A Chromosome-Level Genome Assembly of the Dark Sleeper Odontobutis potamophila

Abstract

The dark sleeper, Odontobutis potamophila, is a commercially valuable fish that widely distributed in China and Southeast Asia countries. The phenomenon of sexual dimorphism in growth is conspicuous, which the males grow substantially larger and faster than the females. However, the high-quality genome resources for gaining insight into sex-determining mechanisms to develop sex-control breeding are still lacking. Here, a chromosomal-level genome assembly of O. potamophila was generated from a combination of Illumina reads, 10× Genomics sequencing, and Hi-C chromatin interaction sequencing. The assembled genome was 1,134.62 Mb with a contig N50 of 22.25 Mb and a scaffold N50 of 24.85 Mb, representing 94.4% completeness (Benchmarking Universal Single-Copy Orthologs). Using Hi-C data, 96.49% of the total contig bases were anchored to the 22 chromosomes, with a contig N50 of 22.25 Mb and a scaffold N50 of 47.68 Mb. Approximately 54.18% of the genome were identified as repetitive elements, and 23,923 protein-coding genes were annotated in the genome. The assembled genome can be used as a valuable resource for molecular breeding and functional studies of O. potamophila in the future.

Keywords: Odontobutis potamophila; gene annotation; sex determination; whole-genome sequence.

Fig. 1

Assemblies and evolution of Odontobutis potamophila genome. (a) An adult dark sleeper. (b) 41-mer frequency distribution in the genomes. The X-axis is the Kmer depth, and Y-axis represents the frequency of the Kmer for a given depth. (c) Venn diagram of shared and unique orthologous gene family for four selected vertebrate genomes. Each number represents the number of orthologous gene families shared by the indicated genomes. (d) Phylogenetic relationship of O. potamophila and 10 other fish species genome using 1,182 single copy orthologous genes. The divergence time is given in millions of years in blue color. The relative rates of molecular evolution are expressed as the branch lengths. Estimates of divergence times (millions of years) calculated from the rate of sequence similarity are indicated at each node.