De novo genome assembly of a Geomyid rodent, Botta's pocket gopher (Thomomys bottae bottae).

IF 3 2区生物学 Q2 EVOLUTIONARY BIOLOGY

Journal of Heredity Pub Date : 2024-08-27 DOI:10.1093/jhered/esae045

Erin R Voss, Merly Escalona, Krzysztof M Kozak, William Seligmann, Colin W Fairbairn, Oanh Nguyen, Mohan P A Marimuthu, Christopher J Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman

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引用次数: 0

Abstract

Botta's pocket gopher (Thomomys bottae) is a common and widespread subterranean rodent of the North American west. The species has been of long interest to evolutionary biologists due to the phenotypic diversity across its range and unusual levels of variation in chromosome number and composition. Here, we present a high-quality reference genome from a male T. b. bottae individual captured in the San Francisco Bay Area. The assembly is comprised of 2,792 scaffolds, with a scaffold N50 value of 23.6 Mb and a BUSCO score of 91.0%. This genome helps fill a significant taxonomic sampling gap in rodent genome resources. With this reference genome, we envision new opportunities to investigate questions regarding the genomics of adaptation to the belowground niche. Further, we can begin to explore the impact of associated life history traits, such as limited dispersal and low population connectivity, on intraspecific genetic and phenotypic variation, genome evolution, speciation, and phylogenetic relationships across the Geomyoidea.

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一种地啮类动物--博塔袋鼠（Thomomys bottae bottae）的全新基因组组装。

博塔袋鼠（Thomomys bottae）是北美西部一种常见的广泛分布的地下啮齿动物。由于该物种在其分布范围内的表型多样性以及染色体数目和组成的异常变异水平，进化生物学家一直对该物种很感兴趣。在这里，我们展示了在旧金山湾区捕获的一只雄性 T. b. bottae 的高质量参考基因组。该基因组由 2,792 个支架组成，支架 N50 值为 23.6 Mb，BUSCO 得分为 91.0%。该基因组有助于填补啮齿动物基因组资源在分类取样方面的重大空白。有了这个参考基因组，我们设想有新的机会来研究有关适应地下生态位的基因组学问题。此外，我们还可以开始探索相关生活史特征（如有限的扩散和较低的种群连通性）对整个革肢动物门的种内遗传和表型变异、基因组进化、物种分化和系统发育关系的影响。

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 生物-遗传学

CiteScore

5.20

自引率

6.50%

发文量

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.