A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.

Abstract:

:Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.

journal_name

Mycologia

journal_title

Mycologia

authors

Spatafora JW,Chang Y,Benny GL,Lazarus K,Smith ME,Berbee ML,Bonito G,Corradi N,Grigoriev I,Gryganskyi A,James TY,O'Donnell K,Roberson RW,Taylor TN,Uehling J,Vilgalys R,White MM,Stajich JE

doi

10.3852/16-042

subject

Has Abstract

pub_date

2016-09-01 00:00:00

pages

1028-1046

issue

5

eissn

0027-5514

issn

1557-2536

pii

16-042

journal_volume

108

pub_type

杂志文章
  • New species and new records of dictyostelids from Ukraine.

    abstract::Three species of dictyostelid cellular slime molds were isolated from forest soil, meadow soil and leaf litter collected from Yalta, Crimea, Ukraine. Dictyostelium globisporum is new to science; D. crassicaule and D. sphaerocephalum are new records from Ukraine. Descriptions and illustrations are given based on the Uk...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/10-253

    authors: Liu P,Li Y

    更新日期:2011-05-01 00:00:00

  • Rhizomarasmius epidryas (Physalacriaceae): phylogenetic placement of an arctic-alpine fungus with obligate saprobic affinity to Dryas spp.

    abstract::As a part of a large-scale biogeographical study we examined the evolutionary relationships and taxonomic position of Marasmius epidryas, one of the most typical circumpolar arctic-alpine fungi, characterized by a specific, saprobic affinity to dead tissues of Dryas spp. A phylogenetic analysis based on nLSU and RPB2 ...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/11-018

    authors: Ronikier M,Ronikier A

    更新日期:2011-09-01 00:00:00

  • The species of Cortinarius, section Bovini, associated with conifers in northern Europe.

    abstract::Cortinarius bovinus and morphologically similar conifer-associated species were studied using material mainly from northern Europe. To stabilize the nomenclature, relevant types were examined. Phylogenetic relationships and species limits were investigated with rDNA ITS and nuclear rpb2 sequences as well as morphologi...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/12-320

    authors: Niskanen T,Kytövuori I,Liimatainen K,Lindström H

    更新日期:2013-07-01 00:00:00

  • Regional and local population structure of the pioneer wood-decay fungus Trichaptum abietinum.

    abstract::The population structure of 11 Fennoscandian geographic populations of the pioneer wood-decay basidiomycete Trichaptum abietinum was assessed with PCR-RFLPs, intersequence simple repeats (ISSRs) and mating studies. The three codominant PCR-RFLP markers (1) internal transcribed spacer 2 (nrDNA), (2) glyceraldehyde-3-ph...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:

    authors: Kauserud H,Schumacher T

    更新日期:2003-05-01 00:00:00

  • The nascent-polypeptide-associated complex alpha subunit regulates the polygalacturonases expression negatively and influences the pathogenicity of Sclerotinia sclerotiorum.

    abstract::Sclerotinia sclerotiorum is a necrotrophic plant-pathogenic fungus that infects more than 400 species of plants. In this study the nascent polypeptide-associated complex α subunit gene of S. sclerotiorum (SsNACα; accession No. XP_001593856.1) was cloned and characterized. The relative transcript expression of SsNACα a...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/14-250

    authors: Li X,Guo M,Xu D,Chen F,Zhang H,Pan Y,Li M,Gao Z

    更新日期:2015-11-01 00:00:00

  • New species of Laboulbenia from Ecuador, with evidence for host switch in the Laboulbeniales.

    abstract::Ten new species of Laboulbenia from Ecuador are described. These are L. barraganii, parasitic on Platamops sp. (Salpingidae); L. biformis, parasitic on Diploharpus rossii Moret (Carabidae); L. davidsonii, parasitic on Odontocheila spp. (Carabidae); L. gregaria, parasitic on Philonthus sp. (Staphylinidae); L. micrandra...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/10-117

    authors: Rossi W

    更新日期:2011-01-01 00:00:00

  • A taxonomic revision of the genus Puccinia on Lycieae, a tribe of Solanaceae.

    abstract::We present a taxonomic and phylogenetic study of Puccinia species (rust fungi) infecting tribe Lycieae (Solanaceae), with focus on the New World taxa. Phylogenetic analyses using nuclear (nuc) rDNA 5.8S-ITS2 (ITS2) and mitochondrial (mt) cytochrome oxidase subunit 3 (CO3) show that Puccinia species occurring on Lyciae...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.1080/00275514.2018.1478538

    authors: Otálora MAG,Berndt R

    更新日期:2018-07-01 00:00:00

  • Life cycle of Puccinia acroptili on Rhaponticum (= Acroptilon) repens.

