Genomic resources for the little pocket mouse (Perognathus longimembris longimembris)

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.

Methods
These files pertain to the SECOND version (1.1) of the primary genome assembly (GCA_024363575.2) of Perognathus longimembris longimembris (Little Pocket Mouse), assembled using the California Conservation Genomics pipeline v5 (HiFi and OmniC data processed with HiFiasm).

mPerLon1.GCA_024363575.2.RepeatModeler2_nonredundant_sequences.fasta: Novel repeat elements identified in the Perognathus longimembris longimembris primary genome assembly GCA_024363575.2 by RepeatModeler v2.03, not redundant with respect to sequences found in public databases (Dfam, RepBase, SINEbase, L1base, msRepDB).

mPerLon1.GCA_024363575.2.repeats_masked.gff3: primary assembly GCA_024363575.2 masked with RepeatMasker.

mPerLon1.GCA_024363575.2.LiftOff_Gene_Annotation.sorted.gff3: Gene annotation lifted over from the P. l. pacificus RefSeq assembly (GCF_023159225.1) using LiftOff.

Perognathus_longimembris_longimembris.mtDNA.annotated.April2023.gb: manuall annotated and inspected mitogenome.

These files pertain to the FIRST version (1.0) of the primary genome assembly (GCA_024363575.1) of Perognathus longimembris longimembris (Little Pocket Mouse), assembled using the California Conservation Genomics pipeline v5 (HiFi and OmniC data processed with HiFiasm).

GCA_024363575.2.longimembris_to_GCF_023159225.1.pacificus_alignment.agp: AGP file for the scaffolding of GCA_024363575.1 by genome-wide alignment to GCF_023159225.1 with RagTag and minimap2.

GCA_024363575.2.longimembris_to_GCF_023159225.1.pacificus_alignment.asm.paf: PAF file for the scaffolding of GCA_024363575.1 by genome-wide alignment to GCF_023159225.1 with RagTag and minimap2.