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G3 (Bethesda). 2018 May 31;8(6):2007-2018. doi: 10.1534/g3.118.200235.

Phylogenetic and Phylogenomic Definition of Rhizopus Species.

Author information

1
Department of Biology, Duke University, Durham, North Carolina, 27708 apg10@duke.edu.
2
Department of Botany and Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, 53706.
3
Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands, 3584.
4
US Department of Energy, Joint Genome Institute, Walnut Creek California, 94598.
5
Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, 92521.
6
School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia, 3010.
7
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland, 02-106.
8
Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland, 02-089.
9
North Florida Research and Educational Center, University of Florida, Quincy, Florida, 32351.
10
Department of Biology, Duke University, Durham, North Carolina, 27708.
11
Department of Natural Resources and Environmental Design, North Carolina Agricultural and Technical State University, Greensboro, North Carolina, 27401.
12
Department of Plant Protection, National University of Life and Environmental Sciences of Ukraine, Kyiv, Ukraine, 03041.
13
M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kyiv, Ukraine, 02000.
14
Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll Institute, Jena, Germany, 07745.
15
Department of Plant Pathology, University of Florida, Gainesville, Florida, 32611.
16
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, 27710.

Abstract

Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R. microsporus as the basal species and the sister lineage to R. stolonifer and two closely related species R. arrhizus and R. delemar A comparative analysis of the mating type locus across Rhizopus reveals that its structure is flexible even between different species in the same genus, but shows similarities between Rhizopus and other mucoralean fungi. The topology of single-gene phylogenies built for two genes involved in mating is similar to the phylogenomic tree. Comparison of the total length of the genome assemblies showed that genome size varies by as much as threefold within a species and is driven by changes in transposable element copy numbers and genome duplications.

KEYWORDS:

genome duplication; orthologs; sexual reproduction; transposons; zygomycete

PMID:
29674435
PMCID:
PMC5982828
DOI:
10.1534/g3.118.200235
[Indexed for MEDLINE]
Free PMC Article

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