    abstract::Russian knapweed (Rhaponticum repens) is a rangeland weed pest in the western United States. One candidate fungus for biological control of R. repens is Puccinia acroptili, which causes a rust disease. Understanding the life cycle of candidate rust fungi for weed biological control is an essential component in risk as...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/08-215

    authors: Bruckart WL 3rd,Eskandari FM,Berner DK,Aime MC

    更新日期:2010-01-01 00:00:00

  • Lignicolous freshwater Ascomycota from Thailand: Hymenoscyphus varicosporoides and its Tricladium anamorph.

    abstract::A Tricladium anamorph for the discomycete Hymenoscyphus varicosporoides was established in culture from both conidia and ascospores collected in KhaoYai National Park, Thailand, and is compared with Tricladium indicum and T. marylandicum. Hymenoscyphus varicosporoides is compared with Cudoniella indica. ...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:

    authors: Sivichai S,Jones EB,Hywel-Jones NL

    更新日期:2003-03-01 00:00:00

  • Penicillium kongii, a new terverticillate species isolated from plant leaves in China.

    abstract::A new Penicillium species isolated from plant leaves, characterized by restricted growth, terverticillate penicilli, ovoid to ellipsoidal conidia and a red soluble pigment on yeast extract sucrose agar is reported here. Penicillium kongii sp. nov. belongs to subgenus Penicillium section Brevicompacta and is morphologi...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/13-022

    authors: Wang B,Wang L

    更新日期:2013-11-01 00:00:00

  • Taxonomic revision of Pseudolachnea and Pseudolachnella and establishment of Neopseudolachnella and Pseudodinemasporium gen. nov.

    abstract::The taxonomy of Pseudolachnea and Pseudolachnella is controversial. Some authors have regarded them as congeneric, whereas others have considered them to be distinct genera differentiated merely on the number of conidial septa. A total of 26 isolates of Pseudolachnea-like fungi were subjected to morphological examinat...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/14-171

    authors: Hashimoto A,Sato G,Matsuda T,Matsumura M,Hatakeyama S,Harada Y,Ikeda H,Tanaka K

    更新日期:2015-03-01 00:00:00

  • A strategy for recovering high quality genomic DNA from a large number of Phytophthora isolates.

    abstract::We present a strategy to recover high molecular weight genomic DNA from large numbers of isolates of Phytophthora. Included are steps for generating mycelial mass in 24-well reuseable deep well plates, efficient lyophilization and disruption of the mycelium and genomic DNA extraction with 96-well glass fiber filter pl...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/mycologia.98.3.514

    authors: Lamour K,Finley L

    更新日期:2006-05-01 00:00:00

  • Two new rhytismatales on Rhododendron from China.

    abstract::The new species Myriophacidium ramosum and Neococcomyces erumpens are described from Rhododendron twigs in the eastern Himalayan Mountains in China. Both are members of the Rhytismatales. ...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/08-092

    authors: Hou CL,Piepenbring M

    更新日期:2009-05-01 00:00:00

  • The endangered Hastings River mouse (Pseudomys oralis) as a disperser of ectomycorrhizal fungi in eastern Australia.

    abstract::Rodents are the most widespread and diverse order of vertebrate mycophagists and are key to the dispersal of mycorrhizal fungi. Rodents consume and subsequently disperse fungi through their feces on every continent except Antarctica. This study examines the fungal taxa consumed by the Hastings River mouse (Pseudomys o...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.1080/00275514.2020.1777383

    authors: Elliott TF,Townley S,Johnstone C,Meek P,Gynther I,Vernes K

    更新日期:2020-11-01 00:00:00

  • An unknown mechanism promotes somatic incompatibility in Ceratobasidium bicorne.

    abstract::Strains of Ceratobasidium bicorne (anamorph uninucleate Rhizoctonia), causing root dieback in nursery-grown conifer seedlings, were fruited in the laboratory and the pairing interactions among sibling, single-basidiospore progeny were investigated. No mating reactions were observed. Instead, a high frequency of somati...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:

    authors: Hietala AM,Korhonen K,Sen R

    更新日期:2003-03-01 00:00:00

  • Morphological and molecular characterization of Phytophthora glovera sp. nov. from tobacco in Brazil.

