an overview of the higher level classification of

An overview of the higher level classification of Pucciniomycotina based oncombined analyses of nuclear large and small subunit rDNA sequences

M. Catherine Aime1

USDA-ARS, Systematic Botany and Mycology Lab,Beltsville, Maryland 20705

P. Brandon MathenyBiology Department, Clark University, Worcester,Massachusetts 01610

Daniel A. HenkUSDA-ARS, Systematic Botany and Mycology Lab,Beltsville, Maryland 20705

Elizabeth M. FriedersDepartment of Biology, University of Wisconsin,Platteville, Wisconsin 53818

R. Henrik NilssonGoteborg University, Department of Plant andEnvironmental Sciences, Goteborg, Sweden

Meike PiepenbringJ.W. Goethe-Universitat Frankfurt, Department ofMycology, Frankfurt, Germany

David J. McLaughlinDepartment of Plant Biology, University of Minnesota,St Paul, Minnesota 55108

Les J. SzaboUSDA-ARS, Cereal Disease Lab, University ofMinnesota, St Paul, Minnesota 55108

Dominik BegerowUniversitat Tubingen, Spezielle Botanik und Mykologie,Tubingen, Germany

Jose Paulo SampaioCREM, SABT, Faculdade de Ciencias e Tecnologia,Universidade Nova de Lisboa, 2829-516 Caparica,Portugal

Robert BauerMichael WeißFranz Oberwinkler

Universitat Tubingen, Spezielle Botanik und Mykologie,Tubingen, Germany

David HibbettBiology Department, Clark University, Worcester,Massachusetts 01610

Abstract: In this study we provide a phylogeneticallybased introduction to the classes and orders ofPucciniomycotina (5Urediniomycetes), one of three

subphyla of Basidiomycota. More than 8000 species ofPucciniomycotina have been described includingputative saprotrophs and parasites of plants, animalsand fungi. The overwhelming majority of these(,90%) belong to a single order of obligate plantpathogens, the Pucciniales (5Uredinales), or rustfungi. We have assembled a dataset of previouslypublished and newly generated sequence data fromtwo nuclear rDNA genes (large subunit and smallsubunit) including exemplars from all known majorgroups in order to test hypotheses about evolutionaryrelationships among the Pucciniomycotina. Theutility of combining nuc-lsu sequences spanning theentire D1-D3 region with complete nuc-ssu sequencesfor resolution and support of nodes is discussed. Ourstudy confirms Pucciniomycotina as a monophyleticgroup of Basidiomycota. In total our results supporteight major clades ranked as classes (Agaricostilbo-mycetes, Atractiellomycetes, Classiculomycetes, Cryp-tomycocolacomycetes, Cystobasidiomycetes, Microbo-tryomycetes, Mixiomycetes and Pucciniomycetes) and18 orders.

Key words: basidiomycetes, molecular phylo-genetics, parasitic fungi, rDNA systematics, Uredi-niomycetes

INTRODUCTION

One-third of described Basidiomycota belong tosubphylum Pucciniomycotina (5Urediniomycetessensu Swann and Taylor 1995). Roughly 7000 ofthese, or ,90%, belong to a single order, Pucciniales(5Uredinales G. Winter) or the rust fungi (Kirk et al2001). The remaining fungi within the Pucciniomy-cotina are remarkably diverse ecologically, biological-ly and physiologically; only with the relatively recentadvent of ultrastructure, biochemical and molecularsystematic studies have the relatedness of the variedfungi now placed in the Pucciniomycotina becomeapparent. These include Microbotryales, phytopatho-gens once classified in the Ustilaginomycotina (truesmuts and relatives, Ustilaginomycetes sensu Bauer etal 2001); numerous basidiomycetous yeasts formerlyallied with Auriculariales and other groups ofAgaricomycotina (mushroom-forming fungi and re-lated taxa; Hymenomycetes sensu Swann and Taylor1993); and at least one species, Mixia osmundae,formerly classified within the Ascomycota (Nishidaet al 1995).

Acepted for publication 7 September 2006.1 Corresponding author. E-mail: [email protected]

Mycologia, 98(6), 2006, pp. 896–905.# 2006 by The Mycological Society of America, Lawrence, KS 66044-8897

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Most species of Pucciniomycotina are parasitic andthe group includes phytopathogens (e.g. Pucciniales,Microbotryales), mycoparasites (e.g. Tuberculina,Spiculogloea) and entomopathogens (e.g. Septobasi-diales). A few are putatively saprotrophic or are ofunknown trophic habit. Pucciniomycotina species arepresent in most habitats including freshwater (Baueret al 2003) and marine environments (Swann et al2001). Dimorphism, cryptic fructifications, heteroe-cism and multiple spore types all have evolved in atleast some lineages of Pucciniomycotina, hamperingthe collection of complete biological and life cycledata for many taxa. Yet species of Pucciniomycotinaare causal agents of some of the most devastatingdiseases of crops, may cause opportunistic disease inhumans and have shown potential as biologicalcontrol organisms of invasive plants and of otherpathogenic fungi (e.g. Evans 1993, Swann et al 2001).

A few Pucciniomycotina species produce basidio-carps, these typically being simple stipitate-capitate(stilboid) or resupinate (FIG. 1b) structures. SomePucciniomycotina species form hyphae (filamentous)or yeasts or both (dimorphic) (FIG. 1d). Members ofthe Pucciniales produce spore-filled fruiting struc-tures termed sori (FIG. 1f ). Basidia of teleomorphicspecies may take the form of teliospores, holobasidiaor phragmobasidia, and basidiospores may be sessile,gasteroid or forcibly discharged. The Pucciniomyco-tina is distinguished from the other two major cladesof Basidiomycota by the possession of simple septalpores that lack membrane-bound caps (Swann et al2001, Weiß et al 2004 and references therein). Inaddition the cell wall sugar composition of thePucciniomycotina differs from that in the Ustilagino-mycotina and Agaricomycotina (Prillinger et al2002).

Diverse approaches have been used to delimit taxawithin the Pucciniomycotina, including studies ofultrastructural, physiological, biochemical and eco-logical characters. Molecular characters have hada major impact on our understanding of thephylogenetic relationships of Pucciniomycotina. Asearly as 1985 Gottschalk and Blanz showed that thesecondary structure of 5S ribosomal RNA in somespecies of Pucciniomycotina differs from that of someother lineages of Basidiomycota. The pioneeringstudies of Swann and colleagues (Swann and Taylor1993, 1995; Swann et al 1999) used nuclear smallsubunit (nuc-ssu) rDNA sequences to support themonophyly of the Pucciniomycotina and a number ofmajor clades. Other studies have employed a regionof about 500–650 bp at the 59 end of the nuclear largesubunit (nuc-lsu) rDNA, containing the highly vari-able divergent domains D1 and D2 (Hassouna et al1984) providing resolution for many clades within the

Pucciniomycotina (e.g. Fell et al 2001, Weiß et al2004, Bauer et al 2006). However D1–D2 sequenceshave provided only weak support for monophyly ofPucciniomycotina (Begerow et al 1997, Berres et al1995), or have resolved the group as a paraphyleticassemblage from which the Ustilaginomycotina andAgaricomycotina have been derived (Weiß et al 2004).Nor were analyses of a third gene, that coding for b-tubulin, able to recover a monophyletic Pucciniomy-cotina (Begerow et al 2004). Because of the publisheddiscrepancies in tree topologies and support values,monophyly for the group has yet to be establishedconclusively by molecular analyses.

Current major classifications of Pucciniomycotinainclude those of Kirk et al (2001), Swann et al (2001),Weiß et al (2004) and Bauer et al (2006). The latterthree classifications have many similarities (SUPPLE-

MENTARY TABLE I). However there are also differencesbetween these systems in both resolution andcomposition of taxa. Kirk et al (2001) divide thePucciniomycotina (as Urediniomycetes) into fiveorders and do not include subclasses; thus theirclassification is quite different from the others.

The goal of the present study is to reassess thehigher level systematics of the Pucciniomycotina withcombined analyses of nuc-lsu rDNA and nuc-ssurDNA sequences. Two other studies have includeda simultaneous analysis of nuc-lsu and nuc-ssu rDNAsequences of Pucciniomycotina (Lutzoni et al 2004,Bauer et al 2006). However the former was focused onrelationships across the Fungi and it included only 14species of Pucciniomycotina, of which 10 weremembers of the Pucciniales and the combinedanalysis in the latter employed only 25 species ofPucciniomycotina and did not cover all majorlineages. In the present study we compile and analyzedatasets containing new and previously publishedsequences that represent 174 species from all majorgroups of Pucciniomycotina. We assess the ability ofdifferent rDNA genes and gene regions to recoverand support each clade, and we provide an overviewof the classes and orders of Pucciniomycotina.

MATERIALS AND METHODS

This study uses both newly generated sequences andsequences that were retrieved from GenBank from morethan 80 studies (SUPPLEMENTARY TABLE II). Some Pucci-niales sequences were generated with the methods de-scribed in Aime (2006); sequences of Jola spp. weregenerated as in Frieders (1997). Descriptions of laboratorymethods pertaining to the majority of new sequencesproduced at Clark University can be found online (SUPPLE-

MENTARY APPENDIX 1).The entire data matrix contains 208 operational taxo-

nomic units (OTUs) including six Ascomycota that were

AIME ET AL: PUCCINIOMYCOTINA OVERVIEW 897

FIG. 1. Representatives of the Pucciniomycotina. a. Jola cf. javensis (Platygloeales) fruiting on Sematophyllum swartzii. b.Septobasidium burtii (Septobasidiales) fungal mat completely covering scale insects. c. Eocronartium muscicola (Platygloeales)fruiting on undetermined moss. d. Yeast and filamentous cells of Sporidiobolus pararoseus (Sporidiobolales). e. Cultures of twoSporidiobolus species in the S. pararoseus clade (Sporidiobolales). f. Phragmidium sp. (Pucciniales) on Rosa rubiginosa.

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used for rooting purposes, nine Ustilaginomycotina, fourAgaricomycotina and 189 Pucciniomycotina that represent174 species (26 species of Pucciniomycotina are representedby two OTUs and one species is represented by threeOTUs). One OTU, Septobasidium sp., is represented bya nuc-lsu rDNA sequence deposited as Septobasidium sp. anda nuc-ssu rDNA sequence deposited as Septobasidiumcanescens. All other OTUs include sequences from the sameputative species and where possible from the samecollection or isolate (SUPPLEMENTARY TABLE II). Alignmentsare available from the first and/or last author on request.We performed analyses using two sets of OTUs. Dataset 1contains the 128 OTUs that have both nuc-lsu and nuc-ssurDNA, including all the Ascomycota, Ustilaginomycotinaand Agaricomycotina, and 109 Pucciniomycotina thatinclude representatives of all the major groups in theclassifications of Swann et al (2001), Weiß et al (2004) andBauer et al (2006) except the Cryptomycocolacomycetes.Dataset 2 contains all 208 OTUs, 74 of which have only nuc-lsu rDNA, including Cryptomycocolax abnormis (Cryptomy-cocolacomycetes), and six OTUs that have only the nuc-ssurDNA. To compare the phylogenetic utility of the short(D1–D2 region only) versus long (D1–D3 region, seeSUPPLEMENTARY APPENDIX 1) nuc-lsu rDNA sequences, aswell as various combinations of data, we assembled a thirddataset (Dataset 3) that contains 20 Pucciniomycotina andtwo other Basidiomycota that have nuc-lsu rDNA sequencesof at least 1117 bp and nuc-ssu rDNA sequences of at least1667 bp (indicated by an asterisk in SUPPLEMENTARY TABLE

II). Datasets were analyzed with equally weighted maximumparsimony (MP); Dataset 1 also was analyzed with neighborjoining (NJ) and Bayesian methods. (Details of analyticalmethods are provided online in SUPPLEMENTARY APPENDIX

1.)

RESULTS AND DISCUSSION

MP analyses of Dataset 1 recovered 36 trees of 8215steps (CI 5 0.345, RI 5 0.731), one of which isdepicted (FIG. 2, an expanded version is available inonline supplementary materials). MP analyses ofDataset 2 recovered 1000 trees of 9748 steps (CI 5

0.310, RI 5 0.729); the strict consensus tree forDataset 2 is presented (SUPPLEMENTARY FIG. 3).Detailed results and discussion of analyses for allthree datasets are provided online (SUPPLEMENTARY

APPENDIX 2).This work brings together data from more than 80

studies along with newly generated data to providethe first multigene molecular analyses for all majorclades of Pucciniomycotina. The present study strong-ly supports monophyly of the Pucciniomycotina(FIG. 2). We recover eight major clades containing18 subclades (SUPPLEMENTARY FIG. 3), which mostclosely correspond to the classification of Bauer et al(2006). All higher taxa of Pucciniomycotina recog-nized in the present study are supported by bootstrapvalues of at least 90% in one or more of our analyses

and have Bayesian posterior probabilities of at least0.98 with the exception of the Sporidiobolales,Agaricostilbomycetes including Spiculogloeales, andthe Cryptomycocolacales which is represented by onlya single nuc-lsu sequence (SUPPLEMENTARY FIG. 3).

