High-Quality Reference Genome for an Arid-Adapted Mammal, the Banner-Tailed Kangaroo Rat (Dipodomys spectabilis)

Abstract

Kangaroo rats in the genus Dipodomys are found in a variety of habitat types in western North America, including deserts, arid and semi-arid grasslands, and scrublands. Many Dipodomys species are experiencing strong population declines due to increasing habitat fragmentation, with two species listed as federally endangered. The precarious state of many Dipodomys populations, including those occupying extreme environments, make species of this genus valuable subjects for studying the impacts of habitat degradation and fragmentation on population genomic patterns and for characterizing the genomic bases of adaptation to harsh conditions. To facilitate exploration of such questions, we assembled and annotated a reference genome for the banner-tailed kangaroo rat (D. spectabilis) using PacBio HiFi sequencing reads, providing a more contiguous genomic resource than two previously assembled Dipodomys genomes. Using the HiFi data for D. spectabilis and publicly available sequencing data for two other Dipodomys species (D. ordii and D. stephensi), we demonstrate the utility of this new assembly for studies of congeners by conducting inference of historic effective population sizes (N e) and linking these patterns to the species’ current extinction risk statuses. The genome assembly presented here will serve as a valuable resource for population and conservation genomic studies of Dipodomys species, comparative genomic research within mammals and rodents, and investigations into genomic adaptation to extreme environments and changing landscapes.

A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

“…2008 ), likely including P. longimembris , which consists of 16 recognized subspecies ( www.itis.gov ; accessed 13 December 2021). Other heteromyids show similar fluctuations and large historical N e , including the federally endangered Stephen’s kangaroo rat ( Dipodomys stephensi ; Harder et al . 2022 ).…”

“…We evaluated genome-wide synteny between PPM and two heteromyid species, Ord’s kangaroo rat ( Dipodomys ordii ) and banner-tailed kangaroo rat ( D. spectabilis ; Harder et al . 2022 , fig.…”

Chromosome-level haplotype-resolved genome assembly for Takifugu ocellatus using PacBio and Hi-C technologies

“…Finally, three preliminary assemblies, including one monoploid assembly and two haploid assemblies, were yielded, which spanned 375.62 Mb (monoploid), 373.25 Mb (Haploid-1) and 372.15 Mb (Haploid-2), with a contig N50 length of 11.55 Mb, 4.86 Mb and 4.87 Mb, respectively (Table 2). The genome assembly was slightly larger than the estimated genome size of 369.48 Mb (Table 1) because some repeat fragments could be assembled by high-precision CCS reads 13 . Juicer 14 and 3D-DNA 15 were implemented to obtain the www.nature.com/scientificdata www.nature.com/scientificdata/ chromosome-level whole genome assembly for T. ocellatus.…”

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

“…Genomic hotspots of accumulation for retrotransposons, regulatory elements, and coding genes are conserved in mammals ( Buckley et al 2017 ). Hence our thorough annotations of these features will aid in understanding the evolution of genome architecture in Perognathus , and broadly in Heteromyidae, a group of ~100 species with only three contiguous genomes available at present ( Harder et al 2022 ; Wilder et al 2022 ).…”