De novo reference genome of a Geomyid rodent, Botta’s pocket gopher (Thomomys bottae)

A well-known subterranean rodent of the North American west, Botta’s pocket gopher (Thomomys bottae) is both a garden pest and an important soil engineer. It is also a fascinating example of intraspecific variation, with considerable phenotypic diversity across its range and unusual levels of variation in chromosome number and composition. Here, we present a high-quality reference genome from a male T. b. bottae captured in the San Francisco Bay Area, representing one of the first two genomes assembled for the rodent family Geomyidae. The assembly, comprised of 2,792 scaffolds, with a scaffold N50 value of 23.6 Mb and a BUSCO score of 91.0%, fills a significant taxonomic sampling gap in rodent genome resources. With this new reference genome, we envision new opportunities to investigate questions regarding the genomics of adaptation to the belowground niche space and the impact of associated life history traits, such as limited dispersal and low population connectivity, on intraspecific genetic and phenotypic variation, genome evolution, speciation, and phylogenetic relationships across the Geomyoidea.

Methods
This dataset was generated in as a preliminary annotation step for the Thomomys bottae genome assembly available at NCBI BioProject ID PRJNA851166. We annotated repetitive elements in the genome using a combination of known repetitive elements and de novo identification of transposable element motifs in the genome. We identified these repetitive elements using RepeatModeler v.2.0.3 (Flynn et al. 2020) with GenomeTools LTR harvest (v.1.6.5), LTR Retriever v.2.9.8 (Ou and Jiang 2018) and DeepTE (version: Commit babd65e950, Yan et al. 2020) to perform de novo identification on the mThoBot1.0 genome. 

Here, we make the the de novo annotated repetitive element library available in fasta format. Code used to perform annotation is also included.