A chromosome-level genome assembly of the blackspotted croaker (Protonibea diacanthus)

Abstract

The blackspotted croaker (Protonibea diacanthus) is an endangered coastal marine fish. It is also a valuable species that is cultured on the southeast coast of China. While some genetic studies have been conducted to protect this species, genomic resources are lacking. Here, we report a chromosome-scale assembly of P. diacanthus genome by high-depth genome sequencing, assembly, and annotation. The genome scale was 635.69 Mb with contig and scaffold N50 length of 3.33 Mb and 25.60 Mb, respectively. Hi-C scaffolding of the genome resulted in 24 chromosomes of 94.15% total genome. We predicted 23,971 protein-coding genes. In addition, we constructed a phylogenetic tree using 2755 single-copy gene families and identified 462 unique gene families in P. diacanthus genome compared to three other sciaenids. What's more, from the analysis of gene families, we found that several gene families related to innate immunity were significantly expanded in the blackspotted croaker genome compared to other teleost genomes. The high-quality genome can improve our understanding of the molecular mechanisms behind economically valuable traits and provide insights into characteristics of the immune system.