An annotated, chromosome-level genome for the spotted turtle, Clemmys guttata.

Abstract

The spotted turtle (Clemmys guttata) is the sole extant member of the genus Clemmys and can be found in shallow wetlands across eastern North America. In recent decades, habitat alterations and poaching have reduced spotted turtle populations by more than 50% range-wide, resulting in federal protection in Canada and state-level protection within the United States. Here, we provide an annotated, chromosome-level assembly of C. guttata derived from long- and ultra-long read data as an addition to the conservation genomics resources for the species. The assembly comprises 2,286,936,868 base pairs, 98.5% of which are assembled in 25 contigs, consistent with published karyotypic data (n = 25) and including 16 gapless, telomere-to-telomere chromosome sequences. BUSCO scores indicate a highly complete assembly (99.4%). Annotation of the genome yielded 21,335 protein-coding genes with a BUSCO completeness score of 98.4%. Comparisons with a separate assembly derived from long-read and Hi-C data show that substituting ultra-long for Hi-C sequencing can improve telomere assembly and reduce structural errors in this taxon at the cost of reduced haplotype phasing, though primary assemblies are highly syntenic overall. PSMC analyses of both assemblies independently revealed a long, essentially identical history of population declines in spotted turtles. Coupled with range-wide genomic sampling, these resources will provide critical data to understand genetic structure, patterns of local adaptation, and demographic history in this species and help stem further declines.