The Genetically Homogeneous Population Structure of Evynnis cardinalis Along the Chinese Coast Revealed by Whole Genome Sequencing

ABSTRACT Evynnis cardinalis is a warm‐water demersal fish inhabiting the northwestern Pacific coastal waters. Previous studies based on limited molecular markers and morphological traits have yielded inconsistent conclusions regarding its phylogenetic position and population differentiation. To address these uncertainties, we assembled a high‐quality chromosome‐level genome using PacBio HiFi and Hi‐C technologies, and then clarified its close phylogenetic relationship with Pagrus major . At the population genomic level, genome‐wide single nucleotide polymorphism (SNP) analysis detected 8,643,907 high‐quality SNPs from three geographically distinct populations (Shantou, Zhuhai, and Hainan). The results revealed weak population structure and extremely low genetic differentiation among the three geographic populations, a pattern consistent with high genetic connectivity in the ocean. However, subsequent analysis showed that chromosome 8 had the most candidate genes for genomic variation among populations, involved in cell structure, energy metabolism, and DNA repair. It suggests that certain genomic regions may provide potential targets for future studies on environmental responses in complex nearshore benthic environments despite the overall population genetic homogeneity. Our study not only provides the first chromosome‐level genome assembly but also clarifies the taxonomic status and single population genetic structure of E. cardinalis in Chinese coastal waters at genome‐wide level. These findings are expected to facilitate the biodiversity conservation and sustainable management of this commercially important species.