Phylogeny Of The Pluteaceae (Agaricales, Basidiomycota .

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ARTICLE IN PRESSf u n g a l b i o l o g y x x x ( 2 0 1 0 ) 1 e2 0journal homepage: www.elsevier.com/locate/funbioPhylogeny of the Pluteaceae (Agaricales, Basidiomycota):taxonomy and character evolutionAlfredo JUSTOa,*,1, Alfredo VIZZINIb,1, Andrew M. MINNISc, Nelson MENOLLI Jr.d,e,Marina CAPELARId, Olivia RODR ıGUEZf, Ekaterina MALYSHEVAg, Marco CONTUh,Stefano GHIGNONEi, David S. HIBBETTaaBiology Department, Clark University, 950 Main St., Worcester, MA 01610, USA di Torino, Viale Mattioli 25, I-10125 Torino, ItalyDipartimento di Biologia Vegetale, UniversitacSystematic Mycology & Microbiology Laboratory, USDA-ARS, B011A, 10300 Baltimore Ave., Beltsville, MD 20705, USAd nica, Caixa Postal 3005, Sa o Paulo, SP 010631 970, Brazil cleo de Pesquisa em Micologia, Instituto de BotaNue o, Cie ncia e Tecnologia de Sa o Paulo, Rua Pedro Vicente 625, Sa o Paulo, SP 01109 010, BrazilInstituto Federal de Educaçaf nica y Zoolog ıa, Universidad de Guadalajara, Apartado Postal 1-139, Zapopan, Jal. 45101, MexicoDepartamento de BotabgKomarov Botanical Institute, 2 Popov St., St. Petersburg RUS-197376, RussiaVia Marmilla 12, I-07026 Olbia (OT), ItalyiInstituto per la Protezione delle Piante, CNR Sezione di Torino, Viale Mattioli 25, I-10125 Torino, Italyharticle infoabstractArticle history:The phylogeny of the genera traditionally classified in the family Pluteaceae (Agaricales,Received 17 June 2010Basidiomycota) was investigated using molecular data from nuclear ribosomal genesReceived in revised form(nSSU, ITS, nLSU) and consequences for taxonomy and character evolution were evaluated.16 September 2010The genus Volvariella is polyphyletic, as most of its representatives fall outside the PluteoidAccepted 26 September 2010clade and shows affinities to some hygrophoroid genera (Camarophyllus, Cantharocybe).Corresponding Editor:Volvariella gloiocephala and allies are placed in a different clade, which represents the sisterJoseph W. Spataforagroup of Pluteus, and a new generic name, Volvopluteus, is proposed to accommodate thesetaxa. Characters such as basidiospore size and pileipellis structure can be used to separateKeywords:Pluteus, Volvariella and Volvopluteus. The genus Pluteus is monophyletic and includes speciesCharacter evolutionwith partial veil traditionally classified in the genus Chamaeota. The evolution of morpho-Phylogenylogical features used in the infrageneric taxonomy of the genus, such as metuloid cystidiaPluteusand pileipellis structure, was analyzed. Agreement between the molecular phylogeny andVolvariellamorphological subdivision of Pluteus is, generally speaking, good, though some rearrange-Volvopluteusments are necessary: (i) species with non-metuloid pleurocystidia and pileipellis as a cutisare placed either in sect. Celluloderma, together with the species characterized by a hymenidermal pipeipellis, or in sect. Pluteus, with the metuloid bearing species; (ii) subdivision ofsect. Celluloderma according to the presence/absence of cystidioid elements in the pileipellis is not supported by molecular data.ª 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.* Corresponding author.E-mail addresses: ajusto@clarku.edu, alfredo.vizzini@unito.it, Drew.Minnis@ars.usda.gov, menollijr@yahoo.com.br, mcapelariibot@yahoo.com, oliviaramx@yahoo.com, ef.malysheva@gmail.com, mecontu@interfree.it, stefano.ghignone@unito.it, dhibbett@clarku.edu1Both authors contributed equally to this work.1878-6146/ e see front matter ª 2010 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.doi:10.1016/j.funbio.2010.09.012Please cite this article in press as: Justo A et al., Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and characterevolution, Fungal Biology (2010), doi:10.1016/j.funbio.2010.09.012

