Chromosome-scale genome assembly and annotation of Xenocypris argentea.

Abstract

Xenocypris argentea is a small to medium-sized freshwater cyprinid fish. It distributes widely in the rivers and lakes of China, and is often used as a tool fish for water quality improvement and optimizing aquaculture structures. In recent years, natural populations of X. argentea have decreased rapidly due to human activities, yet little is known about the genetics and genomics of this fish. In the present work, we reported a chromosome-level reference genome of X. argentea based on PacBio HiFi, Hi-C and Illumina paired-end sequencing technologies. The assembled genome was 984.96 Mb in length, with a contig N50 of 36.02 Mb. Using Hi-C interaction information, 99.47% of the contigs were anchored onto 24 chromosomes, and 18 of the chromosomes were gap-free. Further analysis identified 560.27 Mb of repeat sequences and 28,533 protein-coding genes in the genome, of which, 95.62% (27,284) genes were functionally annotated. This high-quality genome offers an invaluable resource for population genetics and phylogeny, comparative genomics, adaptive evolution and functional exploration of X. argentea.