Chromosome-Level Genome Assembly and Comparative Genomic Analysis of the Barbel Chub (Squaliobarbus curriculus) by Integration of PacBio Sequencing and Hi-C Technology

Abstract

The barbel chub (Squaliobarbus curriculus), the only species in the genus, is widely distributed in freshwater lakes and rivers at different latitudes in East Asia, with fishery and biodiversity importance, and is an emerging commercially important fish in China. However, the resource of this species has dramatically declined due to anthropogenic activities such as over-exploitation, as well as water pollution. Genomic resources for S. curriculus are useful for the management and sustainable utilization of this important fish species, and also for a better understanding of its genetic variation in the region. Here, we report the chromosome-level assembly of the S. curriculus genome obtained from the integration of PacBio long sequencing and Hi-C technology. A total of 155.34 Gb high-quality PacBio sequences were generated, and the preliminary genome assembly was 894.95 Mb in size with a contig N50 being 20.34 Mb. By using Hi-C data, 99.42% of the assembled sequences were anchored to 24 pseudochromosomes, with chromosome lengths ranging from 27.22 to 58.75 Mb. A total of 25,779 protein-coding genes were predicted, 94.70% of which were functionally annotated. Moreover, S. curriculus shows resistance to grass carp haemorrhagic disease (GCHD) caused by grass carp reovirus (GCRV), which seriously hinders the status and future perspectives of commercial grass carp production. Phylogenetic analysis indicated that S. curriculus diverged with grass carp (Ctenopharyngodon idellus) approximately 20.80 million years ago. Annotations of the expanded gene families were found to be largely enriched in immune-related KEGG pathway categories. Moreover, a total of 18 Toll-like receptor (TLR) genes were identified from the whole genome of S. curriculus. The high-quality genome assembled in this study will provide a valuable resource for accelerating ecological, evolutionary, and genetic research on S. curriculus.