Near telomere-to-telomere diploid genome assembly of Acrossocheilus wenchowensis

Acrossocheilus wenchowensis is a lukewarm-water fish found in southern Chinese mountain streams, valued for both ornamental and edible purposes. We assembled a near telomere-to-telomere (T2T) genome using HiFi, ONT, Hi-C and Illumina data. The assembly is approximately 870.69 Mb with a contig N50 of about 21.28 Mb. Among these, 14 chromosomes in Hap1 and 15 chromosomes in Hap2 have reached T2T levels. A total of 24,909 protein-coding genes were predicted in Hap1 and 24,496 in Hap2, with BUSCO scores of 97.4% and 97.6%, respectively. A conserved centromeric satellite sequence (262 bp) derived from an LTR transposon was identified. Comparative genomics showed that Acrossocheilus and Onychostoma diverged approximately 13.7 million years ago (Mya), while A. wenchowensis diverged from A. fasciatus about 5.25 Mya. Resequencing of four geographic populations of A. wenchowensis revealed distinct genetic structure in the LY group compared to the other populations based on SNP and InDel analysis. This genome provides a framework for diploid T2T studies in fish and supports further functional genomics research.