Squirrels (Rodentia; Sciuridae) are a well-known and diverse group of rodents, including the charismatic ground-dwelling members of the Tribe Marmotini. In particular, the California ground squirrel (Otospermophilus beecheyi) is an emerging model system for the study of social and risk-sensitive behaviors in a rapidly changing world, as well as the physiology of resistance to snake venoms. To complement extensive natural history information for O. beecheyi, we provide a chromosome-scale genome to facilitate molecular studies focused on the genetic basis of ecologically important traits, population genetics, comparative genomics, and social evolution. The final scaffolded genome was 2.27 Gb contained in 9,960 contigs and placed into 28 1,383 scaffolds. The scaffold N50 was just over 125 Mb. We used the presence of 10,248 complete genes detected by BUSCO v5 specifically to compare broad patterns of chromosomal synteny between chromosomal scaffolds for O. beecheyi and two other sciurid rodents. The recovered pattern of synteny suggests several fusion and fission events for O. beecheyi to the other two species. This new information should advance our understanding of O. beecheyi, particularly concerning the study of social and risk-taking behaviors, and comparative studies of mammalian genomic biology and evolution.
