A genome assembly for a textbook mammalian study species, the California ground squirrel (Otospermophilus beecheyi).

IF 3 2区 生物学 Q2 EVOLUTIONARY BIOLOGY
Matthew L Holding, Sree Rohit Raj Kolora, Jennifer E Smith, Shana L McDevitt, Peter H Sudmant, Rebecca D Tarvin
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引用次数: 0

Abstract

Squirrels (Rodentia; Sciuridae) are a well-known and diverse group of rodents, including the charismatic ground-dwelling members of the Tribe Marmotini. In particular, the California ground squirrel (Otospermophilus beecheyi) is an emerging model system for the study of social and risk-sensitive behaviors in a rapidly changing world, as well as the physiology of resistance to snake venoms. To complement extensive natural history information for O. beecheyi, we provide a chromosome-scale genome to facilitate molecular studies focused on the genetic basis of ecologically important traits, population genetics, comparative genomics, and social evolution. The final scaffolded genome was 2.27 Gb contained in 9960 contigs and placed into 1383 scaffolds. The scaffold N50 was just over 125 Mb. We used the presence of 10 248 complete genes detected by BUSCO v5 specifically to compare broad patterns of chromosomal synteny between chromosomal scaffolds for O. beecheyi and two other sciurid rodents. The recovered pattern of synteny suggests several fusion and fission events for O. beecheyi in relation to the other two species. Taken together, this new information should advance our understanding of O. beecheyi and comparative studies of mammalian genomic biology and evolution.

一个教科书哺乳动物研究物种的基因组组装,加利福尼亚地松鼠(otospermoophilus beecheyi)。
松鼠(啮齿目;猴科(Sciuridae)是一种众所周知的啮齿类动物,种类繁多,包括有魅力的地栖动物Marmotini部落。特别是,加州地松鼠(otospermoophilus beecheyi)是一个新兴的模型系统,用于研究快速变化的世界中的社会和风险敏感行为,以及对蛇毒的抗性生理。为了补充广泛的自然历史信息,我们提供了一个染色体尺度的基因组,以促进分子研究的重点是生态重要性状的遗传基础,群体遗传学,比较基因组学和社会进化。最终的支架基因组为2.27 Gb,包含在9960个contigs中,放置在1383个支架中。我们利用BUSCO v5特异性检测到的10 248个完整基因,比较了山毛榉鼠和其他两种鼠类染色体支架之间的染色体合群的广泛模式。发现的合群模式表明,与其他两个物种相比,山毛榉有几次融合和裂变事件。综上所述,这些新信息将促进我们对毛毛犀的理解以及哺乳动物基因组生物学和进化的比较研究。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Heredity
Journal of Heredity 生物-遗传学
CiteScore
5.20
自引率
6.50%
发文量
63
审稿时长
6-12 weeks
期刊介绍: Over the last 100 years, the Journal of Heredity has established and maintained a tradition of scholarly excellence in the publication of genetics research. Virtually every major figure in the field has contributed to the journal. Established in 1903, Journal of Heredity covers organismal genetics across a wide range of disciplines and taxa. Articles include such rapidly advancing fields as conservation genetics of endangered species, population structure and phylogeography, molecular evolution and speciation, molecular genetics of disease resistance in plants and animals, genetic biodiversity and relevant computer programs.
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