The names of higher taxa used here follow theclassification formalized in Bauer et al (2006). Theclassification of Bauer et al (2006) is different fromearlier classifications (SUPPLEMENTARY TABLE I) in thatmore groups are named and recognized as formaltaxa (e.g. Cystobasidiomycetes); groups formerlyranked as subclasses were elevated to the rank ofclass (e.g. Microbotryomycetes); and higher levelnames prefixed ‘‘Uredinio-’’ or ‘‘Uredin-’’ have beenreplaced by names based on Puccinia, the largestgenus within the Pucciniomycotina (Kirk et al 2001).

Many of the genera of Pucciniomycotina are notmonophyletic, notably anamorphic yeasts such asRhodotorula and Sporobolomyces (Weiß et al 2004,FIG. 2). One of the obvious obstacles to diagnosePucciniomycotina taxa is the homoplasious nature ofthe micromorphological characters available (Bauerand Oberwinkler 1991a, Bauer et al 2006). Ultrastruc-tural characters, for example, structure of spindlepole body or the presence of colacosomes in manyMicrobotryomycetes (Swann et al 1999) appearpromising for delimiting natural groups. However atpresent the major obstacle to applying meaningfuldiagnoses to these groups is the dearth of ultrastruc-tural, ecological and life-cycle data for most Pucci-niomycotina members.

Descriptions of higher level taxa.—Pucciniomycetes. Thisis the most speciose class of Pucciniomycotina. Wehave resolved four orders (Helicobasidiales, Platy-gloeales s. str., Pucciniales and Septobasidiales). Afifth order, Pachnocybales (Bauer et al 2006), isrepresented by a single species, Pachnocybe ferruginea(SUPPLEMENTARY FIG. 3) although molecular evidencefrom other studies places this taxon within theSeptobasidiales (Berres et al 1995, Frieders 1997,Henk and Vilgalys 2006). With the exception of P.ferruginea, which as a holobasidia-producing sapro-troph (Kropp and Corden 1986, Bauer and Ober-winkler 1990) holds an isolated position within theclass, and Platygloea disciformis, which may besaprotrophic, all known members are parasitic andproduce phragmobasidia or teliospores.

The members of the Helicobasidiales producea dikaryophase (Helicobasidium) that is parasitic onplant roots and a haplophase (Tuberculina) that isparasitic on rust fungi (Lutz et al 2004b). Species ofTuberculina are capable only of infecting rusts in thehaploid stage of development (Thirumalachar 1941)and the host-specificity of some species (Lutz et al


FIG. 2. Phylogenetic relationships in the Pucciniomycotina based on analyses of Dataset 1 (128 OTUs, each with nuc-lsurDNA and nuc-ssu rDNA sequences). Phylogram representing one of 36 equally most parsimonious trees (8215 steps, CI 5

0.345, RI 5 0.731). Nodes with asterisks collapse in the strict consensus of equally most parsimonious trees. Support valuesinclude MP bootstrap frequencies above 70% (first value, before slash), NJ bootstrap frequencies above 70% (second value)

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2004a) might make them candidates for biocontrol.Lutz et al (2004c) discuss the confused taxonomichistory of Tuberculina. The position of H. corticioidescould not be confirmed with nuc-ssu data alone(SUPPLEMENTARY FIG. 3).

Until relatively recently all basidiomycetes withtransversely septate basidia (termed auricularioid)were classified in the rusts, smuts (Ustilaginales) orAuriculariales (Agaricomycotina). Moore (1990) cre-ated the Platygloeales by removing those species thatproduced simple (rather than dolipore) septal poresfrom the Auriculariales. The order now is consideredto contain mostly phytoparasitic species in the generaPlatygloea, Insolibasidium, Herpobasidium, Eocronar-tium and Jola. These last two genera include speciesthat are parasitic on mosses, produce conidia anddevelop basidiomata which, in the case of Eocronar-tium, are clavarioid fruiting bodies that may reach upto 15 mm tall (Atkinson 1902, Frieders and McLaugh-lin 2001) (FIG. 1a, c). Fitzpatrick (1918) providesdescriptions and illustrations of the life cycle,cytology, host-range and taxonomy of E. muscicola,and the host-parasite interaction is described inBoehm and McLaughlin (1988). The columnar typeof fructification (FIG. 1c) similar to that of the rustgenus Cronartium led Atkinson (1902) to hypothesizea close relationship between Eocronartium and thePucciniales, which is supported by molecular analyses(FIG. 2). The unsupported association of Platygloeapustulata with the Septobasidiales (SUPPLEMENTARY

FIG. 3) might be an artifact of our supermatrixapproach (see SUPPLEMENTARY APPENDIX 2) for whichadditional gene sampling might be necessary toresolve.

Species of Septobasidiales are unique in that theyare parasites of scale insects. This is the second largestorder of Pucciniomycotina, with more than 170described species (Kirk et al 2001), nearly all ofwhich belong to the genus Septobasidium. Theprincipal reference is Couch’s 1938 publication‘‘The Genus Septobasidium’’. These fungi are foundas mats of hyphae covering infected scale insects onplants (FIG. 1b). The life cycle (SUPPLEMENTARY FIG. 4)of Septobasidium has been relatively well characterizedand includes the only known occurrence of a yeaststage in the Pucciniomycetes. Members of the orderlive primarily as dikaryons and undergo meiosis

within probasidia (Couch 1938, Olive 1943). Auricu-loscypha, Coccidiodictyon, Uredinella and Ordonia arethe other genera included in the Septobasidiales(Oberwinkler 1989, Henk and Vilgalys 2006).

Pucciniales species are obligate parasites of vascularplants (FIG. 1f) and have developed the mostcomplex life cycles of any Fungi (Cummins andHiratsuka 2003) (SUPPLEMENTARY FIG. 5). Rusts arephenotypically and genetically plastic organisms withmany characters that set them apart from otherBasidiomycota including the development of spermo-gonia, heteroecism and the occurrence of up to sixdifferent spore types (Laundon 1973, Hennen andBuritica 1980, Cummins and Hiratsuka 2003). Ap-proximately 115 (Cummins and Hiratsuka 2003) to163 (Kirk et al 2001) genera of Pucciniales currentlyare recognized and family classification remainscontentious (Hennen and Buritica 1980, Ono andHennen 1983, Kirk et al 2001). Three recent studiesof molecular data from nuc-lsu (Maier et al 2003),nuc-ssu (Wingfield et al 2004) and combined nucrDNA genes (Aime 2006) have provided confirmationfor some families (e.g. Melampsoraceae) and high-lighted others requiring revision (e.g. Pucciniaceae).The origins of the Pucciniales and their relationshipto other Basidiomycota have been a ripe field forconjecture. Many early hypotheses of basidiomyceteevolution consider Pucciniales as the most ‘‘primi-tive’’ Basidiomycota from which all other lineages arederived (e.g. Linder 1940, Savile 1955). Our resultsconfirm other molecular studies (Prillinger et al 2002,Lutzoni et al 2004) that show the Pucciniales asderived from lineages that include insect and non-vascular plant parasites (FIG. 2).

Cystobasidiomycetes.—Our data resolve two orders ofCystobasidiomycetes. A third order, Naohideales, hasbeen proposed (Bauer et al 2006) but it is hererepresented solely by nuc-lsu sequences of Naohideasebacea, a mycoparasite (SUPPLEMENTARY FIG. 3).Three mostly monotypic taxa, Sakaguchia (isolatedfrom marine habitats), Cyrenella and Bannoa, cannotbe placed into orders with our data. The Cystobasi-diales include both anamorphic yeasts and dimorphicyeasts that produce clamp connections and auricular-ioid basidia without basidiocarps. Genera included inthis order are Occultifur (O. internus is a mycoparasite

rand Bayesian posterior probabilities above 0.70 (below branch). Outgroup taxa are condensed into a single branch forAscomycota (six taxa represented); Agaricomycotina (four taxa represented); Ustilaginomycotina (nine taxa represented).Duplicate sequences have been collapsed into a single branch, which are indicated in parentheses after the taxon name, e.g.Occultifer externus (2). The small cladogram depicts the topology of Microbotryomycetidae obtained in Bayesian analyses, withposterior probabilities indicated only for strongly supported nodes that conflict with the MP topology. (An expanded versionof FIG. 2 is presented in the online supplementary materials).


of Dacrymycetales, Bauer et al 2006), Cystobasidium(which like Occultifur produces tremelloid haustorialcells that are indicative of mycoparasitism) andsome Rhodotorula spp. (anamorphic yeasts). TheErythrobasidiales include many yeasts currentlyplaced in Rhodotorula pro parte (p.p.) and Sporobo-lomyces p.p., as well as the monotypic mitosporic yeastErythrobasidium. Other studies (Sampaio 2004, Baueret al 2006) support the inclusion of Bannoa within theErythrobasidiales. No teleomorph has been found inthis order.

Atractiellomycetes.—The Atractiellomycetes containa single order, Atractiellales, originally erected toaccommodate gasteroid auricularioid species withsimple septa formerly placed in the Auriculariales(Oberwinkler and Bandoni 1982). Walker (1984)and Gottschalk and Blanz (1985) recognized theartificiality of this group, which, as supported by ourdata, is limited to include the genera Atractiella,Saccoblastia, Hobsonia, Pleurocolla, Helicogloea, Platy-gloea p.p. and Phleogena. No yeast state is known forthese fungi (Swann et al 2001) but some may produceconidia. Atractiella and Phleogena produce stilboidfruitbodies. All members of this class studied thus farpossess unique ultrastructural organelles of unknownfunction termed symplechosomes (Oberwinkler andBauer 1989, McLaughlin 1990, Bauer and Oberwink-ler 1991b).

Agaricostilbomycetes.—Our data strongly supporta monophyletic Agaricostilbales that is supported assister of the Spiculogloeales in Bayesian analyses(FIG. 2). Blanz and Gottschalk (1986) found thatstructure of the 5S rRNA in Agaricostilbum pulcherri-mum, a small gasteroid fungus found worldwide onpalms, was unique from all examined basidiomycetesand posited that this taxon held an isolated positionwithin the heterobasidiomycetes. Agaricostilbum isalso unusual in that the nuclei divide in the parentcell rather than in the bud cell (Frieders andMcLaughlin 1996), and a similar mitotic pattern wasfound in the closely related Stilbum vulgare but not inthe more distantly related (SUPPLEMENTARY FIG. 3)yeast Bensingtonia yuccicola (McLaughlin et al 2004).The yeast phase of the life cycle of A. pulcherrimum isillustrated in Frieders and McLaughlin (1996). Othergenera placed in the Agaricostilbales include Ben-singtonia, Kondoa, Sterigmatomyces, Sporobolomycesp.p., Chionosphaera, Stilbum, Mycogloea p.p. andKurtzmanomyces. These include gasteroid yeasts withauricularioid basidia (e.g. Agaricostilbum hyphaenes),gasteroid yeasts with holobasidia (e.g. Chionosphaeraapobasidialis), and teliospore-forming yeasts (e.g.Kondoa malvinella). Chionosphaera species produceclamps and microscopic stipitate-capitate fruiting

structures and are mycophilic, associated with lichensand beetle gallery fungi (Kirschner et al 2001a).

The order Spiculogloeales has been placed withinthe Agaricostilbomycetes by Bauer et al (2006) andcontains Mycogloea p.p., Spiculogloea and someanamorphic Sporobolomyces spp. Characters sharedby the teleomorphic species of this order includedimorphism, mycoparasitism and tremelloid hausto-rial cells subtended by clamp connections (Bandoni1998). Mycogloea does not appear monophyletic withthese data (SUPPLEMENTARY FIG. 3) and additionalmolecular (combined nuc-lsu and nuc-ssu sequencescould not be obtained for any Spiculogloea orMycogloea species for this study) and taxonomicsampling, including the type species of Mycogloea,are needed to resolve their placement.

Microbotryomycetes.—This group includes mycopara-sites, phytopathogens and putative saprotrophs witha diversity of micromorphological characters. Manyspecies contain organelles, termed colacosomes, thatare associated with mycoparasitism (Bauer andOberwinkler 1991a). Four orders are recognized:Heterogastridiales (Oberwinkler et al 1990b), whichare mycoparasites and include the aquatic genusHeterogastridium; Leucosporidiales (Sampaio et al2003), which includes the teliospore-forming yeastLeucosporidium and two other genera, Mastigobasi-dium and Leucosporidiella; the Sporidiobolales (Sam-paio et al 2003), including the genera Rhodotorulap.p., Sporidiobolus (FIG. 1d, e), Sporobolomyces p.p. andRhodosporidium (a teliospore-forming yeast illustratedin SUPPLEMENTARY FIG. 6); and the Microbotryales(Bauer et al 1997). Members of Microbotryales areteliospore-forming phytopathogens that once wereclassified within the Ustilaginomycotina and includethe genera Bauerago, Fulvisporium, Aurantiosporium,Rhodotorula p.p., Ustilentyloma, Liroa, Microbotryumand Sphacelotheca. Microbotryum violaceum has be-come an important model organism for co-evolution-ary and population genetics studies between patho-gens and their hosts (e.g. Antonovics et al 2002).

Additional taxa that belong to this class but couldnot be assigned to an order are Colacogloea (amonotypic, mycoparasitic genus that possesses colaco-somes, Oberwinkler et al 1990a), Kriegeria (a mono-typic sedge parasite with an anamorphic yeast stageand unique multiperforate septa, Doubles andMcLaughlin 1991, Swann et al 1999), Camptobasidium(a monotypic aquatic hyphomycete associated withdecaying leaf litter, Marvanova and Suberkropp1990), Rhodotorula p.p., Sporobolomyces p.p., Bensing-tonia yamatoana and Leucosporidium antarcticum.

