Chromosome-level genome assembly of Nemipterus japonicus based on PacBio sequencing and Hi-C technology

TL;DR

This study provides a high-quality chromosome-level genome assembly for the economically important fish Nemipterus japonicus using advanced sequencing technologies.

Contribution

The novel contribution is the first chromosome-level genome assembly of N. japonicus using PacBio and Hi-C technologies.

Findings

The assembled genome has a contig N50 of 30.83 Mb and was anchored onto 22 pseudochromosomes.

23,514 protein-coding genes and 6,532 non-coding RNAs were predicted in the genome.

163 positively selected genes were identified, potentially involved in growth, reproduction, immune response, and DNA repair.

Abstract

Nemipterus japonicus is an economically important demersal fish species inhabiting warm coastal waters of the Indo-West Pacific region, yet its genomic resources remain scarce. Here, we successfully assembled a high-quality chromosome-level reference genome of N. japonicus by integrating Illumina, PacBio, and Hi-C sequencing technologies. The genome assembly spans 723.27 Mb, with a contig N50 of 30.83 Mb, and 97.04% of the contigs were anchored onto 22 pseudochromosomes, yielding a scaffold N50 of 30.96 Mb. A total of 23,514 protein-coding genes and 6,532 non-coding RNAs were predicted, with repetitive sequences accounting for 21.84% of the genome. Comparative genomic analysis revealed that N. japonicus has 218 expanded and 1,076 contracted gene families, with the divergence times of 56.9 to 85.9 million years ago from three Sparidae species. Positive selection analysis further identified 163 positively selected genes potentially involved in growth and development, reproduction, immune response, and DNA repair of N. japonicus. This study provides fundamental data for investigating the genetic evolution of N. japonicus and the genomes of other Nemipterid fish.

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