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The Chinese longsnout catfish ( Leiocassis longirostris Gunther) is one of the most economically important freshwater fish in China. As wild populations have declined sharply in recent years, it is also a valuable model for research on sexual dimorphism, comparative biology, and conservation. However, the current lack of high-quality chromosome-level genome information for the species hinders the advancement of comparative genomic analysis and evolutionary studies. Therefore, we constructed the first high-quality chromosome-level reference genome for L. longirostris. The total genome was 703.19 Mb, with 389 contigs and contig N50 length of 4.29 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome sequences (685.53 Mb) were scaffolded into 26 chromosomes ranging from 17.36 to 43.97 Mb, resulting in a chromosomal anchoring rate for the genome of 97.44%. In total, 23 708 protein-coding genes were identified in the genome. Phylogenetic analysis indicated that L. longirostris and its closest related species P. fulvidraco diverged approximately 26.6 million years ago. This high-quality reference genome of L. longirostris should pave the way for future genomic comparisons and evolutionary research.

The Chinese Longsnout catfish Leiocassis longirostris (L. longirostris) is one of the most economically important freshwater catfish in China. It is a valuable model for studies on sexual dimorphism, comparative and conservation biology since its wild resources have declined sharply. However, there is lack of high-quality chromosome-level genome information for comparative genomic analysis and genome evolutionary studies. Therefore, we constructed the first high-quality chromosome-level reference genome for L. longirostris using a combined strategy of BGI-SEQ500, Nanopore, and Hi-C technologies. The assembled genome of L. longirostris contained a total length of 703.19 Mb with 389 contigs, and an N50 size of 4.29 Mb. Using the Hi-C data, we finally successfully generated 82 chromosome-level scaffolds anchored onto 26 chromosomes with a total length of 685.53 Mb (97.44% of the total genome sequences), ranging in size from 17.36 Mb to 43.97 Mb. A total of 23,708 protein-coding genes were identified in the L. longirostris genome, and up to 97.73% of L. longirostris genes were functionally annotated. In addition, the genome contained 239.11 Mb (33.99% in the total genome) repetitive sequences and 6,303 non-coding RNAs. The phylogenetic analysis indicated that the divergence time between L. longirostris and their closest relative species Pelteobagrus fulvidraco was approximately 26.6 million years. Collinearity analyses showed 26 chromosomes of L. longirostris displayed high homology with the corresponding scaffold (≥3M) of P. fulvidraco and the corresponding chromosomes of the Ictalurus punctatus. The high-quality reference genome of L. longirostris was assembled for the first time and will pave a way for genome-scale selective breeding, genome comparisons and evolution investigations.