Classiculomycetes.—This class contains a single order,the Classiculales, containing aquatic fungi of fresh-

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water habitats (Bauer et al 2003). Classicula fluitans isthe teleomorph of the hyphomycete Naiadellafluitans and produces auricularioid basidia and clampconnections. Jaculispora submersa is an aquatic hy-phomycete for which no teleomorph has beendiscovered. Classicula is unique in forming subapi-cally swollen sterigmata (Bauer et al 2003). Classiculafluitans forms tremelloid haustorial cells that wereobserved to occasionally self-parasitize in culture,which might indicate a mycoparasitic habit for thisfungus (Bauer et al 2003).

Cryptomycocolacomycetes.—This class contains a singleorder, Cryptomycocolacales, represented by the ge-nus Cryptomycocolax, a mycoparasitic fungus thatinfects ascomycete sclerotia (Oberwinkler and Bauer1990) and has been placed in the Ustilaginomycotina(Kirk et al 2001). Our study confirms the placementof this clade within the Pucciniomycotina (SUPPLE-

MENTARY FIG. 3). Cryptomycocolacales species are theonly fungi outside the Microbotryomycetes thatpossess colacosomes, which might indicate a sistergroup relationship between the two. Cryptomycocolaxhas a unique mode of basidium development that onthe other hand might be indicative of a basal positionwithin the Pucciniomycotina (Oberwinkler and Bauer1990). Transmission electron microscopy studies ofanother genus of colacosome-producing mycopara-sites, Colacosiphon, indicate that it belongs in theCryptomycocolacales (Kirschner et al 2001b). Bothgenera are monotypic.

Mixiomycetes.—This class, containing the Mixiales, ismonotypic containing a single fern parasite, Mixiaosmundae. Until recently M. osmundae was classifiedwithin the Ascomycota (Nishida et al 1995) andremains isolated within the Pucciniomycotina with noknown close relatives (Swann et al 1999, 2001; FIG. 2).Mixia osmundae is a blastosporic yeast, although it hasnot been established whether it produces meiosporesor mitospores. The hyphae are multinucleate contain-ing few septa (Kramer 1958, Nishida et al 1995, Swannet al 2001).

Incertae sedis.—Reniforma strues was isolated frombiofilms in a wastewater treatment plant in WestVirginia (Pore and Sorenson 1990). It is a yeast that,unlike any other known basidiomycete, produceskidney-shaped (reniform) somatic cells. Its classifica-tion within the Basidiomycota is confirmed with thesedata, yet its position within the Pucciniomycotinacould not be fully resolved with nuc-lsu data alone(SUPPLEMENTARY FIG. 3).

Concluding remarks.—While our results provide thefirst support for many of the higher level clades ofPucciniomycotina formalized in the classification of

Bauer et al (2006), many nodes, especially along thebackbone, still are not resolved. Future molecularsystematic studies aimed at filling in missing datain Dataset 2 and targeting additional gene regionsfor exemplar taxa from all the groups recovered bythis study should be the next steps toward recoveringa robust phylogenetic hypothesis for these fungi. Ad-ditional taxonomic sampling might benecessary before a fully resolved phylogeny for thePucciniomycotina is attainable. However, excludingthe Pucciniales, we have sampled 54 genera, or nearlythe entire known generic diversity in the subphylum(Kirk et al 2001). The Pucciniales is often consideredone of the best documented groups of fungi. Yetrecent estimates indicate that only 10–30% of theirdiversity in the neotropics alone has been discovered(Hennen and McCain 1993). Many genera ofPucciniomycotina have been discovered and de-scribed only since the 1990s, often from specialtyniches (e.g. beetle galleries, biofilms) or neotropicalhabitats (e.g. Oberwinkler and Bauer 1990; Ober-winkler et al 1990a, 1990b; Pore and Sorenson 1990;Kirschner et al 2001a, 2001b; Sampaio et al 2003).Furthermore many of these are representative oflineages that are monotypic or problematic withregard to phylogenetic resolution (e.g. Reniformastrues). This would indicate that a tremendousamount of diversity still awaits discovery within thisubiquitous group of fungi.

ACKNOWLEDGMENTS

The authors thank Conrad Schoch and CBS for providingseveral cultures and Pat Crane for Pucciniales material usedfor the generation of sequence data. We thank Rytas Vilgalysand Lisa Bukovnik for access to the DNA sequencing facilityat Duke University, Cindy Park for technical support atSBML and Manfred Binder for assistance with Bayesiananalyses. This work was supported in part by grants from theNational Science Foundation, DEB 0228657, DBI 0320875and DEB-0090301, Research Coordination Network: APhylogeny for Kingdom Fungi to M. Blackwell, J.W.Spatafora and J.W. Taylor. Mention of trade names orcommercial products in this publication is solely for thepurpose of providing specific information and does notimply recommendation or endorsement by the U.S. De-partment of Agriculture.

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APPENDIX 1

MATERIAL AND METHODS

DNA extractions, PCR, and sequencing.—New sequenceswere obtained from live or lyophilized cultures, herbariummaterial and fresh collections. DNA was isolated with theEZNA Fungal DNA Kit or EZNA Forensic DNA Kit (OmegaBio-tek, Doraville, Georgia) following the manufacturer’sprotocols. Primer sequences for nuc-ssu are from White et al(1990) and O’Donnell et al (1998) and can be found onlineat http://aftol.org/. Primer pairs PNS1/NS41 and NS19b/NS8 were used to generate two nuc-ssu rDNA products,sequences of which overlap and yield a total product size ofabout 1780 bp. On some occasions NS51 was paired withITS2 to amplify the 39 end of the gene when the primercombination NS19b/NS8 was not optimal. Additionalprimers for sequencing included NS19bc, NS51 and NS6.Due to the presence of multiple introns only partial nuc-ssurDNA sequences were obtained for Colacogloea peniophorae(sample No. 3) and Entyloma holwayi. Only the 18S regionbetween PNS1/NS41 (,1200 bp) at the 59 end of the genewas obtained for Gymnosporangium juniperi-virginianae,Kondoa malvinella, Kuehneola uredinis, Malassezia pachy-dermatis, Sporisorium formosanum and Tilletia controversa.Nuc-lsu rDNA sequences of approximately 1400 bp wereamplified with primers LR0R and LR7 and sequenced withthese primers and LR3R, LR16 and LR5 (Vilgalys andHester 1990; http://www.biology.duke.edu/fungi/mycolab/primers.htm). This region includes the first three divergentdomains (D1–D3) of the large subunit rDNA (Hassouna et al1984, Hopple and Vilgalys 1999) as opposed to mostpublished Pucciniomycotina nuc-lsu rDNA sequences, whichconsist of the first ,600 bp of the region containing thefirst two divergent domains (D1–D2). In several instances,especially for taxa of the Pucciniales, LR16 was not a suitablesequencing primer. For Pileolaria toxicodendri individualnuc-lsu rDNA amplicons were cloned with the TOPO TAcloning kit (Invitrogen, Carlsbad, California) but in all othercases the PCR products were sequenced directly. DNAsequencing reactions were performed with ABI Prism dyeterminator chemistry and were run on an ABI 377XL or 3700automated DNA sequencer (the latter at the DNA sequenc-ing facility of the Duke University Biology Department, R.Vilgalys laboratory).

Assessing conflict.—The nuc-lsu and nuc-ssu rDNA arelinked in the nuclear rDNA repeat, which reduces thechances of phylogenetic conflicts among the loci due tohybridization, lineage sorting or horizontal gene trans-mission. Nevertheless the majority of operational taxonomicunits (OTUs) combine sequences obtained from differentstudies (SUPPLEMENTARY TABLE II) so misidentifications,laboratory errors or differing species concepts could besources of incongruence. To assess conflict we performed1000 replicate bootstrapped neighbor joining (NJ) analysesof the nuc-lsu and nuc-ssu rDNA partitions independently,using PAUP* 4.0b12 (Swofford 2002) with Kimura two-

parameter distances. OTUs with differing placements thatreceived at least 70% NJ bootstrap support in both datapartitions were considered to demonstrate conflict. Poten-tial conflicts were detected between the nuc-lsu and nuc-ssurDNA partitions in Filobasidiella neoformans, Melampsoraeuphorbiae and Mycogloea sp. (trees not shown). One of theconflicting nodes involving F. neoformans was stronglysupported only marginally (bootstrap 5 73%) so the datafor that taxon were combined. The data for M. euphorbiaeand Mycogloea sp. were not combined and only nuc-lsu datawere used for these OTUs in Dataset 2.

Data analyses.—Datasets 1 and 2 were analyzed with equallyweighted maximum parsimony (MP) and bootstrapped MP.Dataset 1 also was analyzed with neighbor joining (NJ) andBayesian methods. MP analyses were implemented inPAUP* with a two-step search strategy consisting of aninitial search with 1000 heuristic searches (each witha starting tree generated by taxon addition with a randomsequence, TBR branch swapping, and keeping up to twotrees per replicate) followed by a second heuristic searchusing the shortest trees found in the initial search as startingtrees, with TBR branch swapping and MAXTREES set to 1000.Bootstrapped MP analyses used 1000 replicates, each withone heuristic search with a starting tree generated byrandom taxon addition, TBR branch swapping, and keepingup to 10 trees per replicate.

Modeltest 3.7 (Posada and Crandall 1998) was used toevaluate models of molecular evolution for use in NJ andBayesian analyses. Optimal models were identified for thenuc-ssu rDNA alone, nuc-lsu rDNA alone and the combineddataset. For each data partition the optimal model accord-ing to the Akaike information criterion was the general timereversible model, with a proportion of invariable sites andamong-site rate heterogeneity modeled with a discretegamma distribution (i.e. the GTR+G+I model). Howeverhierarchical likelihood ratio tests selected the TIM+I+Gmodel for the nuc-ssu rDNA alone and the combineddataset and the TrN+I+G model for the nuc-lsu rDNA datapartition.

NJ and bootstrapped NJ analyses (with 1000 replicates)were implemented in PAUP* with the BIONJ algorithm(Gascuel 1997) with maximum likelihood distances thatwere obtained using the GTR+I+G model. Model parame-ters were fixed based on values obtained from Modeltest, asfollows: base frequencies A 5 0.2498, C 5 0.2045, G 5

0.2772, T 5 0.2685; substitution rates A«C 5 1.1857, A«G5 2.4999, A«T 5 1.5885, C«G 5 1.0903, C«T 5 4.7743,G«T 5 1.0000; proportion of invariable sites 5 0.2680;gamma distribution shape parameter 5 0.5577 (with fourrate classes).

Bayesian analyses were performed using MrBayes 3.0(Ronquist and Huelsenbeck 2003) with the GTR+I+Gmodel with all parameter values allowed to vary. Modelparameters for the nuc-lsu rDNA and nuc-ssu rDNApartitions obtained with Modeltest were similar (values not

shown), so the data were not partitioned. Three indepen-dent Metropolis-coupled Markov chain Monte Carlo anal-yses were performed, each with four chains, three of whichwere ‘‘heated’’ (with default temperature settings). Eachanalysis was run 1 3 106 generations, with trees sampledevery 100 generations. A total of 8500 trees were uploadedfrom each run after a burn-in of the first 1501 trees.Posterior probabilities were calculated from the 25 500 treesproduced by each of the three independent runs.

To assess the phylogenetic resolution and supportafforded by different rDNA regions we performed two setsof partitioned analyses. The first set of partitioned analysesused MP, bootstrapped MP and bootstrapped NJ analyses ofthe nuc-lsu rDNA and nuc-ssu rDNA data partitions ofDataset 1, with the same analytical settings as the combinednuc-lsu/nuc-ssu rDNA analysis. The nuc-lsu rDNA datapartition in Dataset 1 contains many sequences that includeonly the D1–D2 region, as well as sequences up to 1778 bp(SUPPLEMENTARY TABLE II). To compare the phylogeneticutility of the short (D1–D2) versus long (D1–D3) nuc-lsurDNA sequences, as well as various combinations of data, weassembled a third dataset (Dataset 3) that contains 21species of Pucciniomycotina and two other Basidiomycotathat have nuc-lsu rDNA sequences of at least 1117 bp andnuc-ssu rDNA sequences of at least 1667 bp (OTUs selectedfor Dataset 3 are indicated by an asterisk in SUPPLEMENTARY

TABLE II). We performed analyses of Dataset 3 with sixdifferent data partitions, including: (i) The first approxi-mately 650 bp of nuc-lsu rDNA containing the D1–D2region, with the same set of included positions used inanalyses of Datasets 1 and 2; (ii) The D1–D2 region of nuc-lsu rDNA but including two hypervariable regions that wereexcluded in analyses of Datasets 1 and 2 (the hypervariableregions were aligned with Clustal X 1.83 [Thompson et al1997] with default settings); (iii) Longer D1–D3 nuc-lsurDNA sequences (excluding the hypervariable regions); (iv)Complete nuc-ssu rDNA sequences; (v) Combined D1–D2and nuc-ssu rDNA sequences (excluding the hypervariableregions of nuc-lsu rDNA); and (vi) combined D1-D3 nuc-lsurDNA and nuc-ssu rDNA sequences (excluding the hyper-variable regions of nuc-lsu rDNA).

