Genomic Insights into the Population Genetics and Adaptive Evolution of Yellow Seabream (<i>Acanthopagrus latus</i>) with Whole-Genome Resequencing
2025
Yuan Li | Jingyu Yang | Yan Fang | Ran Zhang | Zizi Cai | Binbin Shan | Xing Miao | Longshan Lin | Puqing Song | Jing Zhang
Yellow seabream (<i>Acanthopagrus latus</i>), a species of significant economic importance, predominantly inhabits the warm waters of the Indo-Western Pacific. While previous studies have explored the genetic diversity of <i>A. latus</i> using microsatellites and other nuclear markers, a comprehensive understanding of its genetic characteristics and adaptive evolution using whole-genome resequencing (WGR) remains limited. In this study, we collected 60 individuals from six distinct geographic locations and performed WGR, achieving an average sequencing depth of 12.59×, which resulted in the identification of 19,488,059 high-quality single-nucleotide polymorphisms (SNPs). The nucleotide polymorphism (π<sub>θ</sub>) across all populations was consistent, ranging from 0.003042 to 0.003155, indicating low genetic differentiation among populations. Comparative analyses revealed that populations other than that in Xiamen (XM) have undergone adaptive evolution, potentially linked to traits such as growth and development, feeding, immunity, and movement. This study explores the population genetics and adaptive evolutionary patterns of <i>Acanthopagrus latus</i> at the genomic level, providing an essential foundation for the conservation and management of this economically important species in the future.
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