The pan-genome of 1,107 spotted sea bass accessions reveals gene evolution patterns during domestication selection

Spotted sea bass (Lateolabrax maculatus) is an ecologically and economically important species that supports a large-scale aquaculture industry in China. However, most farmed populations have not undergone systematic breeding programs and are characterized by undocumented empirical selection and poorly defined target traits. Understanding genetic diversity and gene evolutionary patterns for farmed populations is critical for designing appropriate breeding management for the future. In this study, we assembled a chromosome-level reference genome (636.65 Mb) and performed population genetics analyses using 1,107 representative wild and farmed accessions. Significant genetic differentiation and reduced genetic diversity was observed for farmed populations. Pan-genome of 1,107 accessions further identified 86.48 Mb of non-reference novel sequences (NRNS) and 206 novel genes absent from the reference genome. Gene presence/absence variation (PAV) analysis revealed farmed populations encode fewer genes than wild counterparts, implying gene loss and negative selection during domestication process. Lost genes were enriched for immune response and nervous system development, indicating the urgent need introducing wild accessions as essential genetic resources for future breeding programs. Notably, selection signatures and comparative PAV analyses across independent farmed populations revealed parallel domestication effects at both loci and gene levels, suggesting similar selective pressures despite different aquaculture practices and domestication histories. Our study provides the first pan-genome of spotted sea bass that deciphers gene evolution in domestication selection and delivers critical insights for sustainable breeding programs for farmed aquatic species.