Supporting data for "Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise"

The Yangtze finless porpoise (<i>Neophocaena asiaeorientalis asiaeorientalis</i>, YFP) and the East Asian finless porpoise (<i>Neophocaena asiaeorientalis sunameri</i>, EFP) are two subspecies of the narrow-ridged finless porpoise that live in fresh and salt water, respectively. They serve as ideal models for the study of freshwater adaptation and evolution. The main objective of this study was to provide contiguous chromosome-level genome assemblies for YFP and EFP. Here, we generated and upgraded genomes of YFP and EFP at the telomere-to-telomere level by combining PacBio HiFi long reads, ultra-long ONT reads, and Hi-C sequencing data, with a total size of 2.48 Gb and 2.50 Gb respectively. The scaffold N50 of two genomes was 125.12Mb (YFP) and 128Mb (EFP) with one contig for one chromosome. The telomere repeat and centromere position were clearly identified in both YFP and EFP genomes. Telomeric repeat units were detected at 85% and 90% of the chromosome both ends in YFP and EFP genomes, respectively. In total, 5,480 new-found genes were detected in the YFP genome, including 56 genes located in the newly identified centromere regions. Additionally, synteny blocks, comparative genomes, phylogenetic relationships, gene family expansion, and selection pressure were studied in connection with the genomes of other related mammals. Significant improvements were observed in genome contiguity, the number of scaffolds and gaps, and annotation compared to the first drafts of the YFP (GCA_003031525.2) and EFP (GCA_026225855.1) genome assemblies. The telomere-to-telomere gap-free reference genomes will support conservation genetics and population management for finless porpoises.