Near telomere-to-telomere and gap-free reference genome assembly of the WuLi carp (Cyprinus carpio var. Quanzhounensis)

Abstract

Cyprinus carpio var. Quanzhounensis (WuLi carp), a native fish from Quanzhou, Guangxi, China, is well-adapted to mountainous rice-fish farming systems, yet genomic studies on the strain remain scarce. This study presents the first near telomere-to-telomere (T2T) genome and gapless assembly of C. carpio var. Quanzhounensis , generated using PacBio HiFi sequencing, ONT ultra-long reads, and Hi-C data. The final assembly, spanning 1.54 Gb across 68 contigs, features a contig N50 of 29.52 Mb, with 99.37% of sequences anchored to 50 chromosomes. A total of 49,781 protein-coding genes were annotated, and transposable elements account for 42.96% of the genome. The high-quality assembly provides a valuable genomic resource for conservation, germplasm evaluation, and future comparative studies of WuLi carp and related cyprinid fishes.