Data from: A high-quality genome assembly for a desert-adapted rodent, Merriam’s kangaroo rat (Dipodomys merriami)
Data files
Apr 30, 2025 version files 284.74 MB
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. The reference genome sequence is available on NCBI under accession GCA_023159225.1. Here, we share supplementary data, including a a mitochondrial genome assembly and a basic protein-coding gene annotation lifted over from Dipodomys spectabilis, the closest relative of D. merriami with an annotated genome.
https://doi.org/10.5061/dryad.x0k6djhtc
Description of the data and file structure
This dataset corresponds to a genome assembly report for Dipodomys merriami (Voss et al. Journal of Heredity, in review).
The genome assembly is available on NCBI under the identifier mDipMer1.0.p at https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_024711535.1/
Here, we have deposited associated files that were generated for the purposes of preliminary genome annotation.
- GCA_024711535.1_mDipMer1.NCBI.p_ctg.Liftoff_Annotation_polished.gff: GFF file containing preliminary genome feature annotation for D. merriami genome assembly. Genome features were lifted over from the closest relative with a high-quality genome annotation (D. spectabilis, Harder et al. 2022) with Liftoff.
- GCA_024711535.1_DipMer_final_mitogenome.fasta: 17,159 bp mitochondrial genome assembled from PacBio reads using MitoHiFi.
- GCA_024711535.1_DipMer_Mitogenome_Annotation_MITOS2.bed: Mitochondrial genome annotation file indicating position of 13 protein-coding genes, 2 rRNAs, and 22 unique tRNAs generated with MITOS2.
Sharing/Access information
Please contact Erin Voss (erinvoss@berkeley.edu) if there are any questions or concerns about the data shared here.
Code/Software
Flags/options are indicated below where applicable.
MitoHiFi (v.2.2): Mitochondrial genome assembly
mitohifi -r -p 50 -o 1
https://github.com/marcelauliano/MitoHiFi
MITOS2: Mitochondrial genome annotation
https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/mitos2/mitos2/2.1.9+galaxy0
Liftoff (v.1.6.3): Lift over genome annotation from D. spectabilis
liftoff -polish -copies -cds
- Voss, Erin R; Escalona, Merly; Nguyen, Oanh et al. (2025). A high-quality genome assembly for a desert-adapted rodent, Merriam’s kangaroo rat (Dipodomys merriami). Journal of Heredity. https://doi.org/10.1093/jhered/esaf023