    abstract::A root rot disease of cultivated tobacco called yellow stunt has been observed in the burley tobacco production areas of Brazil since the early 1990s. Root infecting fungi and straminipiles were isolated from the roots of diseased tobacco plants, including a semi-papillate, homothallic, slow growing Phytophthora speci...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/09-157

    authors: Abad ZG,Ivors KL,Gallup CA,Abad JA,Shew HD

    更新日期:2011-03-01 00:00:00

  • New species and records of bioluminescent Mycena from Mexico.

    abstract::Seven species of bioluminescent fungi are recorded from the cloud forests in Mexico. Six represent new species belonging to the genus Mycena, whereas Mycena globulispora is a new distribution record for the country. Descriptions, illustrations, photographs, and an identification key to bioluminescent fungi species fro...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.1080/00275514.2018.1554172

    authors: Cortés-Pérez A,Desjardin DE,Perry BA,Ramírez-Cruz V,Ramírez-Guillén F,Villalobos-Arámbula AR,Rockefeller A

    更新日期:2019-03-01 00:00:00

  • Light might regulate divergently depside and depsidone accumulation in the lichen Parmotrema hypotropum by affecting thallus temperature and water potential.

    abstract::Depsides and depsidones are the most common secondary products uniquely produced in lichens by the fungal symbiont, and they accumulate on the outer surface of its hyphae. Their biological roles are subject to debate. Quantitatively the compounds typical of a given lichen can vary dramatically from thallus to thallus....

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/07-162r

    authors: Armaleo D,Zhang Y,Cheung S

    更新日期:2008-07-01 00:00:00

  • Studies in neotropical polypores 15: new and interesting species from Guyana.

    abstract::During fieldwork in Guyana several unusual and distinctive taxa of polypores were collected, three of which are described here as new. The first of these, Amauroderma coltricioides is the first species known in the Ganodermataceae with smooth basidiospores. Coltricia verrucata and Coltriciella navispora also are descr...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.1080/15572536.2004.11833065

    authors: Aime MC,Henkel TW,Ryvarden L

    更新日期:2003-07-01 00:00:00

  • The white-rot fungus Pleurotus ostreatus secretes laccase isozymes with different substrate specificities.

    abstract::Four laccase isozymes (LCC1, LCC2, LCC3 and LCC4) synthesized by Pleurotus ostreatus strain V-184 were purified and characterized. LCC1 and LCC2 have molecular masses of about 60 and 65 kDa and exhibited the same pI value (3.0). Their N termini were sequenced, revealing the same amino acid sequence and homology with l...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.1080/15572536.2004.11833017

    authors: Mansur M,Arias ME,Copa-Patiño JL,Flärdh M,González AE

    更新日期:2003-11-01 00:00:00

  • Freshwater ascomycetes: Natipusillaceae, a new family of tropical fungi, including Natipusilla bellaspora sp. nov. from the Peruvian Amazon.

    abstract::A new ascomycete species, Natipusilla bellaspora, collected from submerged woody debris in a freshwater stream at Los Amigos Biological Station, Madre De Dios in the Peruvian Amazon is described and illustrated. This fungus is characterized by small, globose to subglobose, hyaline ascomata; small, globose to subglobos...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/11-150

    authors: Raja HA,Miller AN,Shearer CA

    更新日期:2012-03-01 00:00:00

  • Talaromyces rubrifaciens, a new species discovered from heating, ventilation and air conditioning systems in China.

    abstract::A new Talaromyces species, T. rubrifaciens, was isolated from supply air outlets of heating, ventilation and air conditioning (HVAC) systems in three kinds of public building in Beijing and Nanjing, China. Morphologically it exhibits many characters of section Trachyspermi but is distinguished from other species of th...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/15-233

    authors: Luo Y,Lu X,Bi W,Liu F,Gao W

    更新日期:2016-07-01 00:00:00

  • Multilocus phylogenetic and coalescent-based methods reveal dilemma in generic limits, cryptic species, and a prevalent intercontinental disjunct distribution in Geopyxis (Pyronemataceae s. l., Pezizomycetes).