ARTICLE IN PRESS2IntroductionThe family Pluteaceae Kotl. & Pouzar (Basidiomycota, Agaricales)comprises three genera of non-mycorrhizal agaric fungi (Chamaeota (W.G. Sm.) Earle, Pluteus Fr. and Volvariella Speg.) thatshare the following combination of morphological characters(Fig 1): basidiocarps with lamellae that are free from the stipe;pink or pinkish brown spore print; basidiospores smooth, inamyloid, non-dextrinoid, cyanophilic; and inverse hymenophoral trama. Pluteus and Chamaeota species grow mostly onwood or other decaying plant material (sawdust, wood chips).The majority of species of Volvariella grow terrestrially in thelitter layer of the soil, in grasslands or in woods, but one mycoparasitic and some lignicolous taxa are also known. The recently described Volvariella terrea Musumeci & A. Riva andVolvariella koreana Seok et al. grow among basidiocarps of Agaricus xanthodermus Genev. and Clitocybe alboinfundibuliformeSeok et al. respectively, but the exact nature of the relationshipbetween both pairs of fungi is not yet known (Musumeci &Riva 2007; Seok et al. 2009). The family is readily morphologically distinguishable among the Agaricales, especially basedon the inverse hymenophoral trama and basidiospore characteristics, and a close relation to the Amanitaceae R. Heim exPouzar has been repeatedly postulated (Singer 1986). Separation of the three genera in the Pluteaceae has relied on the presence or absence of partial and universal veil on thebasidiocarps, with Volvariella having a well-developed volva,Chamaeota showing a distinct annulus on the stipe and Pluteuslacking both volva and annulus (Singer 1986).Pluteus, typified by Pluteus cervinus, includes approximately300 species and is distributed worldwide (Kirk et al. 2008).Infrageneric taxonomy is primarily based on the characteristics of the hymenial cystidia and the pileipellis (Fig 1). Singer(1986) recognized three sections: Sect. Pluteus (with metuloidpleurocystidia and pilepellis as a cutis), Sect. HispidodermaFayod (with non-metuloid pleurocystidia and pileipelliscomposed of elongated elements organized as a cutis, anhymeniderm or a trichoderm) and Sect. Celluloderma Fayod(with non-metuloid pleurocystidia and a pileipellis composedof short, clavate or spheropedunculate elements organized asan hymeniderm, with transitions to an epithelium). Sect. Celluloderma is further subdivided into two subsections accordingto the presence (subsect. Mixtini Singer) or absence (subsect.Eucellulodermini Singer) of elongated cystidioid elements inthe pileipellis. A variation on this taxonomic scheme was proposed by Vellinga & Schreurs (1985) that subdivided sect. Hispidoderma into two taxonomic units: the new sect. VillosiVellinga & Schreurs, which accommodates the species withnon-metuloid cystidia and a pileipellis as a cutis, and the subsection Hispidodermini Vellinga & Schreurs in sect. Celluloderma, for the remaining species, characterized by thepileipellis as a hymeniderm or trichoderm made up of elongated elements.A total of 12 taxa have been classified in Chamaeota, thoughsome have been shown to belong in other genera, likeChamaeota dextrinoidespora Z.S. Bi and Chamaeota sinica J.Z.Ying, that are in fact species of Leucoagaricus Locq. ex Singer(Yang 2007). The type species, Chamaeota xanthogramma(Ces.) Earle, is only known from the plate accompanying theA. Justo et al.original description and its true identity has been subjectedto debate through the decades (Corriol & Moreau 2007;Singer 1986). Only Chamaeota mammillata, from North America, and Chamaeota fenzlii, from Europe, are relatively wellknown.Volvariella comprises about 50 species worldwide (Kirk et al.2008), including the cultivated Volvariella volvacea (‘paddystraw mushroom’). Several morphological/ecological groupscan be differentiated within the genus, more or less corresponding to the ‘stirps’ recognized by Singer (1986): Volvariellagloiocephala-group (basidiospores 11 mm long, pileipellis asan ixocutis), Volvariella bombycina-group (pileus covered withconspicuous fibrills, lignicolous), V. volvacea-group (mediumto large species, i.e. pileus 