A high-quality chromosome-level genome assembly of the common carp (Cyprinus carpio var. Xiangxi)

Cyprinus carpio var. Xiangxi is a regionally farmed rice-field carp endemic to the Xiangxi region of Hunan Province, China. To adapt to the rice-fish farming environment, this variety has developed a range of genetic and physiological adaptations. However, genomic research on this strain remains limited. Here, we assembled a high-quality chromosome-level genome of C. carpio var. Xiangxi to fill this knowledge gap. Using PacBio HiFi, DNBSEQ, and Hi-C technology, We generated a 1.54 Gb genome with a contig N50 of 28.12 Mb. Using Hi-C data, 99.38% of the assembly (1,535.34 Mb) was anchored to 50 pseudochromosomes, yielding a scaffold N50 of 30.26 Mb. The quality value and Benchmarking Universal Single-Copy Ortholog score were 62.32 and 97.4%, respectively, indicating that our genome sequence is of high quality and completeness. A total of 46,362 protein-coding genes were predicted, of which 45,409 (97.94%) were functionally annotated. This study provides a valuable genomic resource for the conservation of C. carpio var. Xiangxi and offers new insights into the evolutionary history of common carp.