A Phylum-Level Phylogenetic Classification of Zygomycete Fungi Based on Genome-Scale Data
Mycologia, 108(5), 2016, pp. 1028–1046. DOI: 10.3852/16-042 # 2016 by The Mycological Society of America, Lawrence, KS 66044-8897 A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data Joseph W. Spatafora1 Jason E. Stajich Ying Chang Department of Plant Pathology & Microbiology and Institute Department of Botany and Plant Pathology, Oregon State for Integrative Genome Biology, University of California– University, Corvallis, Oregon 97331 Riverside, Riverside, California 92521 Gerald L. Benny Katy Lazarus Abstract: Zygomycete fungi were classified as a single Matthew E. Smith phylum, Zygomycota, based on sexual reproduction by Department of Plant Pathology, University of Florida, Gainesville, Florida 32611 zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of Mary L. Berbee coenocytic hyphae, all with some exceptions. Molecular Department of Botany, University of British Columbia, phylogenies based on one or a few genes did not support Vancouver, British Columbia, V6T 1Z4 Canada the monophyly of the phylum, however, and the phylum Gregory Bonito was subsequently abandoned. Here we present phyloge- Department of Plant, Soil, and Microbial Sciences, Michigan netic analyses of a genome-scale data set for 46 taxa, State University, East Lansing, Michigan 48824 including 25 zygomycetes and 192 proteins, and we dem- Nicolas Corradi onstrate that zygomycetes comprise two major clades Department of Biology, University of Ottawa, Ottawa, that form a paraphyletic grade. A formal phylogenetic Ontario, K1N 6N5 Canada classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis Igor Grigoriev of these results, the phyla Mucoromycota and Zoopago- US Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598 mycota are circumscribed.
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