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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

References

    1. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Woodage T, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC. The genome sequence of Drosophila melanogaster. Science 287:2185–2195, doi: 10.1126/science.287.5461.2185 - DOI - PubMed
    1. Bauer R, Garnica S, Oberwinkler F, Reiss K, Weiß M, Begerow D. 2015. Entorrhizomycota: a new fungal phylum reveals new perspectives on the evolution of fungi. PLoS One 10:e0128183, doi: 10.1371/journal.pone.0128183 - DOI - PMC - PubMed
    1. Bauer R, Humber RA, Voigt K. 2014. Zygomycetous fungi: phylum Entomophthoromycota and subphyla Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoopagomycotina. In: McLaughlin DJ, Spatafora JW, eds. Systematics and evolution. Part A New York: Springer-Verlag. The Mycota; VII:209–250.
    1. Benny GL, Humber RA, Voigt K. 2014. Zygomycetous fungi: phylum Entomophthoromycota and subphyla Kickxellomycotina, Mortierellomycotina, Mucoromycotina, and Zoopagomycotina. In: McLaughlin DJ, Spatafora JW, eds. Mycota VII, part A. Systematics and evolution New York: Springer-Verlag; p 209–250.
    1. Benny GL, O’Donnell K 2000. Amoebidium parasiticum is a protozoan, not a Trichomycete. Mycologia 92:1133–1137, doi: 10.2307/3761480 - DOI

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