without statistic support in the trees drawn from the six-gene dataset but polyphyletic in the trees drawn from the rRNA gene and the protein gene datasets (data not shown). The polyphyletic nature of the Exobasidiomycetes was magnified by using the new programs, implying that this group may not represent a single class.

In conclusion, multiple gene phylogenetic analyses and phenotypic comparisons suggest that the species of Malassezia and Moniliella form two independent deep lineages representing sister groups to the recognised classes Ustilaginomycetes and Exobasidiomycetes within Ustilaginomycotina. Therefore, we propose two new classes to accommodate these fungi.

TAXONOMY

Monilielliomycetes Q.M. Wang, F.Y. Bai & Boekhout, class. nov. — MycoBank MB805229

Type order. Moniliellales.

Etymology. The nomenclature of the class is derived from the generic name of Moniliella Stolk & Dakin, Antonie van Leeuwenhoek 32: 399. 1966.

Member of Ustilaginomycotina. Sexual morph unknown. Colonies are smooth or velvety, greyish to olivaceous black. Budding cells are ellipsoidal and form terminally on true hyphae that disarticulate with artroconidia. Pseudohyphae and chlamydospores may be present. Cell walls are multi-lamellar. Hyphal septa typically possess dolipores with an arch of endoplasmic reticulum, but ‘micropore’-like structures may also be present. Sugars are fermented by most species. Nitrate is assimilated. Urease and diazonium blue B (DBB) reactions are positive. Coenzyme Q-9 is present. Xylose and fucose are absent from whole-cell hydrolysates.

Moniliellales Q.M. Wang, F.Y. Bai & Boekhout, ord. nov. — MycoBank MB805230

Type family. Moniliellaceae.

The diagnosis of the order Moniliellales is based on the description of the class Monilielliomycetes. The nomenclature of the order is based on the genus Moniliella Stolk & Dakin, Antonie van Leeuwenhoek 32: 399. 1966.

Moniliellaceae Q.M. Wang, F.Y. Bai & Boekhout, fam. nov. — MycoBank MB805231

Type genus. Moniliella Stolk & Dakin, Antonie van Leeuwenhoek 32: 399. 1966.

The diagnosis of the family Moniliellaceae is based on the description of the order Moniliellales. The nomenclature of the family is based on the genus Moniliella Stolk & Dakin, Antonie van Leeuwenhoek 32: 399. 1966.

Malasseziomycetes Boekhout, Q.M. Wang & F.Y. Bai, class. nov. — MycoBank MB805514

Type order. Malasseziales R.T. Moore with family Malasseziaceae Denchev & R.T. Moore, Mycotaxon 110: 379. 2009, and genus Malassezia Baillon (1889).

Etymology. The nomenclature of the class is derived from the order name of Malasseziales R.T. Moore, Bot. Mar. 23: 371. 1980, emend. Begerow et al., Mycol. Res. 104: 59. 2000.

Member of Ustilaginomycotina. Sexual morph unknown. Cells are globose, ovoid or cylindrical. Budding is typically monopolar on a more or less broad base, enteroblastic and percurrent. The cell wall is multi-lamellate, and the inner layer of the cell wall is corrugated with a groove spiralling from the bud site. The species are lipid dependent or lipophilic. Sugars are not fermented. Urease and diazonium blue B (DBB) reactions are positive. Coenzyme Q-9 is formed. Xylose is absent in whole-cell hydrolysates.

Acknowledgments

This study was supported by grants No. 31010103902 and No. 30970013 from the National Natural Science Foundation of China (NSFC), KSCX2-YW-Z-0936 from the Knowledge Innovation Program of the Chinese Academy of Sciences and grant No. 10CDP019 from the Royal Netherlands Academy of Arts and Sciences (KNAW). TB is supported by grant NPRP 5-298-3-086 of Qatar Foundation. The authors are solely responsible for the content of this manuscript.

