Chromosome-level genome assembly and evolutionary analysis of the Nao-zhou stock of large yellow croaker (Larimichthys crocea)

Abstract

The Nao-zhou stock of large yellow croaker is an indigenous population in the South China Sea and is phenotypically different from the population on the eastern coast of China. The chromosome-level genome assembly presented in this study significantly advances the understanding of Larimichthys crocea by surpassing previous fragmented genome assemblies and genome-wide RAD marker studies. While earlier studies have provided foundational insights into the genetic diversity and population structure of the species, they lack the resolution necessary for in-depth evolutionary, functional, and applied genomic analyses. In this study, the chromosome-level genome assembly of the Nao-zhou stock was constructed by combining MGI (MGISEQ-2000), and PacBio (Pacific Biosciences) HiFi and Hi-C sequencing methods. The results showed that the assembled genome size was 726 Mb, of which 98.27 % (723 Mb) of the sequences were anchored to 24 chromosomes and the proportion of complete genes reached 98.7 %. In the genome annotation, 31.04 % of the repetitive sequences in the genome were identified, with 24,796 protein-coding genes predicted, of which 99.47 % (24,664 genes) were successfully annotated. A total of 867 positively selected genes were identified in the environmental adaptation of the Nao-zhou stock. Gene Ontology (GO) enrichment of these genes showed that they were mainly enriched in DNA replication, rRNA processing, and ubiquinone biosynthesis. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that these genes were mainly involved in cytokine receptor interactions, ribosome generation in eukaryotes, DNA replication, and RNA degradation. These genomic data provide valuable genetic resources for more in-depth evolutionary and functional studies in the future, as well as a basis for molecular breeding and protection of this economically important species.