Assembled and annotated reference genome and demographic history of the eastern chipmunk (Tamias striatus).

The eastern chipmunk (Tamias striatus) is an abundant North American sciurid rodent and the only extant member of the subgenus Tamias. Despite its abundance, a reference genome has not been produced for this species. Here we present an assembled and annotated reference genome for the eastern chipmunk using PacBio HiFi long read sequencing data. We sequenced the genome of a vouchered male eastern chipmunk collected in Maine and stored at the National Museum. We compared the eastern chipmunk's genome with the genome of the Siberian chipmunk (Tamias sibiricus; subgenus Eutamias), the only other species in the Tamias genus with an annotated reference genome. The genomes were similar with 55.45% of genes showing collinearity and chromosomal rearrangements only occurring between chromosomes 4 and 8. We identified 219 genes under positive selection in the eastern chipmunk relative to the Siberian chipmunk. A coalescent analysis inferred the effective population size of the Maine eastern chipmunk may have steadily decreased through the Pleistocene epoch, consistent with a reduction in available habitat. We also generated short-read Illumina sequencing data from two additional eastern chipmunks collected in New Castle County, Delaware and Carbon County, Pennsylvania. We calculated nucleotide diversity over 10 kb windows across the genome (mean = 0.0014 ± 0.0012 s.d.) and identified genes with high nucleotide diversity. The eastern chipmunk reference genome will facilitate future population genetic and evolutionary studies including those investigating its role as a reservoir host for the bacterium that causes Lyme disease.