Chromosome-scale assembly of the Xenocypris davidi using PacBio HiFi reads and Hi-C technologies.

Xenocypris davidi is a benthic fish species widely distributed in the water systems south of the Yellow River in China, playing a significant role in aquatic ecosystems. Despite its ecological and economic importance, genomic resources for X. davidi are limited, hindering a comprehensive understanding of its evolutionary adaptations and genetic improvements. This study presents the first chromosome-level genome assembly of X. davidi, utilizing PacBio long-reads, Illumina short reads, and Hi-C sequencing data. The genome assembly spans 1.05 Gb with a scaffold N50 length of 33.99 Mb, and 95.12% of the genome sequence was successfully anchored onto 24 pseudochromosomes. We identified 27,360 protein-coding genes, of which 26,672 were functionally annotated. This genome sequence provides a valuable resource for exploring the molecular basis of agronomic traits in X. davidi and will facilitate its genetic enhancement.