一种适应沙漠环境的啮齿动物——梅里亚姆更格卢鼠（Dipodomys merriami）的高质量基因组组装。

A high-quality genome assembly for a desert-adapted rodent, Merriam's kangaroo rat (Dipodomys merriami).

作者信息

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

机构信息

Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA.

Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.

出版信息

J Hered. 2025 Apr 17. doi: 10.1093/jhered/esaf023.

DOI:10.1093/jhered/esaf023

PMID:40243028

Abstract

Merriam's kangaroo rat (Dipodomys merriami) is a member of a unique family of primarily desert-adapted North American rodents (Heteromyidae). Of the 20 species in the genus, D. merriami is one of the most wide-ranging and ecologically flexible, inhabiting desert scrub, grassland, sagebrush steppe, and juniper-piñon woodland in the southwestern deserts of the United States and Mexico. We present a de novo reference genome for D. merriami generated from PacBio HiFi long-read and Omni-C chromatin proximity sequencing as a part of the California Conservation Genomics Project. The primary pseudo-haplotype assembly comprises 3,110 scaffolds, with a contig N50 of 8.6 Mb, scaffold N50 of 49.1 Mb, and a total length of 3.57 Gb. Further, a BUSCO completeness score of 97.8% suggests that the assembly is highly complete. This reference genome will serve as a resource for future studies of Dipodomys conservation genomics, desert adaptation, and phylogeography.

摘要

梅里亚姆更格卢鼠（Dipodomys merriami）是北美一个独特的主要适应沙漠环境的啮齿动物家族（异鼠科）的成员。在该属的20个物种中，梅里亚姆更格卢鼠是分布范围最广、生态适应性最强的物种之一，栖息于美国西南部和墨西哥沙漠的灌丛、草原、蒿属植物草原以及杜松-矮松林地。作为加利福尼亚保护基因组计划的一部分，我们展示了一个利用PacBio HiFi长读长测序和Omni-C染色质邻近测序生成的梅里亚姆更格卢鼠的从头参考基因组。主要的假单倍型组装包含3110个支架，重叠群N50为8.6 Mb，支架N50为49.1 Mb，总长度为3.57 Gb。此外，BUSCO完整性评分97.8%表明该组装高度完整。这个参考基因组将作为未来更格卢鼠保护基因组学、沙漠适应性和系统地理学研究的资源。