Phylogenetic and Phylogenomic Definition of Rhizopus Species

被引：52

作者：

Gryganskyi, Andrii P. ^{[1
]}

Golan, Jacob ^{[2
,3
]}

Dolatabadi, Somayeh ^{[4
,18
]}

Mondo, Stephen ^{[5
]}

Robb, Sofia ^{[6
,7
]}

Idnurm, Alexander ^{[8
]}

Muszewska, Anna ^{[9
]}

Steczkiewicz, Kamil ^{[10
]}

Masonjones, Sawyer ^{[6
,7
]}

Liao, Hui-Ling ^{[11
]}

Gajdeczka, Michael T. ^{[1
]}

Anike, Felicia ^{[12
]}

Vuek, Antonina ^{[13
]}

Anishchenko, Iryna M. ^{[14
]}

Voigt, Kerstin ^{[15
]}

de Hoog, G. Sybren ^{[4
]}

Smith, Matthew E. ^{[16
]}

Heitman, Joseph ^{[17
]}

Vilgalys, Rytas ^{[1
]}

Stajich, Jason E. ^{[11
]}

机构：

[1] Duke Univ, Dept Biol, Durham, NC 27708 USA

[2] Univ Wisconsin, Dept Bot, Madison, WI 53706 USA

[3] Univ Wisconsin, Dept Bacteriol, Madison, WI 53706 USA

[4] Westerdijk Fungal Biodivers Inst, NL-3584 Utrecht, Netherlands

[5] US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA

[6] Univ Calif Riverside, Dept Microbiol & Plant Pathol, Riverside, CA 92521 USA

[7] Univ Calif Riverside, Inst Integrat Genome Biol, Riverside, CA 92521 USA

[8] Univ Melbourne, Sch BioSci, Melbourne, Vic 3010, Australia

[9] Polish Acad Sci, Inst Biochem & Biophys, PL-02106 Warsaw, Poland

[10] Univ Warsaw, Ctr New Technol, Lab Bioinformat & Syst Biol, PL-02089 Warsaw, Poland

[11] Univ Florida, North Florida Res & Educ Ctr, Quincy, FL 32351 USA

[12] North Carolina Agr & Tech State Univ, Dept Nat Resources & Environm Design, Greensboro, NC 27401 USA

[13] Natl Univ Life & Environm Sci Ukraine, Dept Plant Protect, UA-03041 Kiev, Ukraine

[14] Natl Acad Sci Ukraine, MG Kholodny Inst Bot, UA-02000 Kiev, Ukraine

[15] Hans Knoell Inst, Leibniz Inst Nat Prod Res & Infect Biol, D-07745 Jena, Germany

[16] Univ Florida, Dept Plant Pathol, Gainesville, FL 32611 USA

[17] Duke Univ, Med Ctr, Dept Mol Genet & Microbiol, Durham, NC 27710 USA

[18] Sabzevar Univ New Technol, Fac Engn, POB 679, Sabzevar, Razavi Khorasan, Iran

来源：

G3-GENES GENOMES GENETICS | 2018年 / 8卷 / 06期

基金：

澳大利亚研究理事会;

关键词：

zygomycete; orthologs; genome duplication; transposons; sexual reproduction; MOLECULAR PHYLOGENY; IDENTIFICATION; ALIGNMENT; SEQUENCE; FUNGI; ORYZAE; GENOME; RDNA; SEX; CLASSIFICATION;

D O I：

10.1534/g3.118.200235

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：2007 / 2018

页数：12

共 64 条

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