Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny

BMC Genomics

Research

Wataru Iwasaki¹  Takashi Sugita²  Nobuyuki Fujita³  Ayane Kayamori³  Naoto Tanaka³  Yuh Shiwa³  Keita Aoki⁴  Yuuki Kobayashi⁴  Masako Takashima⁴  Minenosuke Matsutani⁵ 

[1] Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 277-0882, Kashiwa, Chiba, Japan;Department of Microbiology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, 204-8588, Tokyo, Japan;Department of Molecular Microbiology, Faculty of Life Sciences, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, 156-8502, Tokyo, Japan;Laboratory of Yeast Systematics, Tokyo NODAI Research Institute (TNRI), Tokyo University of Agriculture, 1-1-1 Sakuragaoka, 156-8502, Setagaya, Tokyo, Japan;NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, 156-8502, Setagaya, Tokyo, Japan;

关键词: Comparative genomics;    Genome evolution;    Chromosome rearrangement;    Taxonomy;    Cutaneotrichosporon;    Yeast;    Basidiomycota;   

DOI  :  10.1186/s12864-023-09718-2

 received in 2023-06-15, accepted in 2023-10-05,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundSince DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided fungal identification; however, a barcode sequence alone is often insufficient. Thus, multi-gene- or whole-genome-based methods were developed. We previously isolated Basidiomycota yeasts classified in the Trichosporonales. Some strains were described as Cutaneotrichosporon cavernicola and C. spelunceum, whereas strain HIS471 remained unidentified. We analysed the genomes of these strains to elucidate their taxonomic relationship and genetic diversity.ResultsThe long-read-based assembly resulted in chromosome-level draft genomes consisting of seven chromosomes and one mitochondrial genome. The genome of strain HIS471 has more than ten chromosome inversions or translocations compared to the type strain of C. cavernicola despite sharing identical ITS barcode sequences and displaying an average nucleotide identity (ANI) above 93%. Also, the chromosome synteny between C. cavernicola and the related species, C. spelunceum, showed significant rearrangements, whereas the ITS sequence identity exceeds 98.6% and the ANI is approximately 82%. Our results indicate that the relative evolutionary rates of barcode sequences, whole-genome nucleotide sequences, and chromosome synteny in Cutaneotrichosporon significantly differ from those in the model yeast Saccharomyces.ConclusionsOur results revealed that the relative evolutionary rates of nucleotide sequences and chromosome synteny are different among fungal clades, likely because different clades have diverse mutation/repair rates and distinct selection pressures on their genomic sequences and syntenic structures. Because diverse syntenic structures can be a barrier to meiotic recombination and may lead to speciation, the non-linear relationships between nucleotide and synteny diversification indicate that sequence-level distances at the barcode or whole-genome level are not sufficient for delineating species boundaries.

【 授权许可】

CC BY   
© The Author(s) 2023. corrected publication 2023

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