Each data partition was analyzed with MP, bootstrappedMP and bootstrapped NJ. Analytical settings were the sameas described above, except that the MP analysis used a single-step heuristic search with 1000 replicates, each witha starting tree generated with a random taxon addition

sequence, TBR branch swapping, and MAXTREES set toautoincrease.

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APPENDIX 2

RESULTS AND DISCUSSION

The newly generated nuc-lsu rDNA sequences rangefrom 917 to 1778 bp (SUPPLEMENTARY TABLE II).Seventy percent (140) of the nuc-lsu rDNA sequencesin the complete dataset (Dataset 2) are between 501and 648 bp, reflecting the prevalence of studies thatsolely use the region containing the highly variabledivergent domains D1 and D2 (Hassouna et al 1984).The newly generated nuc-ssu rDNA sequences rangefrom 829 to 2146 bp. Eighty percent (107) of the nuc-ssu rDNA sequences in the Dataset 2 are more than1600 bp (SUPPLEMENTARY TABLE II) and containdivergent domains D1–D3. Introns ranging from255 to 416 bp are present in the nuc-lsu rDNAsequence of Entyloma holwayi and in the nuc-ssurDNA sequences of Bensingtonia ciliata, Colacogloeapeniophorae, Entyloma holwayi and Ustilago maydis.The aligned length of the complete nuc-lsu rDNAsequences is 2069 bp. The analyzed region of nuc-lsurDNA (excluding introns and regions that weconsidered to be of ambiguous alignment) contains1357 positions, of which 699 are variable and 550(40.5%) are parsimony informative (in the context ofDataset 1). The nuc-ssu rDNA has an aligned lengthof 3736 positions. Excluding introns and regions ofambiguous alignment the nuc-ssu rDNA contains1843 positions, including 1007 variable positionsand 710 (38.5%) parsimony informative positions(in the context of Dataset 1; SUPPLEMENTARY TABLE

III).

Analyses of Dataset 1.—MP analyses of Dataset 1recovered 36 trees of 8215 steps (CI 5 0.345, RI 5

0.731; SUPPLEMENTARY TABLE III). Thirty-one of themost parsimonious trees were found in 125 of the1000 heuristic searches in the first part of the analysis.The strict consensus of all equally most parsimonioustrees is highly resolved but there is a large polytomy atthe base of the Microbotryomycetes (FIG. 2). ThePucciniomycotina was supported as monophyleticwith 100% MP and NJ bootstrap support andposterior probability of 1.0 (FIG. 2). The Atractiello-mycetes received MP bootstrap support of 80%, butthe other five classes for which there were at least twoOTUs each received MP bootstrap support of 100%

(FIG. 2 and SUPPLEMENTARY TABLE IV). All six classeswith more than two OTUs received NJ bootstrapsupport of at least 96% and posterior probabilities of1.0. In total 52 nodes in the Pucciniomycotinareceived MP bootstrap support greater than 90%, 62nodes received NJ bootstrap support greater than

90% and 100 nodes received Bayesian posteriorprobabilities greater than 0.95 (FIG. 2). However thebasal nodes in the ‘‘backbone’’ of the Pucciniomyco-tina are weakly supported (FIG. 2).

MP analyses of Dataset 1 using only the nuc-lsurDNA recovered 1000 trees of 3799 steps (CI 5 0.324,RI 5 0.695); 33 nodes received MP bootstrap supportexceeding 90% and 27 nodes received NJ bootstrapsupport exceeding 90% (results summarized inSUPPLEMENTARY TABLE III). MP analyses of Dataset 1using only the nuc-ssu rDNA recovered 1000 trees of4136 steps (CI 5 0.373, RI 5 0.766); 44 nodesreceived MP bootstrap support exceding 90% and 50nodes received NJ bootstrap support exceeding 90%

(SUPPLEMENTARY TABLE III).

Analyses of Dataset 2.—MP analyses of Dataset 2recovered 1000 trees of 9748 steps (CI 5 0.310, RI 5

0.729). Four trees were recovered in two of the 1000heuristic searches in the first part of the analysis.Despite the large number of equally parsimonioustrees the strict consensus is highly resolved (SUPPLE-

MENTARY FIG. 3). For the most part the same majorgroups that are strongly supported in analyses ofDataset 1 were resolved in analyses of Dataset 2, butMP bootstrap support values in analyses of Dataset 2are generally lower than those in analyses of Dataset 1(SUPPLEMENTARY TABLE IV). For example, MP boot-strap support for the Pucciniomycotina dropped from100% (Dataset 1) to 83% (Dataset 2) and support forthe Microbotryomycetes dropped from 100% to 74%

(SUPPLEMENTARY TABLE IV).

Analyses of Dataset 3.—Dataset 3 was analyzed with sixdifferent data partitions (SUPPLEMENTARY TABLE III).The D1–D2 region alone had the worst performance,with only four (MP) or five (NJ) nodes receivingbootstrap support of 90% or greater. The Clustal X-aligned hypervariable subregions of the D1–D2 re-gion had an aligned length of 153 bp, with 97 variablepositions and 81 (53%) parsimony informative posi-tions. Addition of these data to the more conservedpart of the D1–D2 dataset resulted in seven nodesreceiving bootstrap support of at least 90%. Indepen-dent analyses of the longer (D1–D3) nuc-lsu rDNAand nuc-ssu rDNA regions alone yielded similarresults, with 8–10 nodes receiving at least 90%

bootstrap support. Combined analyses of D1–D2 orlonger nuc-lsu sequences and nuc-ssu rDNA se-quences yielded 10 or 11 nodes supported by at least90% of the bootstrap replicates.

Combined vs. independent analyses of nuc-lsu rDNAand nuc-ssu rDNA.—Combined analyses of nuc-lsurDNA and nuc-ssu rDNA sequences provide strongersupport for the phylogenetic relationships of Pucci-niomycotina than is attained through analyses ofeither region alone (SUPPLEMENTARY TABLES III andIV). In analyses of Dataset 1 (with 128 OTUs)combined analyses recovered about twice as manystrongly supported nodes as analyses of nuc-lsu rDNAalone, and about 1.2–1.4 times as many stronglysupported nodes as analyses of nuc-ssu rDNA alone.Combined analyses of Dataset 1 also provide greaterresolution than the single-gene analyses; both single-partition analyses of Dataset 1 recovered 1000 equallymost parsimonious trees (this was the MAXTREES

setting, so there are probably many more equallyparsimonious trees), whereas the combined analysisrecovered only 36 trees.

The nuc-lsu rDNA data partition in Dataset 1includes taxa with a range of nuc-lsu sequence lengths(SUPPLEMENTARY TABLE II). Analyses of Dataset 3 allowassessment of the impact of the longer nuc-lsu rDNAsequences which incorporate divergent domains D1–D3 compared to shorter nuc-lsu sequences coveringonly D1–D2, as well as the resolving power of differentcombinations of data (SUPPLEMENTARY TABLE III). TheD1-D2 region is the smallest data partition analyzed,and not surprisingly it provides the weakest resolu-tion. Inclusion of the hypervariable parts of the D1–D2 region increases the number of strongly sup-ported nodes (SUPPLEMENTARY TABLE III) but theextreme variability of these regions also increases thedanger of making incorrect hypotheses of homologywhen aligning the sequences. The strongest resultswere obtained in the combined analyses of the nuc-lsuand nuc-ssu rDNA sequences. There was essentially nodifference in the strength of support in analyses thatcombined nuc-ssu rDNA sequences with the D1–D2regions vs. those that combined nuc-ssu rDNAsequences with extended-length nuc-lsu rDNA se-quences (SUPPLEMENTARY TABLE III). Nevertheless theextended-length nuc-lsu rDNA sequences have about1.4 times as many variable and parsimony-informative

sites as the D1–D2 region alone, and the extended-length nuc-lsu rDNA provides stronger resolutionthan the D1–D2 region when those regions areanalyzed independently (SUPPLEMENTARY TABLE III).

Analyses of Datasets 1 and 3 indicate that combiningnuc-lsu rDNA and nuc-ssu rDNA sequences improvesphylogenetic resolution and support and also that theutility of D1–D2 sequences can be enhanced signifi-cantly by extending them to include the completeLR0R-LR7 fragment covering D1–D3. Another strategyfor building on the existing data would be to combinethem with a supermatrix approach. Such approaches,where taxon sampling is extensive but not all taxa havebeen sampled at all loci resulting in a large amount ofmissing data, nonetheless have shown potential forphylogenetic reconstruction in large datasets (Driskellet al 2004). Analyses of Dataset 2 (in which 74 OTUshave only nuc-lsu rDNA sequences and six OTUs haveonly nuc-ssu rDNA sequences) resolve the same majorclades as analyses of Dataset 1 (FIG. 2 and SUPPLEMEN-

TARY FIG. 3), but many more equally most parsimoni-ous trees were derived from Dataset 2 than wereobtained in analyses of Dataset 1 and the bootstrapvalues are lower in Dataset 2 (FIG. 2, SUPPLEMENTARY

FIG. 3, and SUPPLEMENTARY TABLE IV). Thus super-matrix analyses might provide a useful means toconstruct comprehensive phylogenetic trees that in-corporate the large database of D1–D2 sequences, butthey probably will not provide the resolution andsupport that could be attained through combinedanalyses that have no missing data.

LITERATURE CITED

Driskell AC, Ane C, Burleigh JG, McMahon MM, O’MearaBC, Sanderson MJ. 2004. Prospects for building thetree of life from large sequence databases. Science 306:1172–1174.

Hassouna N, Michot B, Bachellerie J. 1984. The completenucleotide sequence of mouse 28S rRNA. Implicationsfor the process of size increase of the large subunitrRNA in higher eukaryotes. Nucleic Acid Res 12:3563–3583.

LITERATURE CITED

Bauer R, Begerow D, Sampaio JP, Weiß M, Oberwinkler F.2006. The simple-septate basidiomycetes: a synopsis.Mycol Progress 5:41–66.

Swann EC, Frieders EM, McLaughlin DJ. 2001. Uredinio-mycetes. In: McLaughlin DJ, McLaughlin EG, Lemke

PA, eds. Systematics and Evolution. Berlin: Springer-Verlag, The Mycota VIIB: 37–56.

Weiß M, Bauer R, Begerow D. 2004. Spotlights on

heterobasidiomycetes. In: Agerer R, Piepenbring M,

Blanz P, eds. Frontiers in Basidiomycote Mycology.

Eching, Germany: IHW-Verlag. p 7–48.

SUPPLEMENTARY TABLE I. Comparison of classifications of higher taxa of Pucciniomycotina. Exact compositions of taxa varyacross classification. Major lineages in each classification are indicated by boldface.

Swann et al (2001) Weiß et al (2004) Bauer et al (2006)

UREDINIOMYCETES UREDINIOMYCETES PUCCINIOMYCOTINA

Urediniomycetidae Urediniomycetidae PucciniomycetesUredinales Uredinales PuccinialesHelicobasidium Helicobasidium subgroup HelicobasidialesPlatygloeales s. str. Platygloeales PlatygloealesSeptobasidiales Septobasidiales Septobasidiales

Pachnocybaceaea Pachnocybaceae PachnocybalesErythrobasidiumb clade Cystobasidiaceae lineage CystobasidiomycetesCystobasidiumc Cystobasidiaceae group Cystobasidiales

Erythrobasidium Erythrobasidium subgroup ErythrobasidialesNaohidea Naohidea subgroup Naohideales

Atractiellales Atractiellales lineage AtractiellomycetesAttractiellales

Agaricostilbomycetidae Agaricostilbomycetidae AgaricostilbomycetesAgaricostilbales Agaricostilbales AgaricostilbalesMycogloea Mycogloea group Spiculogloeales

Microbotryomycetidae Microbotryomycetidae MicrobotryomycetesHeterogastridiales Heterogastridiales HeterogastridialesSporidiobolaceae p.p. Leucosporidiales LeucosporidialesMicrobotryales Microbotryales MicrobotryalesSporidiobolaceae p.p. Sporidiobolales SporidiobolalesCamptobasidiaceae Camptobasidiaceae group incertae sedisd

Cryptomycocolacales Cryptomycocolacales CryptomycocolacomycetesCryptomycocolacales

Naiadellac Classiculales lineage ClassiculomycetesClassiculales

Mixiaceae Mixiaceae lineage MixiomycetesMixiales

a Placed within Septobasidiales.b Full name: Erythrobasidium, Naohidea, Sakaguchia clade.c Placed incertae sedis within Urediniomycetes.d Placed within Microbotryomycetes.

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LITERATURE CITED

Bauer R, Begerow D, Sampaio JP, Weiß M, Oberwinkler F.2006. The simple-septate basidiomycetes: a synopsis.Mycol Progress 5:41–66.


Fell JW, Boekhout T, Fonseca A, Sampaio JP. 2001.Basidiomycetous yeasts. In: McLaughlin DJ, McLaugh-lin EG, Lemke PA, eds. Systematics and Evolution.Berlin: Springer-Verlag, The Mycota VIIB: 3–35.

Lutzoni F, Kauff F, Cox CJ, 41 others. 2004. Assembling theFungal Tree of Life: progress, classification, andevolution of subcellular traits. Am J Bot 91:1446–1480.

