Phylogenetic and Phylogenomic Definition of Rhizopus Species

Andrii P. Gryganskyi; Jacob Golan; Somayeh Dolatabadi; Stephen Mondo; Sofia Robb; Alexander Idnurm; Anna Muszewska; Kamil Steczkiewicz; Sawyer Masonjones; Hui-Ling Liao; Michael T. Gajdeczka; Felicia Anike; Antonina Vuek; Iryna M. Anishchenko; Kerstin Voigt; G. Sybren de Hoog; Matthew E. Smith; Joseph Heitman; Rytas Vilgalys; Jason E. Stajich

doi:10.1534/g3.118.200235

Phylogenetic and Phylogenomic Definition of Rhizopus Species

Andrii P. Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, Kamil Steczkiewicz, Sawyer Masonjones, Hui-Ling Liao, Michael T. Gajdeczka, Felicia Anike, Antonina Vuek, Iryna M. Anishchenko, Kerstin Voigt, G. Sybren de Hoog, Matthew E. Smith, Joseph Heitman, Rytas Vilgalys, Jason E. Stajich

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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.

Original language	English
Title of host publication	G3: Genes\|Genomes\|Genetics
Pages	2007-2018
Number of pages	12
DOIs	https://doi.org/10.1534/g3.118.200235
Publication status	Published - Jun 2018

Publication series

Name	G3: Genes\|Genomes\|Genetics
Volume	8

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Gryganskyi, A. P., Golan, J., Dolatabadi, S., Mondo, S., Robb, S., Idnurm, A., Muszewska, A., Steczkiewicz, K., Masonjones, S., Liao, H.-L., Gajdeczka, M. T., Anike, F., Vuek, A., Anishchenko, I. M., Voigt, K., de Hoog, G. S., Smith, M. E., Heitman, J., Vilgalys, R., & Stajich, J. E. (2018). Phylogenetic and Phylogenomic Definition of Rhizopus Species. In G3: Genes|Genomes|Genetics (pp. 2007-2018). (G3: Genes|Genomes|Genetics; Vol. 8). https://doi.org/10.1534/g3.118.200235

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title = "Phylogenetic and Phylogenomic Definition of Rhizopus Species",

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.",

author = "Gryganskyi, {Andrii P.} and Jacob Golan and Somayeh Dolatabadi and Stephen Mondo and Sofia Robb and Alexander Idnurm and Anna Muszewska and Kamil Steczkiewicz and Sawyer Masonjones and Hui-Ling Liao and Gajdeczka, {Michael T.} and Felicia Anike and Antonina Vuek and Anishchenko, {Iryna M.} and Kerstin Voigt and {de Hoog}, {G. Sybren} and Smith, {Matthew E.} and Joseph Heitman and Rytas Vilgalys and Stajich, {Jason E.}",

year = "2018",

month = jun,

doi = "10.1534/g3.118.200235",

language = "English",

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Gryganskyi, AP, Golan, J, Dolatabadi, S, Mondo, S, Robb, S, Idnurm, A, Muszewska, A, Steczkiewicz, K, Masonjones, S, Liao, H-L, Gajdeczka, MT, Anike, F, Vuek, A, Anishchenko, IM, Voigt, K, de Hoog, GS, Smith, ME, Heitman, J, Vilgalys, R & Stajich, JE 2018, Phylogenetic and Phylogenomic Definition of Rhizopus Species. in G3: Genes|Genomes|Genetics. G3: Genes|Genomes|Genetics, vol. 8, pp. 2007-2018. https://doi.org/10.1534/g3.118.200235

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AU - Gryganskyi, Andrii P.

AU - Golan, Jacob

AU - Dolatabadi, Somayeh

AU - Mondo, Stephen

AU - Robb, Sofia

AU - Idnurm, Alexander

AU - Muszewska, Anna

AU - Steczkiewicz, Kamil

AU - Masonjones, Sawyer

AU - Liao, Hui-Ling

AU - Gajdeczka, Michael T.

AU - Anike, Felicia

AU - Vuek, Antonina

AU - Anishchenko, Iryna M.

AU - Voigt, Kerstin

AU - de Hoog, G. Sybren

AU - Smith, Matthew E.

AU - Heitman, Joseph

AU - Vilgalys, Rytas

AU - Stajich, Jason E.

PY - 2018/6

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N2 - 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.

AB - 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.

U2 - 10.1534/g3.118.200235

DO - 10.1534/g3.118.200235

M3 - Chapter

C2 - 29674435

SN - 0000000262231

T3 - G3&#58; Genes|Genomes|Genetics

SP - 2007

EP - 2018

BT - G3: Genes|Genomes|Genetics

ER -

Phylogenetic and Phylogenomic Definition of Rhizopus Species

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