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. 2016 Sep;108(5):1028-1046.
doi: 10.3852/16-042.

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

Joseph W Spatafora  1 , Ying Chang  2 , Gerald L Benny  3 , Katy Lazarus  3 , Matthew E Smith  3 , Mary L Berbee  4 , Gregory Bonito  5 , Nicolas Corradi  6 , Igor Grigoriev  7 , Andrii Gryganskyi  8 , Timothy Y James  9 , Kerry O'Donnell  10 , Robert W Roberson  11 , Thomas N Taylor  12 , Jessie Uehling  13 , Rytas Vilgalys  13 , Merlin M White  14 , Jason E Stajich  15
Affiliations

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

Joseph W Spatafora et al. Mycologia. 2016 Sep.

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.

Keywords: Entomophthoromycotina; Glomeromycotina; Kickellomycotina; Mortierellomycotina; Mucoromycota; Mucoromycotina; Zoopagomycota Zoopagomycotina; fungi; paraphyly; systematics.

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Figures

FIG. 1.
FIG. 1.
RAxML phylogenetic tree of KingdomFungi based on the concatenated alignment of 192 conserved orthologous proteins. All branches received 100%bootstrap partitions except where noted by number above or below respective branches. Example images include: a. Rhizopus sporangium(SEM). b. Phycomyces zygospore (LM). c. Mortierella chlamydospores (SEM). d. Rhizophagus spores and hyphae (LM). e. Conidiobolus secondary (replicative) conidia forming on primary conidium (SEM). f. Basidiobolus ballistosporic conidium (SEM). g. Piptocephalis merosporangia (SEM). h. Linderina merosporangium (SEM). LM: light micrograph, SEM: scanning electron micrograph.1032 MYCOLOGIA
FIG. 2.
FIG. 2.
ASTRAL consensus cladogram of Kingdom Fungi based on analyses of individual bootstrap trees for each of 192 conserved orthologous proteins. All branches received 100% ASTRAL branch support except where noted by number above or below respective branches
See this image and copyright information in PMC

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