McLaughlin DJ, Berres ME, Szabo LJ. 1995. Molecules and

morphology in basidiomycete phylogeny. Can J Bot73(1):S684–692.

Sampaio JP. 2004. Diversity, phylogeny and classification of

basidiomycetous yeasts. In: Agerer R, Piepenbring M,

Blanz P, eds. Frontiers in Basidiomycote Mycology.

Eching, Germany: IHW-Verlag. p 49–80.Swann EC, Frieders EM, McLaughlin DJ. 1999. Microbo-

tryum, Kriegeria and the changing paradigm in basid-iomycete classification. Mycologia 91:51–66.

Weiß M, Bauer R, Begerow D. 2004. Spotlights onheterobasidiomycetes. In: Agerer R, Piepenbring M,Blanz P, eds. Frontiers in Basidiomycote Mycology.Eching, Germany. IHW-Verlag. p 7–48.


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ank

no

.le

ngt

h(b

p)

Ref

eren

ce(c

ited

inG

enb

ank)

AS

CO

MY

CO

TA

Leo

tia

lubr

ica

(Sco

p.)

Per

s.A

Y544

644

1396

Lu

tzo

ni

etal

(200

4)A

Y544

687

1729

Lu

tzo

ni

etal

(200

4)

Mor

chel

lacf

.el

ata

Fr.

AY5

4466

513

86L

utz

on

iet

al(2

004)

AY5

4470

917

29L

utz

on

iet

al(2

004)

Neo

lect

avit

elli

na

(Bre

s.)

Ko

rf&

J.K

.R

oge

rsA

F27

9401

1252

Bh

atta

char

yaet

al(2

000)

Z27

393*

*17

22L

and

vik

etal

(199

3)

Sacc

haro

myc

esce

revis

iae

Mey

enex

E.C

.H

anse

nJ0

1355

3911

Bay

evet

al(1

981)

J013

5317

98R

ub

tso

vet

al(1

980)

Sor

dari

afi

mic

ola

(Ro

ber

geex

Des

m.)

Ces

.&

De

No

t.A

Y545

728

1343

Lu

tzo

ni

etal

(200

4)X

6985

1**

1796

Wil

mo

tte

etal

(199

3)

Taphri

na

wie

sner

i(R

ath

ay)

Mix

AY5

4829

214

11L

utz

on

iet

al(2

004)

AY5

4829

317

25L

utz

on

iet

al(2

004)

BA

SID

IOM

YC

OT

AA

GA

RIC

OM

YC

OT

INA

Au

ricu

lari

asp

.A

Y634

277

1433

Mat

hen

yet

al(2

004)

un

pu

bli

shed

DQ

2345

4217

64M

ath

eny

etal

(200

5)u

np

ub

lish

ed

Bot

ryob

asi

diu

mbo

tryo

sum

(Bre

s.)

J.E

riks

s.D

Q08

9013

1297

Nil

sso

net

al(2

005)

un

pu

bli

shed

AY6

6266

717

66N

ilss

on

etal

(200

5)u

np

ub

lish

ed

Calo

cera

corn

ea(B

atsc

h)

Fr.

*A

Y701

526

1367

Mat

hen

yet

al(2

004)

un

pu

bli

shed

AY7

7161

017

64M

ath

eny

etal

(200

4)u

np

ub

lish

ed

Fil

obasi

die

lla

neo

form

an

sK

wo

n-C

hu

ng

AJ5

5129

072

4K

idd

(200

3)u

np

ub

lish

edX

6018

3**

1769

Van

de

Pee

ret

al(1

992)

US

TIL

AG

INO

MY

CO

TIN

A

En

tylo

ma

hol

wayi

Syd

.A

Y745

721

1778

Mat

hen

yet

al(2

004)

un

pu

bli

shed

DQ

2345

6220

45M

ath

eny

etal

(200

5)u

np

ub

lish

ed

Mala

ssez

iafu

rfu

r(C

.P.

Ro

bin

)B

aill

.*A

Y745

725

1373

Mat

hen

yet

al(2

004)

un

pu

bli

shed

AY0

8322

3**

1628

McI

lhat

ton

and

Cu

rran

(200

2)u

np

ub

lish

edM

ala

ssez

iapach

yder

mati

s(W

eid

man

)C

.W.

Do

dge

AY7

4572

413

89M

ath

eny

etal

(200

4)u

np

ub

lish

edD

Q45

7640

1179

this

stu

dy

Spor

isor

ium

form

osan

um

(Saw

ada)

Van

kyA

Y740

134

594

Sto

llet

al(2

005)

DQ

8322

2610

96th

isst

ud

y

Til

leti

aco

ntr

over

saJ.

G.

Ku

hn

DQ

8322

4413

73th

isst

ud

yD

Q83

2245

829

this

stu

dy

Til

leti

ari

aan

omala

Ban

do

ni

&B

.N.

Joh

riA

Y745

715

1381

Mat

hen

yet

al(2

004)

un

pu

bli

shed

AY8

0375

217

71M

ath

eny

etal

(200

4)u

np

ub

lish

ed

Til

leti

opsi

sm

inor

Nyl

and

AY7

4571

314

04M

ath

eny

etal

(200

4)u

np

ub

lish

edD

8319

017

27T

akas

him

aan

dN

akas

e(1

996)

Til

leti

opsi

sw

ash

ingt

onen

sis

Nyl

and

AY7

4571

413

97M

ath

eny

etal

(200

4)u

np

ub

lish

edD

8319

217

30T

akas

him

aan

dN

akas

e(1

996)

Ust

ilago

mayd

is(D

C.)

Co

rda

AF

4539

3811

15P

iep

enb

rin

get

al(2

002)

X62

396*

*21

83D

eW

ach

ter

etal

(199

2)P

UC

CIN

IOM

YC

OT

INA

Aga

rico

stil

bum

hyp

haen

es(H

ar.

&P

at.)

Ob

erw

.&

Ban

do

ni*

AY6

3427

813

69M

ath

eny

etal

(200

4)u

np

ub

lish

edA

Y665

775

1774

Mat

hen

yet

al(2

004)

un

pu

bli

shed

Aga

rico

stil

bum

pu

lcher

rim

um

(Ber

k.&

Bro

om

e)B

.L.

Bra

dy,

B.

Sutt

on

&Sa

mso

nL

2027

753

9B

erre

set

al(1

995)

AY3

7339

1**

1760

McL

augh

lin

etal

(200

4)A

tract

iell

aso

lan

i(C

oh

n&

J.Sc

hro

t.)

Ob

erw

.&

Ban

do

ni

AY5

1283

155

4B

eger

ow

etal

(200

3)u

np

ub

lish

edA

ura

nti

ospor

ium

subn

iten

s(J

.Sc

hro

t.&

Hen

n.)

M.

Pie

pen

br.

,V

anky

&O

ber

w.

AF

0098

4656

0B

eger

ow

etal

(199

7)B

an

noa

hahaji

men

sis

Ham

am.,

Th

anh

&N

akas

eA

B08

2571

648

Nag

aham

aet

al(2

002)

un

pu

bli

shed

Spec

ies

nu

c-ls

urD

NA

nu

c-ss

urD

NA

Gen

Ban

kn

o.

len

gth

(bp

)R

efer

ence

(cit

edin

Gen

ban

k)G

enB

ank

no

.le

ngt

h(b

p)

Ref

eren

ce(c

ited

inG

enb

ank)

Ben

sin

gton

iach

an

gbaie

nsi

sF

.Y.

Bai

&Q

.M.

Wan

gA

Y233

342

639

Wan

get

al(2

003)

Ben

sin

gton

iaci

liata

Ingo

ld*

AY7

4573

014

02M

ath

eny

etal

(200

4)u

np

ub

lish

edD

3823

320

93T

akas

him

aet

al(1

995a

)

Ben

sin

gton

iain

gold

iiN

akas

e&

Ito

hA

F18

9888

631

Fel

let

al(2

000)

D38

234

1746

Tak

ash

ima

etal

(199

5a)

Ben

sin

gton

iam

isca

nth

i(N

akas

e&

M.

Suzu

ki)

Nak

ase

&B

oek

ho

ut

AF

1898

9164

0F

ell

etal

(200

0)D

3823

617

49T

akas

him

aet

al(1

995a

)B

ensi

ngt

onia

mu

sae

M.

Tak

ash

.,S.

O.

Suh

&N

akas

eA

Y512

833

628

Beg

ero

wet

al(2

003)

un

pu

bli

shed

D43

946*

*17

39T

akas

him

aet

al(1

995b

)B

ensi

ngt

onia

naga

noe

nsi

s(N

akas

e&

M.

Suzu

ki)

Nak

ase

&B

oek

ho

ut

AF

1898

9363

4F

ell

etal

(200

0)D

3836

617

53T

akas

him

aet

al(1

995a

)B

ensi

ngt

onia

phyl

lada

(Van

der

Wal

t&

Y.Ya

mad

a)V

and

erW

alt,

Nak

agaw

a&

Y.Ya

mad

aex

Bo

ekh

ou

tA

Y512

836

642

Beg

ero

wet

al(2

003)

un

pu

bli

shed

D38

237a

**17

48T

akas

him

aet

al(1

995a

)B

ensi

ngt

onia

saka

guch

iiSu

gita

,M

.T

akas

h.,

Ham

am.

&N

akas

eA

F36

3646

599

Sco

rzet

tiet

al(2

002)

AB

0017

4626

53Su

gita

etal

(199

7)

Ben

sin

gton

iaso

rbi

F.Y

.B

ai&

Q.M

.W

ang

AY2

3334

563

1W

ang

etal

(200

3)B

ensi

ngt

onia

subr

osea

(Nak

ase

&M

.Su

zuki

)N

akas

e&

Bo

ekh

ou

tA

F18

9895

640

Fel

let

al(2

000)

D38

238

1744

Tak

ash

ima

etal

(199

5a)

Ben

sin

gton

iaya

mato

an

a(N

akas

e,M

.Su

zuki

&It

oh

)N

akas

e&

Bo

ekh

ou

tA

F18

9896

619

Fel

let

al(2

000)

D38

239

2658

Tak

ash

ima

etal

(199

5a)

Ben

sin

gton

iayu

ccic

ola

(Nak

ase

&M

.Su

zuki

)N

akas

e&

Bo

ekh

ou

t*A

Y745

727

1388

Mat

hen

yet

al(2

004)

un

pu

bli

shed

DQ

2345

4317

75M

ath

eny

etal

(200

5)u

np

ub

lish

edC

am

pto

basi

diu

mhyd

rophil

um

Mar

van

ova

&Su

ber

kr.

[1]

AY2

1299

157

0Sa

mp

aio

etal

(200

3)

Cam

pto

basi

diu

mhyd

rophil

um

[2]

AY5

1283

754

1B

eger

ow

etal

(200

3)u

np

ub

lish

ed

Chio

nos

phaer

aapob

asi

dia

lis

D.E

.C

ox

[1]

AF

3934

7048

7K

irsc

hn

eret

al(2

001)

Chio

nos

phaer

aapob

asi

dia

lis

[2]

AF

1774

0763

2Sa

mp

aio

etal

(199

9b)

U77

662*

*16

58Sw

ann

etal

(199

9)C

hio

nos

phaer

acu

nic

uli

cola

R.

Kir

sch

ner

,B

eger

ow

&O

ber

w.

AF

3934

7348

3K

irsc

hn

eret

al(2

001)

Chry

som

yxa

arc

tost

aphyl

iD

iete

l*A

Y700

192

1180

Mat

hen

yet

al(2

004)

un

pu

bli

shed

AY6

5700

916

67M

ath

eny

etal

(200

4)u

np

ub

lish

edC

lass

icu

lafl

uit

an

sR

.B

auer

,B

eger

ow

,O

ber

w.

&M

arva

no

vaA

Y512

838

559

Beg

ero

wet

al(2

003)

un

pu

bli

shed

AY1

2447

815

16B

auer

etal

(200

3)C

olaco

gloe

apen

iophor

ae

(Bo

urd

ot

&G

alzi

n)

Ob

erw

.,R

.B

auer

&B

and

on

i[1

]A

F18

9898

621

Fel

let

al(2

000)

Col

aco

gloe

apen

iophor

ae

[2]

AY5

1283

961

6B

eger

ow

etal

(200

3)u

np

ub

lish

ed

Col

aco

gloe

apen

iophor

ae

[3]*

AY6

2931

313

15M

ath

eny

etal

(200

4)u

np

ub

lish

edD

Q23

4565

2146

Mat

hen

yet

al(2

005)

un

pu

bli

shed

Col

eosp

oriu

mast

eru

m(D

iete

l)Sy

d.

&P

.Sy

d.

AF

5221

6495

1Sz

aro

and

Bru

ns

(200

2)u

np

ub

lish

edA

Y123

286

1760

Win

gfie

ldet

al(2

004)

Cro

nart

ium

ribi

cola

J.C

.F

isch

.A

F52

2166

963

Szar

oan

dB

run

s(2

002)

un

pu

bli

shed

M94

338

1753

Bru

ns

etal

(199

2)

Cry

pto

myc

ocol

ax

abn

orm

isO

ber

w.

