A highly contiguous genome assembly for the California vole, Microtus californicus, provides insight into phylogenetic relationships and patterns of synteny among voles.

IF 2.5 2区生物学 Q2 EVOLUTIONARY BIOLOGY

Journal of Heredity Pub Date : 2025-09-17 DOI:10.1093/jhered/esaf067

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

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引用次数: 0

Abstract

The California vole (Microtus californicus) is a small cricetid rodent and one of 20 species of Microtus in North America and 60 worldwide. Several subspecies are listed as being of conservation concern in California, and one is federally protected. Here we present the first de novo genome assembly for the California vole, generated as a part of the California Conservation Genomics Project. The M. californicus genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. Our high-quality genome is one of the most complete vole assemblies available, with a contig N50 of 49.8 Mb, scaffold N50 of 83.7 Mb, and BUSCO completeness score of 96.4%. Analysis of this genome together with genomes of closely related species revealed phylogenetic relationships and high levels of synteny among voles. The California vole genome provides an important new resource for comparative work across cricetid and muroid genomes. It will also serve as a reference for the analysis of within-species genetic diversity across widespread subspecies as well as more restricted populations of conservation concern.

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加利福尼亚田鼠（Microtus californicus）的高度连续基因组组装，为田鼠之间的系统发育关系和合群模式提供了见解。

加州田鼠（Microtus californicus）是一种小型的环状啮齿动物，是北美20种和全球60种鼠属动物之一。几个亚种在加州被列为保护物种，其中一个受到联邦保护。在这里，我们展示了加利福尼亚田鼠的第一个从头基因组组装，作为加利福尼亚保护基因组计划的一部分产生。利用PacBio HiFi长读数和Omni-C染色质近距离测序技术的组合，生成了加利福尼亚加利福尼亚螨基因组。我们的高质量基因组是目前最完整的田鼠基因组组合之一，序列N50为49.8 Mb，支架N50为83.7 Mb， BUSCO完整性评分为96.4%。该基因组与近缘种基因组的分析揭示了田鼠之间的系统发育关系和高水平的共系性。加州田鼠基因组为跨蟋蟀和鼠类基因组的比较工作提供了重要的新资源。它还将为分析广泛分布的亚种以及更受限制的种群的种内遗传多样性提供参考。

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.