A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus.
A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus.
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DOI：
10.1093/g3journal/jkad028
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发表时间：
2023-04-11
影响因子：
2.6
通讯作者：
Du, Li-Lin
中科院分区：
文献类型：
--
作者：
Jia, Guo-Song;Zhang, Wen-Cai;Liang, Yue;Liu, Xi-Han;Rhind, Nicholas;Pidoux, Alison;Brysch-Herzberg, Michael;Du, Li-Lin
关键词：
裂变酵母菌是一种古老的真菌物种，在数千万到数亿年前彼此分离。其中，杰出的模式生物裂糖菌（Schizosaccharomyces pombe）为我们理解基本细胞过程的分子机制做出了重大贡献。利用S. pombe和其他3种裂变酵母物种S. japonicus、S. octosporus和S. cryophilus的基因组，可以进行跨物种比较，从而深入了解基因、途径和基因组的进化。在这里，我们对最近发现的裂变酵母菌种S. osmophilus进行了基因组测序，获得了完整的线粒体基因组和仅在rRNA基因阵列上存在缺口的核基因组组装。共注释了5098个蛋白编码核基因，鉴定出95%以上的同源基因。基于基因组的系统发育分析表明，嗜锇葡萄球菌与章鱼孢子葡萄球菌的亲缘关系最为密切，这两个物种大约在1600万年前分化。为了证明该嗜酸葡萄球菌参考基因组的实用性，我们对着丝粒、端粒、转座子、交配型区域、Cbp1家族蛋白和线粒体基因组进行了跨物种比较分析。这些分析揭示了着丝粒核心重复序列和序列基序的保守性，鉴定了由2种重复组成的端粒序列，描绘了Tf1/sushi组反转录转座子之间的关系，表征了Cbp1家族驯化转座子的进化起源和轨迹，并发现了2种线粒体自私元件的种间转移迹象。在这项研究中，作者建立了一个高质量的染色体水平的参考基因组，为最近发现的分裂酵母物种分裂糖菌（Schizosaccharomyces osmophilus），该物种与著名的模式生物分裂糖菌（Schizosaccharomyces pombe）属于同一属。他们利用这个新的参考基因组进行了比较基因组分析，揭示了着丝粒、端粒、反转录转座子、交配型区域和线粒体基因组进化的新见解。
Fission yeasts are an ancient group of fungal species that diverged from each other from tens to hundreds of million years ago. Among them is the preeminent model organism Schizosaccharomyces pombe, which has significantly contributed to our understandings of molecular mechanisms underlying fundamental cellular processes. The availability of the genomes of S. pombe and 3 other fission yeast species S. japonicus, S. octosporus, and S. cryophilus has enabled cross-species comparisons that provide insights into the evolution of genes, pathways, and genomes. Here, we performed genome sequencing on the type strain of the recently identified fission yeast species S. osmophilus and obtained a complete mitochondrial genome and a nuclear genome assembly with gaps only at rRNA gene arrays. A total of 5,098 protein-coding nuclear genes were annotated and orthologs for more than 95% of them were identified. Genome-based phylogenetic analysis showed that S. osmophilus is most closely related to S. octosporus and these 2 species diverged around 16 million years ago. To demonstrate the utility of this S. osmophilus reference genome, we conducted cross-species comparative analyses of centromeres, telomeres, transposons, the mating-type region, Cbp1 family proteins, and mitochondrial genomes. These analyses revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, delineated relationships among Tf1/sushi group retrotransposons, characterized the evolutionary origins and trajectories of Cbp1 family domesticated transposases, and discovered signs of interspecific transfer of 2 types of mitochondrial selfish elements. In this study, the authors established a high-quality chromosome-level reference genome for the recently discovered fission yeast species Schizosaccharomyces osmophilus, which belongs to the same genus as the renowned model organism Schizosaccharomyces pombe. They took advantage of this new reference genome to perform comparative genomic analysis and revealed new insights into the evolution of centromeres, telomeres, retrotransposons, the mating type region, and the mitochondrial genome.
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