50 mm in diameter, with darklycolored, usually grey-brown, basidiocarps), Volvariella taylorii-group (small species, i.e. pileus 50 mm in diameter,with darkly colored, usually grey-brown, basidiocarps) andVolvariella pusilla-group (small species, with white basidiocarps, including the type species of the genus, Volvariellaargentina Speg. and the mycoparasitic Volvariella surrecta).Moncalvo et al. (2002) performed a phylogenetic analysis ofthe Agaricales based on nLSU data that included 17 sequencesof Pluteus and two of Volvariella. Pluteus appeared well supported as monophyletic and subdivided into two major clades:one with only representatives of sect. Pluteus and the othera mixture of species of sections Celluloderma and Hispidodermasensu Singer (1986). No representatives of subsect. Mixtiniwere included. The genus Melanoleuca Pat., represented bytwo sequences, was placed as the sister group of Pluteus,which was rather unexpected based on morphological data.Melanoleuca has been traditionally classified in the Tricholomataceae R. Heim ex Pouzar (Singer 1986) and is characterized bya white spore print, basidiospores with amyloid ornamentation and regular hymenophoral trama. More surprising wasthe placement of Volvariella (V. volvacea, Volvariella hypophytis)in a very distant position, clustering (with no statistical support) with Fistulina Bull. and Schizophyllum Fr.Matheny et al. (2006) presented the results of a six genephylogeny of the Agaricales, including three taxa of Pluteus,one of Volvariella (V. gloiocephala) and one of Melanoleuca. Inthis analysis Pluteus appears as monophyletic with V. gloiocephala as its sister group, and Melanoleuca closely related. Thethree genera were placed together with members of the hner, the aquatic basidiomyceteAmanitaceae, Pleurotaceae KuLimnoperdon G.A. Escobar and some ‘orphan’ agaric genera(Tricholomopsis Singer, Cantharocybe H.E. Bigelow & A.H. Sm.,Macrocystidia Joss.), in one major group named the ‘Pluteoid’clade. However, the authors pointed out that this generalgrouping was poorly supported and some of its constituentsfell outside the Pluteoid clade in some of the analysis. Binderet al. (2010) recovered a similar topology for Pluteus, V. gloiocephala and Melanoleuca, with Amanita Pers. as the sister group ofthe ‘core’ pluteoid genera, but in this study Tricholomopsis andCantharocybe were placed outside the Pluteoid clade.Minnis et al. (2006) generated new nLSU data for the American C. mammillata and performed a phylogenetic analysis,showing that this annulate species clusters inside Pluteus,and questioned the taxonomic status of the genus Chamaeota.Chamaeota mammillata and the other North American speciesPlease cite this article in press as: Justo A et al., Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and characterevolution, Fungal Biology (2010), doi:10.1016/j.funbio.2010.09.012

ARTICLE IN PRESSPhylogeny of the Pluteaceae3Fig 1 e Morphological characters of the Pluteaceae. a. Pluteus petasatus (sect. Pluteus); b. Pluteus plautus (sect. Hispidoderma);c. Pluteus aurantiorugosus (sect. Celluloderma); d. Pluteus mammillatus ([Chamaeota); e. Volvopluteus gloiocephalus; f. Volvariellavolvacea; geh. Metuloid cystidia (Pluteus sect. Pluteus); iej. Non-metuloid cystidia (Pluteus sect. Hispidoderma andCelluloderma); ken. Pileipellis types in Pluteus: k. Cutis (sect. Pluteus), l. Trichoderm (sect. Hispidoderma), m. Hymeniderm(sect. Celluloderma subsect. Eucellulodermini), n. Hymeniderm with cystidioid elements (sect. Celluloderma subsect. Mixtini);o. Basidiospores of Volvopluteus; p. Basidiospores of Volvariella; q. Pileipellis (ixocutis) of Volvopluteus; r. Pileipellis (cutistrichoderm) of Volvariella. Photos a, b, c, e and f courtesy of Agust ın Caballero. Photo d courtesy of Walter J. Sundberg.of the genus, Chamaeota sphaerospora, were placed in synonymy and the new combination Pluteus mammillatus wasproposed. Based on morphological data alone, the EuropeanC. fenzlii was also transferred to Pluteus, and the subsectionAnnularia (Schulzer) Corriol & P.-A. Moreau was introducedin sect. Hispidoderma to accommodate this species (Corriol &Moreau 2007). Morphology-based phylogenies of Pluteus(Banerjee & Sundberg 1995; Minnis & Sundberg 2009) andPlease cite this article in press as: Justo A et al., Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and characterevolution, Fungal Biology (2010), doi:10.1016/j.funbio.2010.09.012