REFERENCES

  • Baillon EH. 1889. Traité de Botanique Médicale Cryptogamique. Doin, Paris. [Google Scholar]
  • Bauer R, Begerow D, Sampaio JP, Weiß M, Oberwinkler F. 2006. The simple-septate basidiomycetes: a synopsis. Mycological Progress 5: 41–66. [Google Scholar]
  • Bauer R, Oberwinkler F, Vánky K. 1997. Ultrastructural markers and systematics in smut fungi and allied taxa. Canadian Journal of Botany 75: 1273–1314. [Google Scholar]
  • Bauer R, Oberwinkler F, Piepenbring M, Berbee ML. 2001. Ustilaginomycetes. In: McLaughlin DJ, McLaughlin EG, Lemke PA. (eds), Systematics and evolution. The mycota VII part B: 57–83 Springer-Verlag, Berlin. [Google Scholar]
  • Begerow D, Bauer R, Boekhout T. 2000. Phylogenetic placements of ustilaginomycetous anamorphs as deduced from nuclear LSU rDNA sequences. Mycology Research 104: 53–60. [Google Scholar]
  • Begerow D, Bauer R, Oberwinkler F. 1997. Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxa. Canadian Journal of Botany 75: 2045–2056. [Google Scholar]
  • Begerow D, Stoll M, Bauer R. 2006. A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data. Mycologia 98: 906–916. [PubMed] [Google Scholar]
  • Boekhout T. 1991. A revision of ballistoconidia-forming yeasts and fungi. Studies in Mycology 33: 1–194. [Google Scholar]
  • Boekhout T. 1995. Pseudozyma bandoni emend. Boekhout, a genus for yeast-like anamorphs of Ustilaginales. The Journal of General and Applied Microbiology 41: 359–366. [Google Scholar]
  • Boekhout T. 1998. Diagnostic descriptions and key to presently accepted heterobasidiomycetous genera. In: Kurtzman CP, Fell JW. (eds), The yeasts, a taxonomic study, 4th ed: 627–634 Elsevier, Amsterdam. [Google Scholar]
  • Boekhout T, Fell JW, O’Donnell K. 1995. Molecular systematics of some yeast-like anamorphs belonging to the Ustilaginales and Tilletiales. Studies in Mycology 38: 175–183. [Google Scholar]
  • Boekhout T, Fonseca A, Sampaio JP, Bandoni RJ, Fell JW, et al. 2011. Discussion of teleomorphic and anamorphic basidiomycetous yeasts. In: Kurtzman CP, Fell JW, Boekhout T. (eds), The yeasts, a taxonomic study, 5th ed: 1339–1372 Elsevier, Amsterdam. [Google Scholar]
  • Boekhout T, Theelen B, Houbraken J, Robert V, Scorzetti G, et al. 2003. Novel anamorphic mite-associated fungi belonging to the Ustilaginomycetes: Meira geulakonigii gen. nov., sp. nov., Meira argovae sp. nov. and Acaromyces ingoldii gen. nov., sp. nov. International Journal of Systematic and Evolutionary Microbiology 53: 1655–1664. [PubMed] [Google Scholar]
  • Boekhout T, Yamada Y, Weijman ACM, Roeijmans HJ, Batenburg-van der Vegte WH. 1992. The significance of coenzyme Q, carbohydrate composition and septal ultrastructure for the taxonomy of ballistoconidia-forming yeasts and fungi. Systematic and Applied Microbiology 15: 1–10. [Google Scholar]
  • Bolano A, Stinchi S, Preziosi R, Bistoni F, Allegrucci M, et al. 2001. Rapid methods to extract DNA and RNA from Cryptococcus neoformans. FEMS Yeast Research 1: 221–224. [PubMed] [Google Scholar]
  • Denchev CM, Moore RT. 2009. Validation of Malasseziaceae and Ceraceosoraceae (Exobasidiomycetes). Mycotaxon 110: 379–382. [Google Scholar]
  • Dörfler C. 1990. Vergleichende Untersuchungen zum biochemischen Aufbau der Zellwand an Hefestadien von niederen und höheren Basidiomyceten. Bibliotheca Mycologica 129: 1–163. [Google Scholar]
  • Driel KGA van, Humbel BM, Verkleij AJ, Stalpers J, Müller WH, Boekhout T. 2009. Variation of septal pore complex morphology in Cantharellales and Hymenochaetales (Agaricomycotina). Mycology Research 113: 559–576. [PubMed] [Google Scholar]