    abstract::Species limits in the small genus Geopyxis are debatable because of problems with interpreting the few phenotypic features and poor documentation of types. To clarify species boundaries and diversity, we studied the morphology of 74 specimens of Geopyxis from the Northern Hemisphere, including five types, and sequence...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/16-100

    authors: Wang XH,Huhtinen S,Hansen K

    更新日期:2016-11-01 00:00:00

  • Species recognition, geographic distribution and host-pathogen relationships: a case study in a group of lignicolous basidiomycetes, Phellinus s.l.

    abstract::Morphological, phylogenetic (sequencing of the ribosomal ITS region) and, if applicable, biological (pairings of single-spore testers) species recognition have been used to resolve relationships among 69 collections belonging to the Hymenochaetales genera Phellinus s.str. and Fomitiporia. The isolates originate from a...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.1080/15572536.2005.11832927

    authors: Fischer M,Binder M

    更新日期:2004-07-01 00:00:00

  • Phytophthora xserendipita sp. nov. and P. xpelgrandis, two destructive pathogens generated by natural hybridization.

    abstract::The first natural hybrids in the genus Phytophthora were described in 1998, and they were the result of hybridization between P. nicotianae and P. cactorum. They were described formally as Phytophthora × pelgrandis in 2009. In 2007 a second type of P. cactorum hybrid species was described, generated by hybridization b...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/11-272

    authors: Man In 't Veld WA,Rosendahl KC,Hong C

    更新日期:2012-11-01 00:00:00

  • Ribosomal DNA phylogenies of Cyathus: is the current infrageneric classification appropriate?

    abstract::Phylogenetic relationships within the genus Cyathus (bird's nest fungi) were investigated with neighbor joining, maximum likelihood, weighted maximum parsimony and MrBayes analyses of ITS and LSU ribosomal DNA sequences datasets. Twenty-two taxa of Cyathus were used in the analyses based primarily on type and authenti...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/mycologia.99.3.385

    authors: Zhao RL,Jeewon R,Desjardin DE,Soytong K,Hyde KD

    更新日期:2007-05-01 00:00:00

  • Novel taxa in Cladochytriales (Chytridiomycota): Karlingiella (gen. nov.) and Nowakowskiella crenulata (sp. nov.).

    abstract::Six Nowakowskiella species from Brazil were identified and purified on corn meal agar (CMA) plus glucose and Peptonized Milk-Tryptone-Glucose (PmTG) media and placed into a phylogenetic framework for the genus. New sequence data are presented for four species: N. elongata, N. multispora, and N. ramosa and the new spec...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.1080/00275514.2019.1588583

    authors: Jerônimo GH,Jesus AL,Simmons DR,James TY,Pires-Zottarelli CLA

    更新日期:2019-05-01 00:00:00

  • New Boletaceae taxa from Guyana: Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov., Singerocomus rubriflavus gen. and sp. nov., and a new combination for Xerocomus inundabilis.

    abstract::Binderoboletus segoi gen. and sp. nov., Guyanaporus albipodus gen. and sp. nov. and Singerocomus rubriflavus gen. and sp. nov. (Boletaceae, Boletales, Basidiomycota) are described from the Pakaraima Mountains and adjacent lowlands of Guyana. Xerocomus inundabilis, originally described from the central Brazilian Amazon...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/15-075

    authors: Henkel TW,Obase K,Husbands D,Uehling JK,Bonito G,Aime MC,Smith ME

    更新日期:2016-01-01 00:00:00

  • Anthracoidea caricis-meadii is a new North American smut fungus on Carex sect. Paniceae.

    abstract::The morphology and phylogeny of Anthracoidea on Carex meadii (sect. Paniceae) collected in Illinois, Iowa, Wisconsin, USA, were studied by light microscopy, scanning electron microscopy and LSU rDNA sequence analyses. As a result A. caricis-meadii sp. nov. is described. The fungus differs morphologically from Anthraco...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/12-074

    authors: Savchenko KG,Lutz M,Piatek M,Heluta VP,Nevo E

    更新日期:2013-01-01 00:00:00

  • Culturing and direct PCR suggest prevalent host generalism among diverse fungal endophytes of tropical forest grasses.

    abstract::Most studies examining endophytic fungi associated with grasses (Poaceae) have focused on agronomically important species in managed ecosystems or on wild grasses in subtropical, temperate and boreal grasslands. However grasses first arose in tropical forests, where they remain a significant and diverse component of u...

    journal_title:Mycologia

    pub_type: 杂志文章

    doi:10.3852/09-158

    authors: Higgins KL,Coley PD,Kursar TA,Arnold AE

    更新日期:2011-03-01 00:00:00