Data from: 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.