The Pan-Genome of 1107 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 characterised by undocumented empirical selection. Understanding genetic diversity dynamics and gene evolution patterns for farmed populations is critical for designing appropriate breeding strategies. Here, we assembled a chromosome-level reference genome using HiFi and Hi-C sequencing technologies, resulting in a highly contiguous assembly with a total size of 636.65 Mb and a scaffold N50 of 27.27 Mb. Furthermore, we performed population genomic analyses using 1107 representative wild and farmed individuals. Significant genetic differentiation and reduced genetic diversity were observed in farmed populations relative to wild populations. Pan-genome of 1107 accessions further captured 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 that farmed populations harbour fewer genes than wild counterparts, implying gene loss and negative selection during the domestication process. Lost genes were enriched in functions related to immune response and nervous system development, highlighting wild populations as important genetic resources for future breeding programs. Notably, selection signatures and comparative PAV analyses across independent farmed populations revealed parallel domestication effects at both SNP and gene PAV levels, suggesting similar selective pressures despite varied aquaculture practices and domestication histories. Our study provides the first pan-genome of spotted sea bass that deciphers genetic diversity dynamics and gene evolution patterns during domestication selection and establishes valuable genomic resources for sustainable genetic improvement of this species.