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

By J. Spatafora, Ying Chang, G. Benny, Katherine L. Lazarus, Matthew E. Smith, M. Berbee, G. Bonito, N. Corradi, Igor V. Grigoriev, A. Gryganskyi and 8 more. Mycologia, 2016

1,087 citations recorded by the source corpus.

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.

Subfields: Cell Biology, Pharmacology, Plant Science

View Paper: https://www.semanticscholar.org/paper/71b143c0de2cb8c3bc9191e539636f1381cc1d10

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Citations in the corpus

Fungal diversity notes 603–708: taxonomic and phylogenetic notes on genera and species (2017, methodology): “Spatafora et al. (2016b) introduced some necessary species combinations by using morphological analysis.”
Role of Arbuscular Mycorrhizal Fungi in Plant Growth Regulation: Implications in Abiotic Stress Tolerance (2019, background): “A majority of the species of AMF belong to the sub-phylum Glomeromycotina, of the phylum Mucoromycota (Spatafora et al., 2016).”
Fungal diversity notes 491–602: taxonomic and phylogenetic contributions to fungal taxa (2017, background): “The genus Gongronella, proposed by Ribaldi (1952), belongs to the phylum Mucoromycota, subphylum Mucoromycotina, order Mucorales and family Cunninghamellaceae (Benny et al. 2016; Spatafora et al. 2016).”
Roles of Arbuscular Mycorrhizal Fungi on Plant Growth and Performance: Importance in Biotic and Abiotic Stressed Regulation (2020, background): “AMF belong to 11 families, 25 genera, and nearly 250 species [5,6].”
High-level classification of the Fungi and a tool for evolutionary ecological analyses (2018, methodology): “The formerly known phyla Mucoromycota and Zoopagomycota are emended so that these are comprised of the subphylum Mucoromycotina and Zoopagomycotina, respectively (sensu Spatafora et al. 2016).”
NCBI Taxonomy: a comprehensive update on curation, resources and tools (2020, background): “Currently, the NCBI classification contains nine phyla based on genome comparisons (56) but up to 16 are accepted in the literature (57, 58).”
Fungal community homogenization, shift in dominant trophic guild, and appearance of novel taxa with biotic invasion (2017, background): “…Zygomycota (as formerly known) is not fully resolved (Hibbett et al. 2007), we amended our taxonomic outputs for such clades to reclassify the Zygomycota into two phyla (Mucoromycota and Zoopagomycota), with the glomeromycetes as a clade within the Mucoromycota (Spatafora et al. 2016).”
Harnessing Soil Microbes to Improve Plant Phosphate Efficiency in Cropping Systems (2019, positive): “In contrast to AM fungi, ECM fungi belong to the fungal phyla Basidiomycota, Ascomycota, and Mucoromycota (sub-phylum Mucoromycotina) [92,93].”
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes (2018, background): “Its composition is Rozella, Microsporidia, Aphelida, Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Mucoromycota, Zoopagomycota, Ascomycota and Basidiomycota (Hibbett et al. 2007, Karpov et al. 2014, Spatafora et al. 2016).”
Fungal diversity notes 709–839: taxonomic and phylogenetic contributions to fungal taxa with an emphasis on fungi on Rosaceae (2018, background): “Currently, the subphylum contains three orders: Endogonales, Mucorales, and Umbelopsidales (Spatafora et al. 2016).”
Arbuscular mycorrhizal fungi as mediators of ecosystem responses to nitrogen deposition: A trait‐based predictive framework (2018, background): “The phylum Glomeromycota (or subphylum Glomeromycotina, Spatafora et al., 2016) contains most currently described AMF taxa (Redecker et al., 2013).”
The ranking of fungi: a tribute to David L. Hawksworth on his 70th birthday (2017, background): “2016), although even DNA sequence data are not unproblematic (James et al. 2006; Beimforde et al. 2014; Jeewon and Hyde 2016; Liu et al. 2016; Hongsanan et al. 2016; Spatafora et al. 2016).”