Chromosome-level genome assemblies of five Sinocyclocheilus species.

Abstract

Sinocyclocheilus, a genus of tetraploid fishes endemic to Southwest China's karst regions, are classified as second-class nationally protected species due to their fragile habitat. Limited high-quality genomic resources have hampered studies on their phylogenetic relationships and the origin of their polyploidy. Here, we present a high-quality genome assembly of the most abundant Sinocyclocheilus species, the golden-line barbel (Sinocyclocheilus grahami), by integrating PacBio long-read and Hi-C sequencing. The resulting scaffold-level genome-assembly is 1.6 Gb long, with a scaffold N50 of up to 30.7 Mb. We annotated 42,806 protein-coding genes. Also, 93.1% of the assembled genome sequences (about 1.5 Gb) and 93.8% of the total predicted genes were successfully anchored onto 48 chromosomes. Furthermore, we obtained chromosome-level genome assemblies for four other Sinocyclocheilus species (S. anophthalmus, S. maitianheensis, S. anshuiensis, and S. rhinocerous) based on homologous comparisons. These genomic resources will enable in-depth investigations on cave adaptation, improvement of economic values, and conservation of diverse Sinocyclocheilus fishes.