ARTICLE IN PRESS4description of new taxa based on morphological and molecular data (Menolli et al., 2010; Rodr ıguez et al. 2009, 2010) havealso been published in recent years.The present study has two major objectives. First, it aims toresolve the conflicting results about the evolutionary relationships of the genera Pluteus and Volvariella; second it focuses oncharacter evolution in Pluteus, especially in relation to the proposed infrageneric classifications (Singer 1986; Vellinga &Schreurs 1985). For these purposes, new molecular data ofthree nuclear ribosomal loci, 18S (nSSU), ITS1 þ 5.8S þ ITS2(ITS), and 25S (nLSU), were generated for all the majormorphological/ecological groups of Pluteus and Volvariella.Phylogenetic analyses were performed on single gene andmulti-gene datasets and consequences for morphological evolution and taxonomy in the Pluteaceae were examined. Duringthe course of this study we gained some insights about severalspecies-complexes in the Pluteaceae, including newly discovered taxa, but they will be discussed in detail in a separate paper (Justo et al. 2010).Materials and methodsFungal collectionsA total of 182 fresh or dried specimens of Pluteus and Volvariella were selected for molecular sampling (Table 1). The geographic origin of the collections includes Africa, Asia,Europe, North and South America. In many cases, morphological study and identification of the collections were done previously to this work (Justo & Castro 2007a, 2010; Menolli et al.2010, Minnis & Sundberg 2010), but most specimens were reexamined during the course of this study. Newly collected materials, and all the Asian and African herbarium collections,were studied using standard procedures for morphological examination of the Pluteaceae (e.g. Justo & Castro 2007b; Minnis &Sundberg 2010). Descriptive terms for morphological featuresfollow Vellinga (1988). ‘Q’ is used for the quotient of length andwidth, and ‘avQ’ is the average quotient. Herbarium acronymsfollow Thiers (2010).Taxon sampling for the molecular analysesSelection of taxa for the analyses was aimed to maximize therepresentation of the different morphological and ecologicalgroups (‘stirps’) of Pluteus and Volvariella as recognized bySinger (1986) and, in the case of Pluteus, a wide geographic representation. After examining the results from a preliminaryanalysis of the nLSU dataset, the gene was found to be toohighly conserved to address the infrageneric taxonomy ofPluteus and to resolve the relationships between Pluteus andthe Volvariella gloicephala group, and molecular samplingthen focused on the ITS. Representatives of the major lineagesrecognized in the analysis of the ITS dataset of Pluteus and inthe nLSU dataset of Volvariella, were selected for obtainingnSSU data. A total of 22 nSSU, 180 ITS and 42 nLSU sequenceswere generated for this study (Table 1).Additional sequences (2 nSSU, 32 ITS and 36 nLSU) were retrieved from GenBank (Table 2). The nLSU sequence labeled asPluteus pallidus (Moncalvo et al. 2002), a member of sect.A. Justo et al.Celluloderma, corresponds in fact to Pluteus albineus, a memberof sect. Pluteus (Menolli et al. 2010). Comparison with the sequences generated in this study indicates that at least an additional four nLSU and four ITS sequences deposited inGenbank are also misidentified, and they were renamedaccording to their placement in the phylogenetic analyses(Table 2). In order to find unidentified environmental samplespotentially belonging to Pluteus or Volvariella, all newly generated