Chromosome-Scale Genome Assembly and Genome-Wide Identification of Antimicrobial Peptide-Containing Genes in the Endangered Long-Finned Gudgeon Fish (Rhinogobio ventralis)

TL;DR

This study provides a high-quality genome assembly and identifies antimicrobial peptide genes in the endangered long-finned gudgeon fish to aid conservation and research.

Contribution

The study presents the first chromosome-scale genome assembly and genome-wide identification of antimicrobial peptide genes in Rhinogobio ventralis.

Findings

A chromosome-level genome assembly of 1015.9 Mb was constructed with high completeness (99.72%).

561 putative antimicrobial peptide-containing genes were identified and categorized into 185 functional groups.

The genome resource supports conservation and bioactive compound development for this endangered species.

Abstract

Long-finned gudgeon fish, Rhinogobio ventralis, is an economically important cyprinid species with a native distribution in the upper tributaries of the Yangtze River, China. Its natural population has significantly declined due to overfishing and habitat destruction in recent decades, and it is therefore classified as endangered in China. Despite its ecological and economic importance, the lack of genomic resources has restricted comprehensive studies in various areas including population conservation, ecological adaptation, and aquaculture development. To resolve this limitation, we established a high-quality chromosome-level genome assembly of Rhinogobio ventralis in this study. Furthermore, genome-wide prediction and localization of antimicrobial peptides (AMPs) containing genes were performed using some reference sequences from public databases. Our findings hence provide a valuable genetic resource for understanding innate immunity and developing novel bioactive compounds.

As an economically important species endemic to the upper tributaries of Yangtze River in China, long-finned gudgeon fish (Rhinogobio ventralis) has been classified as endangered due to habitat destruction and population decline. In this study, we constructed a chromosome-level genome assembly of R. ventralis by integration of MGI, PacBio and Hi-C sequencing technologies. The final genome assembly was 1015.9 Mb in length (contig N50: 25.91 Mb; scaffold N50: 39.99 Mb), and 97.19% of the haplotypic genome sequences were anchored onto 25 chromosomes. Repetitive elements accounted for 51.00% of the entire genome assembly. A total of 23,220 protein-coding genes were predicted for the assembled genome, of which 99.79% were functionally annotated. Genome evaluation revealed 99.72% completeness for the genome assembly. Through genome-wide prediction of antimicrobial peptides (AMPs), we identified and localized 561 putative AMP-containing genes in the R. ventralis genome. These genes were further classified into 185 distinct functional categories based on public databases, with the top ten components of Penetratin (21.74%), Histone (5.70%), E6AP (4.09%), Scolopendin 1 (2.67%), D38 (2.31%), WBp-1 (2.13%), Defensin (2.13%), Claudin 1 (1.96%), Azurocidin (AZU1, 1.78%), and Ubiquitin (1.60%). Our data presented here provide a potential genetic resource for promoting fundamental research and wild population conservation of this endangered fish species.

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