  • Fell JW, Boekhout T, Fonseca A, Scorzetti G, Statzell-Tallman A. 2000. Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis. International Journal of Systematic and Evolutionary Microbiology 50: 1351–1372. [PubMed] [Google Scholar]
  • Findley K, Oh J, Yang J, Conlan S, Deming C, et al. 2013. Topographic diversity of fungal and bacterial communities in human skin. Nature 498: 367–370. [PMC free article] [PubMed] [Google Scholar]
  • Gaitanis G, Magiatis P, Hantschke M, Bassukas ID, Velegraki A. 2012. The Malassezia genus in skin and systemic diseases. Clinical Microbiology Reviews 25: 106–141. [PMC free article] [PubMed] [Google Scholar]
  • Guého-Kellermann E, Batra R, Boekhout T. 2011. Malassezia Baillon (1889). In: Kurtzman CP, Fell JW, Boekhout T. (eds), The yeasts, a taxonomic study, 5th ed: 1807–1832 Elsevier, Amsterdam. [Google Scholar]
  • Guého-Kellermann E, Boekhout T, Begerow D. 2010. Biodiversity, phylogeny and ultrastructure. In: Boekhout T, Guého E, Mayser P, Velegraki A. (eds), Malassezia and the skin: 17–63 Springer-Verlag, Berlin, Heidelberg. [Google Scholar]
  • Haskins RH. 1975. Septa ultrastructure and hyphal branching in the pleomorphic imperfect fungus Trichosporonoides oedocephalis. Canadian Journal of Botany 53: 1139–1148. [Google Scholar]
  • Haskins RH, Spencer JFT. 1967. Trichosporonoides oedocephalis n. gen., n. sp. I. Morphology, development, and taxonomy. Canadian Journal of Botany 45: 515–520. [Google Scholar]
  • Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, et al. 2007. A higher-level phylogenetic classification of the fungi. Mycology Research 111: 509–547. [PubMed] [Google Scholar]
  • Hocking AD, Pitt JI. 1981. Trichosporonoides nigrescens sp. nov., a new xerophilic yeast-like fungus. Antonie van Leeuwenhoek 47: 411–421. [PubMed] [Google Scholar]
  • Hoog GS de. 1979a. Taxonomic review of Moniliella, Trichosporonoides and Hyalodendron. Studies in Mycology 19: 1–36. [Google Scholar]
  • Hoog GS de. 1979b. The taxonomic position of Moniliella, Trichosporonoides and Hyalodendron – an essay. Studies in Mycology 19: 81–90. [Google Scholar]
  • Hoog GS de, Smith MT. 1998a. Moniliella Stolk & Dakin. In: Kurtzman CP, Fell JW. (eds), The yeasts, a taxonomic study, 4th ed: 785–788 Elsevier, Amsterdam. [Google Scholar]
  • Hoog GS de, Smith MT. 1998b. Trichosporonoides Haskins & Spencer. In: Kurtzman CP, Fell JW. (eds), The yeasts, a taxonomic study, 4th ed: 873–877 Elsevier, Amsterdam. [Google Scholar]
  • Hoog GS de, Smith MT, Rosa CA. 2011. Moniliella Stolk & Dakin (1966). In: Kurtzman CP, Fell JW, Boekhout T. (eds), The yeasts, a taxonomic study, 5th ed: 1837–1846 Elsevier, Amsterdam. [Google Scholar]
  • James TY, Kauff F, Schoch C, Matheny B, Hofstetter V, et al. 2006. Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443: 818–822. [PubMed] [Google Scholar]
  • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution 30: 772–780. [PMC free article] [PubMed] [Google Scholar]
  • Klei I van der, Veenhuis M, Brul S, Klis FM, Groot PWJ de , et al. 2011. Cytology, cell walls and septa: A summary of yeast cell biology from a phylogenetic perspective. In: Kurtzman CP, Fell JW, Boekhout T. (eds), The yeasts, a taxonomic study, 5th ed: 111–128 Elsevier, Amsterdam. [Google Scholar]
  • Martínez AT. 1979. Ultrastructure of Moniliella, Trichosporonoides and Hyalodendron. Studies in Mycology 19: 50–57. [Google Scholar]
  • Martínez AT, Hoog GS de, Smith MT. 1979. Physiological characteristics of Moniliella, Trichosporonoides and Hyalodendron. Studies in Mycology 19: 58–68. [Google Scholar]
