DOI: 10.5061/dryad.x0k6djhtc
title: Data from: A high-quality genome assembly for a desert-adapted rodent, Merriam’s kangaroo rat (Dipodomys merriami)

description: 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. 
description: # Data from: A high-quality genome assembly for a desert-adapted rodent,
 Merriam’s kangaroo rat (Dipodomys merriami)
 [https://doi.org/10.5061/dryad.x0k6djhtc](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/](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.  1. 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.  2. GCA_024711535.1_DipMer_final_mitogenome.fasta: 17,159 bp mitochondrial genome assembled from PacBio reads using MitoHiFi.  3. 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](mailto:phbenham@gmail.com)) 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](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](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 [https://github.com/agshumate/Liftoff](https://github.com/agshumate/Liftoff)