A high-quality genome assembly for a desert-adapted rodent, Merriam’s kangaroo rat (<i>Dipodomys merriami</i>)
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.
Authors
- Mohan P A Marimuthu (ORCID: https://orcid.org/0000-0001-6121-3286)
- James L. Patton (ORCID: https://orcid.org/0000-0002-8709-7196)
- Rauri C. K. Bowie (ORCID: https://orcid.org/0000-0001-8328-6021)
- Erin Voss (ORCID: https://orcid.org/0000-0003-2662-1190)
- William Seligmann (ORCID: https://orcid.org/0000-0002-5762-3095)
- Colin W Fairbairn (ORCID: https://orcid.org/0009-0007-8129-0095)
- Eric Beraut (ORCID: https://orcid.org/0000-0002-4443-6282)
- Noravit Chumchim (ORCID: https://orcid.org/0000-0003-1139-9427)
- Michael W. Nachman (ORCID: https://orcid.org/0000-0003-4321-5135)
- Oanh Nguyen (ORCID: https://orcid.org/0000-0003-1492-2084)
- Merly Escalona (ORCID: https://orcid.org/0000-0003-0213-4777)
- Christopher J Conroy
Institutions
- Museum of Vertebrate Zoology (US)
- University of California, Santa Cruz (US)
- Acupuncture & Integrative Medicine College (US)
- University of California, Davis (US)
- University of California, Berkeley (US)
Publication Details
- Journal
- Journal of Heredity
- Published
- 2025-04-17
- DOI
- https://doi.org/10.1093/jhered/esaf023
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- University of California, Santa Cruz
- National Institutes of Health
- University of California, Davis
- Genome Center, University of California, Davis