&R

.B

auer

AY5

1284

160

9B

eger

ow

etal

(200

3)u

np

ub

lish

ed

Cyr

enel

lael

egan

sG

och

.A

Y512

842

573

Beg

ero

wet

al(2

003)

un

pu

bli

shed

SUP

PL

EM

EN

TA

RY

TA

BL

EII

.C

on

tin

ued

Spec

ies

nu

c-ls

urD

NA

nu

c-ss

urD

NA

Gen

Ban

kn

o.

len

gth

(bp

)R

efer

ence

(cit

edin

Gen

ban

k)G

enB

ank

no

.le

ngt

h(b

p)

Ref

eren

ce(c

ited

inG

enb

ank)

Cys

toba

sidiu

mfi

met

ari

um

(Sch

um

ach

.)P

.R

ob

erts

AY5

1284

363

3B

eger

ow

etal

(200

3)u

np

ub

lish

edA

Y124

479

1624

Bau

eret

al(2

003)

En

doc

ron

art

ium

hark

nes

sii

Hir

ats.

*A

Y700

193

1200

Mat

hen

yet

al(2

004)

un

pu

bli

shed

AY6

6578

517

64M

ath

eny

etal

(200

4)u

np

ub

lish

ed

Eoc

ron

art

ium

mu

scic

ola

(Per

s.)

Fit

zp.

[1]

AF

0148

2591

4B

run

san

dSz

aro

(199

7)u

np

ub

lish

edA

Y123

323

1763

Win

gfie

ldet

al(2

004)

Eoc

ron

art

ium

mu

scic

ola

[2]

AY5

1284

462

2B

eger

ow

etal

(200

3)u

np

ub

lish

edE

ryth

roba

sidiu

mhase

gaw

ian

um

Ham

am.,

Sugi

y.&

Ko

mag

.[1

]A

F13

1058

603

Sam

pai

oet

al(1

999a

)

Ery

thro

basi

diu

mhase

gaw

ian

um

[2]

AF

1898

9959

8F

ell

etal

(200

0)D

1280

3**

1755

Suh

and

Sugi

yam

a(1

993)

Fu

lvis

por

ium

rest

ifaci

ens

(D.E

.Sh

aw)

Van

kyA

F00

9860

561

Beg

ero

wet

al(1

997)

Gym

nos

por

an

giu

mju

nip

eri-

vir

gin

ian

ae

Sch

wei

n.

AY6

2931

613

48M

ath

eny

etal

(200

4)u

np

ub

lish

edD

Q66

7158

1145

this

stu

dy

Hel

icob

asi

diu

mco

rtic

ioid

esB

and

on

iU

7530

317

47Sw

ann

and

McL

augh

lin(1

996)

un

pu

blis

hed

Hel

icob

asi

diu

mlo

ngi

spor

um

Wak

ef.

AY2

2204

611

32L

utz

etal

(200

4b)

Hel

icob

asi

diu

mm

ompa

Tan

aka

[1]

AY2

5417

811

28L

utz

etal

(200

4a)

Hel

icob

asi

diu

mm

ompa

[2]*

AY2

5417

911

17L

utz

etal

(200

4a)

U77

064

1657

Swan

net

al(1

999)

Hel

icob

asi

diu

mpu

rpu

reu

m(T

ul.

)P

at.

[1]

AY2

2204

911

06L

utz

etal

(200

4b)

Hel

icob

asi

diu

mpu

rpu

reu

m[2

]A

Y254

180

1121

Lu

tzet

al(2

004a

)

Hel

icog

loea

lage

rhei

mii

Pat

.A

Y512

849

510

Beg

ero

wet

al(2

003)

un

pu

bli

shed

AY1

2447

617

21B

auer

etal

(200

3)

Hel

icog

loea

vari

abi

lis

K.

Wel

lsL

2028

255

7B

erre

set

al(1

995)

U78

043

1769

Swan

net

al(1

999)

Her

pob

asi

diu

mfi

lici

nu

m(R

ost

r.)

Lin

d[1

]A

F42

6193

506

Mai

eret

al(2

003)

Her

pob

asi

diu

mfi

lici

nu

m[2

]A

Y512

850

619

Beg

ero

wet

al(2

003)

un

pu

bli

shed

Het

erog

ast

ridiu

mpyc

nid

ioid

eum

Ob

erw

.&

R.

Bau

erA

Y512

851

599

Beg

ero

wet

al(2

003)

un

pu

bli

shed

U41

567*

*16

51Sw

ann

and

Tay

lor

(199

5)

Hob

son

iam

irabi

lis

(Pec

k)L

ind

erA

F28

9663

1720

Sika

roo

di

etal

(200

1)

Hya

lopso

rapol

ypod

ii(P

ers.

)M

agn

.A

Y512

852

516

Beg

ero

wet

al(2

003)

un

pu

bli

shed

AB

0110

1517

47Sj

amsu

rid

zal

etal

(199

9)In

soli

basi

diu

mdef

orm

an

s(C

.J.

Go

uld

)O

ber

w.

&B

and

on

i*A

Y646

099

1413

Mat

hen

yet

al(2

004)

un

pu

bli

shed

AY1

2329

2**

1756

Win

gfie

ldet

al(2

004)

Jacu

lisp

ora

subm

ersa

H.J

.H

ud

s.&

Ingo

ldA

Y512

853

595

Beg

ero

wet

al(2

003)

un

pu

bli

shed

AY1

2447

716

69B

auer

etal

(200

3)

Jola

cf.

javen

sis

Pat

.D

Q41

6207

570

this

stu

dy

DQ

4162

0617

17th

isst

ud

y

Jola

hoo

keri

aru

mA

.M

øll

erD

Q41

6208

568

this

stu

dy

Kon

doa

aer

iaA

.F

on

seca

,J.

P.

Sam

p.

&F

ell

AF

1899

0263

8F

ell

etal

(200

0)K

ondoa

malv

inel

la(F

ell

&I.

L.

Hu

nte

r)Y.

Yam

ada,

Nak

agaw

a&

I.B

ann

oA

Y745

720

1440

Mat

hen

yet

al(2

004)

un

pu

bli

shed

DQ

6671

6411

90th

isst

ud

y

Kon

doa

sp.

AF

1899

0463

7F

ell

etal

(200

0)

Kri

eger

iaer

iophor

iB

res.

[1]*

AY7

4572

813

97M

ath

eny

etal

(200

4)u

np

ub

lish

edD

Q41

9918

1766

this

stu

dy

Kri

eger

iaer

iophor

i[2

]A

F18

9905

b61

9F

ell

etal

(200

0)U

7706

3b**

1684

Swan

net

al(1

999)

Ku

ehn

eola

ure

din

is(L

ink)

Art

hu

rA

Y745

696

1385

Mat

hen

yet

al(2

004)

un

pu

bli

shed

DQ

0929

1913

10M

ath

eny

etal

(200

5)u

np

ub

lish

ed

Ku

rtzm

an

omyc

esin

soli

tus

J.P

.Sa

mp

.&

Fel

lA

F17

7408

630

Sam

pai

oet

al(1

999b

)

SUP

PL

EM

EN

TA

RY

TA

BL

EII

.C

on

tin

ued

Spec

ies

nu

c-ls

urD

NA

nu

c-ss

urD

NA

Gen

Ban

kn

o.

len

gth

(bp

)R

efer

ence

(cit

edin

Gen

ban

k)G

enB

ank

no

.le

ngt

h(b

p)

Ref

eren

ce(c

ited

inG

enb

ank)

Ku

rtzm

an

omyc

esn

ecta

irei

(Ro

dr.

Mir

.)Y.

Yam

ada,

Ito

h,

H.

Kaw

as.,

I.B

ann

o&

Nak

ase

AF

1774

0962

9Sa

mp

aio

etal

(199

9b)

D64

122*

*17

39Su

het

al(1

996b

)

Ku

rtzm

an

omyc

esta

rdu

sG

im.-J

ura

do

&U

den

AF

1774

1062

9Sa

mp

aio

etal

(199

9b)

Leu

cosp

orid

iell

acr

eati

niv

ora

(Go

lub

ev)

J.P

.Sa

mp

.A

F18

9925

c61

9F

ell

etal

(200

0)L

euco

spor

idie

lla

fraga

ria

(J.A

.B

arn

ett

&B

uh

agia

r)J.

P.

Sam

p.

AY5

1287

959

4B

eger

ow

etal

(200

3)u

np

ub

lish

edL

euco

spor

idie

lla

mu

scor

um

(Di

Men

na)

J.P

.Sa

mp

.A

Y213

008

589

Sam

pai

oet

al(2

003)

Leu

cosp

orid

iell

aya

kuti

ca(G

olu

bev

)J.

P.

Sam

p.

AY2

1300

158

3Sa

mp

aio

etal

(200

3)L

euco

spor

idiu

man

tarc

ticu

mF

ell,

Stat

zell

,I.

L.

Hu

nte

r&

Ph

aff

AY5

1285

562

2B

eger

ow

etal

(200

3)u

np

ub

lish

ed

Leu

cosp

orid

ium

fell

iiG

im.-J

ura

do

&U

den

AY5

1285

661

7B

eger

ow

etal

(200

3)u

np

ub

lish

edL

euco

spor

idiu

msc

otti

iF

ell,

Stat

zell

,I.

L.

Hu

nte

r&

Ph

aff

[1]

AF

0704

1961

9F

ell

etal

(199

8)X

5349

9**

1765

Hen

dri

kset

al(1

991)

Leu

cosp

orid

ium

scot

tii

[2]*

AY6

4609

813

89M

ath

eny

etal

(200

4)u

np

ub

lish

edA

Y707

092

1803

Mat

hen

yet

al(2

004)

un

pu

bli

shed

Lir

oaem

oden

sis

(Ber

k.)

Cif

.[1

]A

Y512

858

565

Beg

ero

wet

al(2

003)

un

pu

bli

shed

Lir

oaem

oden

sis

[2]

AY2

1299

258

7Sa

mp

aio

etal

(200

3)

Mast

igob

asi

diu

min

term

ediu

mG

olu

bev

[1]

AF

1898

8961

9F

ell

etal

(200

0)

Mast

igob

asi

diu

min

term

ediu

m[2

]A

Y512

859

603

Beg

ero

wet

al(2

003)

un

pu

bli

shed

D38

235*

*17

44T

akas

him

aet

al(1

995a

)

Mel

am

pso

raeu

phor

biae

(C.

Sch

ub

.)C

asta

gne

DQ

4375

0411

00th

isst

ud

yM

icro

botr

yum

cord

ae

(Lir

o)

G.

Dem

l&

Pri

llin

ger

AY2

1300

258

9Sa

mp

aio

etal

(200

3)M

icro

botr

yum

reti

cula

tum

(Lir

o)

R.

Bau

er&

Ob

erw

.A

Y213

003

586

Sam

pai

oet

al(2

003)

U79

566*

*92

5Sw

ann

etal

(199

9)M

icro

botr

yum

vio

lace

um

(Per

s.)

G.

Dem

l&

Ob

erw

.A

Y512

864

620

Beg

ero

wet

al(2

003)

un

pu

bli

shed

U77

062*

*17

27Sw

ann

and

Tay

lor

(199

5)

Mix

iaos

mu

ndae

(Nis

hid

a)C

.L.

Kra

mer

[1]

AB

0528

4060

0Sj

amsu

rid

zal

etal

(200

2)D

1416

317

80N

ish

ida

etal

(199

5)

Mix

iaos

mu

ndae

[2]

AY5

1286

761

3B

eger

ow

etal

(200

3)u

np

ub

lish

edM

ycog

loea

macr

ospor

a(B

erk.

&B

roo

me)

McN

abb

U41

848

1601

Swan

nan

dT

aylo

r(1

995)

Myc

oglo

ean

ippon

ica

Ban

do

ni

AY1

5965

060

2K

irsc

hn

eret

al(2

002)

un

pu

bis

hed

Myc

oglo

easp

.A

Y512

868

629

Beg

ero

wet

al(2

003)

un

pu

bli

shed

Naoh

idea

seba

cea

(Ber

k.&

Bro

om

e)O

ber

w.

[1]

AF

1310

6154

1Sa

mp

aio

etal

(199

9a)

Naoh

idea

seba

cea

[2]*

AF

5221

7612

03Sz

aro

and

Bru

ns

(200

2)u

np

ub

lish

edA

Y123

302

2094

Win

gfie

ldet

al(2

004)

Occ

ult

ifu

rex

tern

us

J.P

.Sa

mp

.,R

.B

auer

&O

ber

w.

[1]*

AY7

4572

314

23M

ath

eny

etal

(200

4)u

np

ub

lish

edD

Q45

7639

1774

this

stu

dy

Occ

ult

ifu

rex

tern

us

[2]

AF

1899

1162

9F

ell

etal

(200

0)A

Y124

475*

*16

29B

auer

etal

(200

3)

Pach

noc

ybe

ferr

ugi

nea

Ber

k.L

2028

455

4B

erre

set

al(1

995)

SUP

PL

EM

EN

TA

RY

TA

BL

EII

.C

on

tin

ued

Spec

ies

nu

c-ls

urD

NA

nu

c-ss

urD

NA

Gen

Ban

kn

o.

len

gth

(bp

)R

efer

ence

(cit

edin

Gen

ban

k)G

enB

ank

no

.le

ngt

h(b

p)

Ref

eren

ce(c

ited

inG

enb

ank)

Phle

ogen

afa

gin

ea(F

r.)

