A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris.

IF 3 2区生物学 Q2 EVOLUTIONARY BIOLOGY

Journal of Heredity Pub Date : 2024-02-03 DOI:10.1093/jhered/esad060

Krzysztof M Kozak, Merly Escalona, Noravit Chumchim, Colin Fairbairn, Mohan P A Marimuthu, Oanh Nguyen, Ruta Sahasrabudhe, William Seligmann, Chris Conroy, James L Patton, Rauri C K Bowie, Michael W Nachman

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引用次数: 0

Abstract

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.

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一个高度连续的口袋鼠长颚鼠基因组组装。

这种名为Perognathus longimembris的小口袋鼠和它的九个同类是在北美西部干旱和季节性干旱地区发现的小型异食啮齿动物。该属的特征是对干燥且通常恶劣的环境的行为和生理适应，包括夜间、季节性迟钝、食物缓存、渗透调节增强和发育良好的听觉。在这里，作为加州保护基因组学项目的一部分，我们展示了由PacBio-HiFi长读和Omni-C染色质接近测序产生的长颌长颌的基因组组装。该组装体的长度为2.35Gb，重叠群N50为11.6Mb，支架N50为73.2Mb，并包括93.8%的BUSCO Glires基因。散布的重复元件占基因组的41.2%。与高度濒危的太平洋袋鼠太平洋太平洋袋鼠的比较揭示了广泛的同源性。这些新资源将有助于研究当地的适应、遗传多样性和受威胁类群的保护。

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.