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

Area of Science:

• Genomics
• Conservation Biology
• Herpetology

Background:

• The spotted turtle (Clemmys guttata) faces significant population declines due to habitat loss and poaching.
• Existing conservation efforts are hampered by a lack of comprehensive genomic resources for the species.

Purpose of the Study:

• To generate a high-quality, chromosome-level genome assembly for the spotted turtle.
• To provide essential genomic data for conservation efforts and population studies.

Main Methods:

• Utilized long- and ultra-long read sequencing data for genome assembly.
• Performed annotation to identify protein-coding genes.
• Employed Population Size Skimmed Coverage (PSMC) analyses to assess demographic history.

Main Results:

• A highly complete chromosome-level genome assembly (2.29 Gb) was achieved, with 25 contigs matching the species' karyotype.
• The assembly includes 16 gapless, telomere-to-telomere chromosome sequences.
• Annotation identified 21,335 protein-coding genes, with high completeness scores (99.4% and 98.4%).
• Comparative analysis indicated ultra-long reads improve telomere assembly over Hi-C data.
• PSMC analyses revealed a consistent history of population decline.

Conclusions:

• The new genome assembly is a valuable resource for spotted turtle conservation genomics.
• This data will facilitate research into genetic structure, adaptation, and demographic history.
• The findings support targeted conservation actions to mitigate population declines.