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Fungal Genet Biol. 2019 Sep;130:31-42. doi: 10.1016/j.fgb.2019.04.013. Epub 2019 Apr 23.

Recognition and delineation of yeast genera based on genomic data: Lessons from Trichosporonales.

Author information

1
Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan. Electronic address: masako@jcm.riken.jp.
2
Comprehensive Genomic Analysis Team, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
3
Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Ibaraki 305-0074, Japan.
4
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Research Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok 10330, Thailand; Computational Molecular Biology Group, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok 10330, Thailand.
5
Department of Microbiology, Meiji Pharmaceutical University, Kiyose, Tokyo 204-8588, Japan.
6
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8568, Japan; Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba 277-8564, Japan; Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. Electronic address: iwasaki@bs.s.u-tokyo.ac.jp.

Abstract

Delineation and characterization of genera in Trichosporonales (Agaricomycotina, Basidiomycota) was performed using 24 haploid and 3 naturally occurring hybrid genomes, with 3 Tremellales genomes used as outgroups. Orthologous group analysis of those genomes showed presence-absence patterns of orthologs that were consistent with the genus classifications. Many shared unique orthologs were identified in the well-supported lineages (genera Apiotrichum and Trichosporon), supporting the definitions of the genera Apiotrichum and Trichosporon from a genomic perspective. Specifically, we obtained 24 and 285 genus-specific genes from eight Apiotrichum and five Trichosporon species, respectively, and propose that these genus-specific genes can be used for delineation of those genera. On the other hand, the genus Cutaneotrichosporon shared only one genus-specific gene among eight genomes, indicating that this genus definition might require re-examination based on genomic data. In addition, taxonomic revisions are presented in this study, including the proposal of two genera, Pascua and Prillingera. Because genomic data can be systematically obtained and analyzed to compare species from a comprehensive viewpoint, they can be used not only to reconstruct reliable phylogenetic trees, but also to re-examine the definitions of taxonomic classifications. To our knowledge, this is the first report to discuss the 'natural system' of genus level classification in fungi based on genomic data.

KEYWORDS:

Backbone tree; Genus delineation; Hybrid genome; Trichosporonales; Yeast systematics

PMID:
31026590
DOI:
10.1016/j.fgb.2019.04.013

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