ITS sequences were used for BLAST searches (http://blast.ncbi.nlm.nih.gov/Blast.cgi), yielding seven additional sequences of Pluteus that were included in the ITS dataset.Genbank sequences, for taxa other than Pluteus andVolvariella, employed in the combined nSSU þ ITS þ nLSUdatasets, are the same ones used in the study of Mathenyet al. (2006). Accession numbers for the sequences used inthe nLSU analysis are given on the tree (Fig 2).DNA extraction, PCR, sequencing and alignmentsApproximately 0.05e0.10 g of tissue (preferably gills) from eachcollection were ground directly in a 1.5 ml eppendorf tube, usingplastic pestles, or in a mortar with liquid nitrogen. DNA wasextracted using 3 % SDS extraction buffer and then isolated bythe sequential addition of phenolechloroform and chloroformeisoamyl alcohol; finally, isopropyl alcohol and 3 M sodium acetate were added to precipitate the DNA, which waswashed with 70 % ethanol and resuspended in sterile water.Primer pairs LR0ReLR5 or LR0ReLR7 were used to amplifya portion of the nLSU gene (Vilgalys Lab, ; ITS1FeITS4 for the ITS(Gardes & Bruns 1993; White et al. 1990) and PNS1eNS8 forthe nSSU (Hibbett 1996; White et al. 1990). For some samples,the nSSU was amplified in two separate fragments usingprimer pairs PNS1eNS41 and NS19beNS8 (Bruns Lab,http://plantbio.berkeley.edu/ bruns/tour/primers.html). Theamplification products were sequenced using ABI PRISM BigDye Terminator Cycle Sequencing Ready Reaction reagentswith the following primer combinations: nLSU forwardprimers (LR0R, LR3R), nLSU reverse primers (LR3, LR5 andLR7 if that primer was used for PCR) (Vilgalys Lab); ITS1F(forward) and ITS4 (reverse) were used for the ITS; nSSU forward primers (PNS1, NS19b, NS51), nSSU reverse primers(NS19bc, NS41, NS8 or alternatively NS6, if NS8 did not yielda good result) (White et al. 1990; Bruns Lab). Sequencing wascarried out on an ABI model 3130 Genetic Analyzer. Rawdata were processed using Sequencher 4.7 (GeneCodes, AnnArbor, Michigan).Sequences were aligned using MAFFT er/). The strategy GeINSeiwas selected for the nLSU and nSSU datasets, and theQeINSei option for the ITS dataset. The alignments werethen examined and manually corrected using MacClade 4.05(Maddison & Maddison 2002). For all the combined datasetseach gene was aligned separately and then concatenated inMacClade. In these datasets only the 5.8S portion of the ITS region was used in the analyses. Alignments have been deposited in TREEbase S10635).Three different datasets were assembled for the phylogenetic analyses:Please cite this article in press as: Justo A et al., Phylogeny of the Pluteaceae (Agaricales, Basidiomycota): taxonomy and characterevolution, Fungal Biology (2010), doi:10.1016/j.funbio.2010.09.012

ARTICLE IN PRESSPhylogeny of the Pluteaceae5Table 1 e New sequences generated for this study with GenBank accession numbers. P [ Pluteus, V [ Volvariella; Vp[ Volvopluteus. An asterisk (*) indicates names being published concurrently with the present article. The symbol ‘!’indicates a type collection (holotypus, epitypus or paratypus).TaxonP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinusP. aff. cervinus (white basidiocarp)P. aff. cinereofuscusP. aff. ephebeusP. aff. ephebeusP. aff. leoninus IP. aff. leoninus IP. aff. leoninus IIP. aff. nothopellitusP. aff. nothopellitusP. aff. phlebophorusP. aff. podospileusP. aff. pouzarianusP. aff. pouzarianusP. aff. semibulbosusP. albostipitatus (Dennis) SingerP. albostipitatus (Dennis) SingerP. albostipitatus (Dennis) P.P.P.P.P.P.P. hneratromarginatus (Singer) Ku hneratromarginatus (Singer) Ku hneratromarginatus (Singer) Kuatropungens A.H. Sm. & Bartelliaurant

Phylogeny Pluteus Volvariella Volvopluteus abstract The phylogeny of the genera traditionally classified in the family Pluteaceae (Agaricales, Basidiomycota) was investigated using molecular data from nuclear ribosomal genes (nSSU, ITS, nLSU) and consequences for

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