Lin

kA

Y512

869

537

Beg

ero

wet

al(2

003)

un

pu

bli

shed

AY3

7339

2**

1833

McL

augh

lin

etal

(200

4)P

ileo

lari

ato

xico

den

dri

(Ber

k.&

Rav

enel

)A

rth

ur

[1]

AY7

4569

911

73M

ath

eny

etal

(200

4)u

np

ub

lish

ed

Pil

eola

ria

toxi

coden

dri

[2]

AY7

4569

814

14M

ath

eny

etal

(200

4)u

np

ub

lish

edD

Q09

2921

1774

Mat

hen

yet

al(2

005)

un

pu

bli

shed

Pla

tygl

oea

dis

cifo

rmis

(Fr.

)N

euh

off

*A

Y629

314

1355

Mat

hen

yet

al(2

004)

un

pu

bli

shed

DQ

2345

6317

63M

ath

eny

etal

(200

5)u

np

ub

lish

ed

Pla

tygl

oea

pu

stu

lata

G.W

.M

arti

n&

Cai

nA

Y512

871

585

Beg

ero

wet

al(2

003)

un

pu

bli

shed

Pla

tygl

oea

ves

tita

Bo

urd

ot

&G

alzi

nA

Y512

872

593

Beg

ero

wet

al(2

003)

un

pu

bli

shed

AY1

2448

016

02B

auer

etal

(200

3)

Ple

uro

coll

aco

mpre

ssa

(Ell

is&

Eve

rh.)

Die

hl

AY3

8258

150

1K

irsc

hn

eret

al(2

004)

un

pu

bli

shed

Pu

ccin

iaaru

ndin

ari

ae

Sch

wei

n.

DQ

4152

7710

42th

isst

ud

y

Pu

ccin

iahor

dei

G.H

.O

tth

DQ

3545

2710

74A

ime

(200

6)D

Q41

5278

this

stu

dy

Pu

ccin

iast

rum

goep

per

tian

um

(Ku

ehn

)K

leb

.A

F52

2180

940

Szar

oan

dB

run

s(2

002)

un

pu

bli

shed

AY1

2330

517

54W

ingf

ield

etal

(200

4)

Ren

ifor

ma

stru

esP

ore

&So

ren

son

AF

1899

1255

7F

ell

etal

(200

0)R

hod

ospor

idiu

mdio

bovatu

mS.

Y.N

ewel

l&

I.L

.H

un

ter

AF

1899

1459

7F

ell

etal

(200

0)R

hod

ospor

idiu

mfl

uvia

leF

ell,

Ku

rtzm

an,

Tal

lman

&J.

D.

Bu

ck[1

]A

F07

0422

604

Fel

let

al(1

998)

Rhod

ospor

idiu

mfl

uvia

le[2

]*A

Y745

719

1362

Mat

hen

yet

al(2

004)

un

pu

bli

shed

U77

395*

*17

37Sw

ann

etal

(199

9)R

hod

ospor

idiu

msp

haer

ocarp

um

S.Y.

New

ell

&F

ell

AY5

1287

556

9B

eger

ow

etal

(200

3)u

np

ub

lish

ed

Rhod

ospor

idiu

mto

rulo

ides

Ban

no

AF

0704

2660

3F

ell

etal

(199

8)D

1280

6**

1759

Suh

and

Sugi

yam

a(1

993)

Rhod

otor

ula

arm

enia

caR

.G.

Shiv

as&

Ro

dr.

Mir

.A

F18

9920

629

Fel

let

al(2

000)

AB

1266

4417

83N

agah

ama

etal

(200

3)u

np

ub

lish

ed

Rhod

otor

ula

au

ran

tiaca

(Sai

to)

Lo

dd

erA

Y512

877

626

Beg

ero

wet

al(2

003)

un

pu

bli

shed

AB

0303

54**

1757

Tak

ash

ima

etal

(200

0)R

hod

otor

ula

bogo

rien

sis

(Dei

nem

a)A

rx&

Wei

jman

AF

1899

2359

2F

ell

etal

(200

0)

Rhod

otor

ula

cres

olic

aM

idd

elh

ove

n&

Spaa

ijA

F18

9926

619

Fel

let

al(2

000)

Rhod

otor

ula

dif

flu

ens

(Ru

inen

)T

.H

aseg

.,B

ann

o&

Yam

auch

iA

Y512

878

621

Beg

ero

wet

al(2

003)

un

pu

bli

shed

Rhod

otor

ula

foli

oru

m(R

uin

en)

Ro

dr.

Mir

.&

Wei

jma

AF

3178

0461

9F

ell

(200

0)u

np

ub

lish

ed

Rhod

otor

ula

glu

tin

is(F

rese

n.)

F.C

.H

arri

son

[1]

AF

0704

3060

4F

ell

etal

(199

8)

Rhod

otor

ula

glu

tin

is[2

]*A

Y646

097

1349

Mat

hen

yet

al(2

004)

un

pu

bli

shed

DQ

8321

9417

62th

isst

ud

y

Rhod

otor

ula

gram

inis

Di

Men

na

AF

0704

3160

4F

ell

etal

(199

8)X

8382

7**

1803

Cai

etal

(199

6)

Rhod

otor

ula

hor

dea

Ro

dr.

Mir

.&

Wei

jman

[1]

AY5

1288

162

3B

eger

ow

etal

(200

3)u

np

ub

lish

ed

Rhod

otor

ula

hor

dea

[2]*

AY6

3190

114

12M

ath

eny

etal

(200

4)u

np

ub

lish

edA

Y657

013

1777

Mat

hen

yet

al(2

004)

un

pu

bli

shed

Rhod

otor

ula

lact

osa

T.

Has

eg.

AF

1899

3660

1F

ell

etal

(200

0)D

4536

617

48Su

het

al(1

996a

)

Rhod

otor

ula

lary

ngi

sR

eier

sol

AF

1899

4262

9F

ell

etal

(200

0)A

B12

6649

1782

Nag

aham

aet

al(2

003)

un

pu

bli

shed

Rhod

otor

ula

mari

na

Ph

aff,

Mra

k&

O.B

.W

illi

ams

AF

1899

4462

9F

ell

etal

(200

0)A

B12

6645

1784

Nag

aham

aet

al(2

003)

un

pu

bli

shed

Rhod

otor

ula

min

uta

(Sai

to)

F.C

.H

arri

son

AF

1899

4562

9F

ell

etal

(200

0)D

4536

717

52Su

het

al(1

996a

)

SUP

PL

EM

EN

TA

RY

TA

BL

EII

.C

on

tin

ued

Spec

ies

nu

c-ls

urD

NA

nu

c-ss

urD

NA

Gen

Ban

kn

o.

len

gth

(bp

)R

efer

ence

(cit

edin

Gen

ban

k)G

enB

ank

no

.le

ngt

h(b

p)

Ref

eren

ce(c

ited

inG

enb

ank)

Rhod

otor

ula

mu

cila

gin

osa

(A.

Jorg

.)F

.C.

Har

riso

nA

F07

0432

600

Fel

let

al(1

998)

AB

0216

68**

1760

Ham

amo

toan

dN

akas

e(2

000)

Rhod

otor

ula

pall

ida

Lo

dd

erA

F18

9962

629

Fel

let

al(2

000)

AB

1266

5117

84N

agah

ama

etal

(200

3)u

np

ub

lish

edR

hod

otor

ula

pin

icol

aF

.Y.

Bai

,L

.D.

Gu

o&

J.H

.Z

hao

AF

4442

9362

7Z

hao

etal

(200

2)A

B12

6652

1783

Nag

aham

aet

al(2

003)

un

pu

bli

shed

Rhod

otor

ula

sloo

ffia

eE

.K.

No

vak

&V

oro

s-F

elka

iA

F18

9968

629

Fel

let

al(2

000)

AB

1266

53**

1781

Nag

aham

aet

al(2

003)

un

pu

bli

shed

Rhod

otor

ula

son

ckii

(Ho

psu

-Hav

u,

Tu

nn

ela

&Ya

rro

w)

Ro

dr.

Mir

.&

Wei

jman

[1]

AF

1899

6962

7F

ell

etal

(200

0)

Rhod

otor

ula

son

ckii

[2]

AY2

1300

959

2Sa

mp

aio

etal

(200

3)

Rhod

otor

ula

sp.

1A

B05

5196

d63

6Sj

amsu

rid

zal

etal

(200

1)u

np

ub

lish

edA

B05

5191

d17

42Sj

amsu

rid

zal

etal

(200

1)u

np

ub

lish

ed

Rhod

otor

ula

sp.

2A

B05

5197

d63

6Sj

amsu

rid

zal

etal

(200

1)u

np

ub

lish

edA

B05

5192

d17

43Sj

amsu

rid

zal

etal

(200

1)u

np

ub

lish

ed

Rhod

otor

ula

sp.

3A

B17

6591

e59

1N

akas

eet

al(2

004)

un

pu

bli

shed

AB

1765

30e

1783

Nak

ase

etal

(200

4)u

np

ub

lish

ed

Rhod

otor

ula

sp.

4A

B05

5194

f63

7Sj

amsu

rid

zal

etal

(200

1)u

np

ub

lish

edA

B05

5189

f17

36Sj

amsu

rid

zal

etal

(200

1)u

np

ub

lish

ed

Rhod

otor

ula

sp.

5A

B05

5195

g63

4Sj

amsu

rid

zal

etal

(200

1)u

np

ub

lish

edA

B05

5190

g17

19Sj

amsu

rid

zal

etal

(200

1)u

np

ub

lish

ed

Sacc

obla

stia

fari

nace

a(H

oh

n.)

Do

nk

AJ4

0640

190

3L

ange

r(2

000)

un

pu

bli

shed

Saka

guch

iadacr

yoid

ea(F

ell,

I.L

.H

un

ter

&T

allm

an)

Y.Ya

mad

a,K

.M

aed

a&

Mik

ata

[1]

AF

1899

7257

1F

ell

etal

(200

0)

Saka

guch

iadacr

yoid

ea[2

]A

F18

9973

571

Fel

let

al(2

000)

Sep

toba

sidiu

mbu

rtii

Llo

ydA

Y373

388

1430

McL

augh

lin

etal

(200

4)

Sep

toba

sidiu

mca

nes

cen

sB

urt

AY3

7338

917

87M

cLau

ghli

net

al(2

004)

Sep

toba

sidiu

mca

rest

ian

um

Bre

s.L

2028

954

8B

erre

set

al(1

995)

Sep

toba

sidiu

msp

.hA

Y254

182

570

Lu

tzet

al(2

004a

)A

Y123

320*

*17

29W

ingf

ield

etal

(200

4)Sphace

loth

eca

pol

ygon

i-per

sica

riae

G.

Dem

l&

Ob

erw

.A

F18

9974

619

Fel

let

al(2

000)

Sphace

loth

eca

pol

ygon

i-se

rru

lati

Mai

reA

Y512

884

620

Beg

ero

wet

al(2

003)

un

pu

bli

shed

Sphen

ospor

ake

vor

kian

iiL

ind

erD

Q35

4521

1205

Aim

e(2

006)

Spic

ulo

gloe

asp

.A

Y512

885

601

Beg

ero

wet

al(2

003)

un

pu

bli

shed

Spor

idio

bolu

sjo

hn

son

iiN

ylan

d[1

]A

Y167

608

604

Alv

arez

-Ro

dri

guez

etal

(200

3)L

2226

1**

1760

Swan

nan

dT

aylo

r(1

993)

Spor

idio

bolu

sjo

hn

son

ii[2

]*A

Y745

718

1371

Mat

hen

yet

al(2

004)

un

pu

bli

shed

AB

0216

72**

1807

Ham

amo

toan

dN

akas

e(2

000)

Spor

idio

bolu

spara

rose

us

Fel

l&

Tal

lman

[1]

AF

0704

3760

1F

ell

etal

(199

8)A

B02

1689

**17

59H

amam

oto

and

Nak

ase

(200

0)

Spor

idio

bolu

spara

rose

us

[2]

AF

1899

7860

1F

ell

etal

(200

0)A

B02

1694

**17

58H

amam

oto

and

Nak

ase

(200

0)

Spor

idio

bolu

ssa

lmon

icol

orF

ell

&T

allm

anA

F07

0439

604

Fel

let

al(1

998)

AB

0216

9717

81H

amam

oto

and

Nak

ase

(200

0)

Spor

obol

omyc

esbl

um

eae

M.

Tak

ash

.&

Nak

ase

AY2

1301

057

3Sa

mp

aio

etal

(200

3)A

B03

0321

1756

Tak

ash

ima

and

Nak

ase

(200

0)

Spor

obol

omyc

esco

pro

smae

Ham

am.

&N

akas

eA

F18

9980

629

Fel

let

al(2

000)

D66

880

1757

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

esco

pro

smic

ola

Ham

am.

&N

akas

e[1

]A

F18

9981

630

Fel

let

al(2

000)

D66

879

1749

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

esco

pro

smic

ola

[2]

AY5

1288

863

2B

eger

ow

etal

(200

3)u

np

ub

lish

ed

Spor

obol

omyc

esdra

cophyl

liH

amam

.&

Nak

ase

AF

1899

8263

0F

ell

etal

(200

0)D

6688

217

57H

amam

oto

and

Nak

ase

(200

0)

SUP

PL

EM

EN

TA

RY

TA

BL

EII

.C

on

tin

ued

Spec

ies

nu

c-ls

urD

NA

nu

c-ss

urD

NA

Gen

Ban

kn

o.

len

gth

(bp

)R

efer

ence

(cit

edin

Gen

ban

k)G

enB

ank

no

.le

ngt

h(b

p)

Ref

eren

ce(c

ited

inG

enb

ank)

Spor

obol

omyc

esel

onga

tus

R.G

.Sh

ivas

&R

od

r.M

ir.