  • Matheny PB, Gossman JA, Zalar P, Arun Kumar TK, Hibbett DS. 2006. Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota. Canadian Journal of Botany 84: 1794–1805. [Google Scholar]
  • Moore RT. 1980. Taxonomic proposals for the classification of marine yeasts and other yeast-like fungi including the smuts. Botanica Marina 23: 361–373. [Google Scholar]
  • Posada D, Crandall KA. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817–818. [PubMed] [Google Scholar]
  • Prillinger H, Lopandic K, Suzuki M, Kock JLF, Boekhout T. 2011. Chemotaxonomy of yeasts. In: Kurtzman CP, Fell JW, Boekhout T. (eds), The yeasts, a taxonomic study, 5th ed: 129–136, Elsevier, Amsterdam. [Google Scholar]
  • Ronquist F, Teslenko M, Mark P van der, Ayres D, Darling A, et al. 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542. [PMC free article] [PubMed] [Google Scholar]
  • Rosa CA, Jindamorakot S, Limtong S, Nakase T, Lachance MA, et al. 2008. Synonymy of the yeast genera Moniliella and Trichosporonoides and proposal of Moniliella fonsecae sp. nov. and five new species combinations. International Journal of Systematic and Evolutionary Microbiology 59: 425–429. [PubMed] [Google Scholar]
  • Scorzetti G, Fell JW, Fonseca A, Statzell-Tallman A. 2002. Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions. FEMS Yeast Research 2: 495–517. [PubMed] [Google Scholar]
  • Stolk AC, Dakin JC. 1966. Moniliella, a new genus of Moniliales. Antonie van Leeuwenhoek 32: 399–409. [PubMed] [Google Scholar]
  • Sugita T, Suzuki M, Goto S, Nishikawa A, Hiruma M, et al. 2010. Quantitative analysis of the cutaneous Malassezia microbiota in 770 healthy Japanese by age and gender using a real-time PCR assay. Medical Mycology 48: 229–233. [PubMed] [Google Scholar]
  • Sun S, Hagen F, Xu J, Dawson T, Heitman J, et al. 2013. Ecogenomics of human and animal basidiomycetous yeast pathogens. In: Martin F. (ed), The ecological genomics of fungi: 215–242 Wiley & Sons. [Google Scholar]
  • Swofford DL. 2002. PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Sinauer Associates, Sunderland MA. [Google Scholar]
  • Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56: 564–577. [PubMed] [Google Scholar]
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony methods. Molecular Biology and Evolution 28: 2731–2739. [PMC free article] [PubMed] [Google Scholar]
  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24: 4876–4882. [PMC free article] [PubMed] [Google Scholar]
  • Wang QM, Bai FY, Zhao JH, Jia JH. 2003. Bensingtonia changbaiensis sp. nov. and Bensingtonia sorbi sp. nov., novel ballistoconidium-forming yeast species from plant leaves. International Journal of Systematic and Evolutionary Microbiology 53: 2085–2089. [PubMed] [Google Scholar]
  • Weijman ACM. 1979. Carbohydrate patterns of Moniliella, Trichosporonoides and Hyalodendron. Studies in Mycology 19: 76–80. [Google Scholar]
  • Weiß M, Bauer R, Begerow D. 2004. Spotlights on heterobasidiomycetes. In: Agerer R, Piepenbring M, Blanz P. (eds), Frontiers in basidiomycote mycology: 7–48 IHW Verlag, Eching. [Google Scholar]
  • Xu J, Saunders CW, Hu P, Grant RA, Boekhout T, et al. 2007. Dandruff-associated Malassezia species reveals convergent and divergent virulence traits with plant and human fungal pathogens. Proceedings of the National Academy of Sciences of the United States of America 104: 18730–18735. [PMC free article] [PubMed] [Google Scholar]
Articles from Persoonia : Molecular Phylogeny and Evolution of Fungi are provided here courtesy of Naturalis Biodiversity Center & Centraalbureau voor Schimmelcultures