A near-telomere-to-telomere genome assembly of the Chinese soft-shelled turtle (Pelodiscus sinensis)

Pelodiscus sinensis (Chinese soft-shelled turtle) is a freshwater species with economic and biomedical value. Here, we report a near-telomere-to-telomere (near-T2T) chromosome-level genome assembly. Using a combination of PacBio HiFi, Oxford Nanopore ultra-long reads, and Hi-C data, we assembled a 2.27 Gb genome (contig N50 = 132.52 Mb). Hi-C contact maps guided scaffolding and curation, anchoring 40 contigs to 34 chromosomes and resolving telomeres for 61 out of the 68 chromosomal ends. Gap filling and polishing yielded a chromosome-level assembly with no ambiguous bases (QV = 41.19; GC = 45.8%). BUSCO analysis indicated 97.9% completeness. Mapping rates for BGI short reads (99.4%), ONT long reads (100%), and HiFi reads (99.98%) confirm high accuracy across platforms. We annotated 21,124 protein-coding genes (97.77% functionally annotated) and 12,868 non-coding RNAs, with support from RNA-seq and full-length transcript data. Sex chromosomes (chrZ and chrW) were inferred from male-to-female depth ratios and validated using two known sex-linked SNP markers. This high-quality genome provides an essential resource for studying reptilian chromosome evolution, sex determination, and molecular breeding.