AF

1899

8360

1F

ell

etal

(200

0)A

B02

1669

1761

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

esfa

lcatu

sN

akas

e,It

oh

&M

.Su

zuki

AF

0754

9062

1F

ell

etal

(199

9)A

B02

1670

1758

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

esfo

liic

ola

R.G

.Sh

ivas

&R

od

r.M

ir.

AF

1899

8462

9F

ell

etal

(200

0)A

B02

1671

1781

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

esgr

aci

lis

Der

xA

F18

9985

629

Fel

let

al(2

000)

AB

1784

8017

87N

agah

ama

etal

(200

4)u

np

ub

lish

ed

Spor

obol

omyc

esgr

iseo

flavu

sN

akas

e&

M.

Suzu

kiA

F20

7888

610

Ho

ng

etal

(200

0)D

6688

417

58H

amam

oto

and

Nak

ase

(200

0)Spor

obol

omyc

esin

osit

ophil

us

Nak

ase

&M

.Su

zuki

AF

1899

8761

9F

ell

etal

(200

0)A

B02

1673

1781

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

eskl

uyv

eri-

nie

lii

Van

der

Wal

tA

F18

9988

629

Fel

let

al(2

000)

AB

0216

7417

53H

amam

oto

and

Nak

ase

(200

0)Spor

obol

omyc

esla

ctop

hil

us

Nak

ase,

Ito

h,

M.

Suzu

ki&

Ban

do

ni

AF

1774

1162

1Sa

mp

aio

etal

(199

9b)

AB

0216

7516

68H

amam

oto

and

Nak

ase

(200

0)Spor

obol

omyc

esli

nder

ae

Nak

ase,

M.

Tak

ash

.&

Ham

am.

[1]

AF

1899

8963

1F

ell

etal

(200

0)

Spor

obol

omyc

esli

nder

ae

[2]

AF

2078

9062

1H

on

get

al(2

000)

D66

885

1753

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

esn

ylan

dii

M.

Tak

ash

.&

Nak

ase

AF

3871

2357

3V

aler

ioet

al(2

002)

AB

0303

1917

56T

akas

him

aan

dN

akas

e(2

000)

Spor

obol

omyc

esor

yzic

ola

Nak

ase

&M

.Su

zuki

AF

1899

9062

9F

ell

etal

(200

0)A

B02

1677

1756

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

esphyl

lom

ati

sV

and

erW

alt

&Y.

Yam

ada

AF

1899

9162

9F

ell

etal

(200

0)A

B02

1685

1761

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

espoo

nso

okia

eM

.T

akas

h.

&N

akas

eA

F38

7124

570

Val

erio

etal

(200

2)A

B03

0320

1757

Tak

ash

ima

and

Nak

ase

(200

0)Spor

obol

omyc

esru

ber

(Nak

ase,

G.

Oka

da

&Su

giy.

)B

oek

ho

ut

AF

1899

9262

6F

ell

etal

(200

0)A

B02

1686

2072

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

essa

lici

nu

s(B

.N.

Joh

ri&

Ban

do

ni)

Nak

ase

&S.

Ito

AF

1899

9562

5F

ell

etal

(200

0)A

B02

1687

1760

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

essa

sico

laN

akas

e&

M.

Suzu

kiA

F20

7889

613

Ho

ng

etal

(200

0)A

B02

1688

2088

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

essi

ngu

lari

sP

haf

f&

Car

mo

Sou

zaA

F20

7885

609

Ho

ng

etal

(200

0)A

B02

1690

**17

63H

amam

oto

and

Nak

ase

(200

0)Spor

obol

omyc

essu

bbru

nn

eus

Nak

ase

&M

.Su

zuki

*A

Y745

717

1431

Mat

hen

yet

al(2

004)

un

pu

bli

shed

AB

0216

9117

44H

amam

oto

and

Nak

ase

(200

0)

Spor

obol

omyc

esta

upoe

nsi

sH

amam

.&

Nak

ase

AF

1774

1362

3Sa

mp

aio

etal

(199

9b)

D66

886

2044

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

ests

uga

e(P

haf

f&

Car

mo

Sou

za)

Nak

ase

&It

oh

AF

1899

9862

1F

ell

etal

(200

0)A

B02

1692

1760

Ham

amo

toan

dN

akas

e(2

000)

Spor

obol

omyc

esxa

nth

us

(Nak

ase,

G.

Oka

da

&Su

giy.

)B

oek

ho

ut

AF

1774

1461

6Sa

mp

aio

etal

(199

9b)

D64

118

1730

Suh

etal

(199

6b)

Spor

obol

omyc

esyu

nn

an

ensi

sF

.Y.

Bai

,M

.T

akas

h.,

Ham

am.

&N

akas

eA

Y335

162

601

Bai

etal

(200

4)A

F22

9176

1777

Bai

etal

(200

1)

Ste

rigm

ato

myc

esel

via

eSo

nck

&Ya

rr[1

]A

F18

9999

632

Fel

let

al(2

000)

Ste

rigm

ato

myc

esel

via

e[2

]A

F19

0000

632

Fel

let

al(2

000)

AY3

7339

0**

1047

McL

augh

lin

etal

(200

4)

SUP

PL

EM

EN

TA

RY

TA

BL

EII

.C

on

tin

ued

Spec

ies

nu

c-ls

urD

NA

nu

c-ss

urD

NA

Gen

Ban

kn

o.

len

gth

(bp

)R

efer

ence

(cit

edin

Gen

ban

k)G

enB

ank

no

.le

ngt

h(b

p)

Ref

eren

ce(c

ited

inG

enb

ank)

Ste

rigm

ato

myc

eshalo

phil

us

Fel

l*A

Y745

716

1400

Mat

hen

yet

al(2

004)

un

pu

bli

shed

D64

119

1749

Suh

etal

(199

6b)

Sti

lbu

mvu

lgare

To

de

AY3

7338

717

99M

cLau

ghli

net

al(2

004)

Than

ato

phyt

um

croc

oru

m(P

ers.

)N

ees

AY8

8516

8i91

7M

ath

eny

etal

(200

5)u

np

ub

lish

edD

8564

8i **17

42K

un

inag

a(1

996)

un

pu

bli

shed

Tri

phra

gmiu

mu

lmari

ae

(DC

.)L

ink

AF

4262

1951

2M

aier

etal

(200

3)A

Y125

401

1698

Win

gfie

ldet

al(2

004)

Tu

berc

uli

na

maxi

ma

Ro

str.

[1]

AY2

2204

411

19L

utz

etal

(200

4b)

Tu

berc

uli

na

maxi

ma

[2]

AY2

9240

811

08L

utz

etal

(200

4a)

Tu

berc

uli

na

sbro

zzii

Cav

ara

&Sa

cc.

[1]

AY2

2204

559

3L

utz

etal

(200

4b)

Tu

berc

uli

na

sbro

zzii

[2]

AY2

9242

559

3L

utz

etal

(200

4a)

Uro

myc

esappen

dic

ula

tus

(Per

s.ex

Per

s.)

Un

ger*

AY7

4570

413

68M

ath

eny

etal

(200

5)u

np

ub

lish

edD

Q35

4510

1775

Aim

e(2

006)

Ust

ilen

tylo

ma

flu

itan

s(L

iro

)V

anky

AF

0098

8257

9B

eger

ow

etal

(199

7)A

Y124

481

2059

Bau

eret

al(2

003)

aas

Ben

sin

gton

iaphyl

ladu

sY.

Yam

ada,

Nak

agaw

a&

Van

der

Wal

t.bas

Zym

oxen

oglo

eaer

iophor

iD

.J.

McL

augh

lin

&D

ou

ble

s.cas

Rhod

otor

ula

crea

tin

ivor

aG

olu

bev

.d

asR

hod

otor

ula

cass

iico

la(S

jam

suri

dza

let

alu

np

ub

lish

ed).

eas

Rhod

otor

ula

fush

an

ensi

s(N

akas

eet

alu

np

ub

lish

ed).

fas

Rhod

otor

ula

nym

phaea

e(S

jam

suri

dza

let

alu

np

ub

lish

ed).

gas

Rhod

otor

ula

sam

an

eae

(Sja

msu

rid

zal

etal

un

pu

bli

shed

).h

25S

isfr

om

Sep

toba

sidiu

msp

.;18

Sis

fro

mS.

can

esce

ns.

ias

Hel

icob

asi

diu

mpu

rpu

reu

m.

SUP

PL

EM

EN

TA

RY

TA

BL

EII

.C

on

tin

ued

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SUPPLEMENTARY FIG. 2A (Expanded). Phylogenetic relationships of Pucciniomycotina based on analyses of Dataset 1 (128OTUs, each with nuc-lsu rDNA and nuc-ssu rDNA sequences). Phylogram representing one of 36 equally most parsimonioustrees (8215 steps, CI 5 0.345, RI 5 0.731). Nodes with asterisks collapse in the strict consensus of equally most parsimonioustrees. Support values include MP bootstrap frequencies above 70% (first value, before slash), NJ bootstrap frequencies above70% (second value) and Bayesian posterior probabilities above 0.70. A. Ascomycete outgroups, Ustilaginomycotina,Agaricomycotina, and Pucciniomycotina p.p.

SUPPLEMENTARY FIG. 2B (Expanded). Phylogenetic relationships of Pucciniomycotina based on analyses of Dataset 1 (128OTUs, each with nuc-lsu rDNA and nuc-ssu rDNA sequences). Phylogram representing one of 36 equally most parsimonioustrees (8215 steps, CI 5 0.345, RI 5 0.731). Nodes with asterisks collapse in the strict consensus of equally most parsimonioustrees. Support values include MP bootstrap frequencies above 70% (first value, before slash), NJ bootstrap frequencies above70% (second value) and Bayesian posterior probabilities above 0.70. B. Pucciniomycotina p.p. The small cladogram depicts thetopology of Microbotryomycetidae obtained in Bayesian analyses, with posterior probabilities indicated only for stronglysupported nodes that conflict with the MP topology.

SUPPLEMENTARY FIG. 3A. Phylogenetic relationships in the Pucciniomycotina based on analyses of Dataset 2 (208 OTUs, 128with nuc-lsu rDNA and nuc-ssu rDNA sequences, 74 with only nuc-lsu rDNA sequences, indicated by ‘‘(lsu)’’ after taxon name,and 6 with only nuc-ssu rDNA sequences, indicated by ‘‘(ssu)’’ after taxon name). Strict consensus of 1000 equally mostparsimonious trees (9748 steps, CI50.31, RI50.729). MP bootstrap values above 70% are indicated. A. Ascomycete outgroups,Ustilaginomycotina, Agaricomycotina, and Pucciniomycotina p.p.

SUPPLEMENTARY FIG. 3B. Phylogenetic relationships in the Pucciniomycotina based on analyses of Dataset 2 (208 OTUs, 128with nuc-lsu rDNA and nuc-ssu rDNA sequences, 74 with only nuc-lsu rDNA sequences, indicated by ‘‘(lsu)’’ after taxon name,and 6 with only nuc-ssu rDNA sequences, indicated by ‘‘(ssu)’’ after taxon name). Strict consensus of 1000 equally mostparsimonious trees (9748 steps, CI50.31, RI50.729). MP bootstrap values above 70% are indicated. B. Pucciniomycotina p.p.

SUPPLEMENTARY FIG. 4. Life cycle of Septobasidium meredithae (Septobasidiales). A. Transversely septate basidium givesrise to forcibly discharged spores. B. Spores are subdivided by septa, and each section gives rise to bud cells that also bud toform yeast colonies in culture. C. When spores encounter a young scale insect, the clusters of bud cells form hyphae thatpenetrate the cuticle of the scale insect and begin to form coiled structures called haustoria. Infected scale insect settles on thehost plant and becomes completely invaded by the fungus. The fungus grows out of the insect to form a mycelial mat thatcovers the host plant and adjacent uninfected scale insects, producing basidia along the upper surface. SUPPLEMENTARY FIG. 5.Life cycle of the rust Gymnosporangium juniperi-virginianae (Pucciniales). A. Teliospores germinate to produce basidia andhaploid basidiospores that are wind-borne to the leaf of a rosaceous host. B. Spermogonia containing haploid spermatia onthe adaxial leaf surface. C. The products from compatible spermatia fuse to form limited dikaryotic hyphae that emerge fromthe abaxial leaf surface forming spore-filled sori known as aecia. The aecia contain long chains of dikaryotic aeciospores thatare wind-borne to the alternate host. D. Juniperus spp. are infected with aeciospores, producing galls from which gelatinouscolumns of telia emerge. Karyogamy occurs within the teliospores. SUPPLEMENTARY FIG. 6. Life cycle of Rhodosporidiumtoruloides (Sporidiobolales). A. A transversely septate basidium gives rise to spores. B. The spores bud and persist as yeasts. C.Yeast cells of the proper mating types fuse via a thin hyphal connection to form a dikaryon. D. The dikaryon forms hyphae thatwill eventually give rise to teliospores.

an overview of the higher level classification of

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