Chromosome-level genome assembly of the Chinese Longsnout catfish
Leiocassis longirostris
Abstract
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.