Background: Understanding population structure and adaptive history is critical for designing appropriate management regulations for fisheries and conserving adaptive potential for the future. However, this is not straightforward for marine fish, particularly those with long-distance migratory capabilities.
Method: In this study, we constructed a high-quality reference genome for Japanese Spanish mackerel (Scomberomorus niphonius) and explored its population structure using whole genomic and epigenomic data.
Result: Despite the high depth of sequence data, we failed to identify geographical genetic differentiation in Japanese Spanish mackerel across Chinese coastal waters. However, whole-genome bisulphite sequencing classified this species into the Bohai-Yellow Sea group and the East China Sea-South China Sea group. Genes associated with embryonic skeletal system development, limb morphogenesis functions, and adult locomotory behaviour were differentially methylated in the southern (Zhanjiang, ZJ) and northern (Western Dalian, WDL) populations, suggesting these may act as key drivers of population structure in Japanese Spanish mackerel.
Conclusion: Our study not only provides the first reference genome for the Japanese Spanish mackerel and elucidates population differentiation at the epigenomic level, but also establishes a methylome-based framework for population structure analyses of marine fish with long-distance migratory abilities. These findings are anticipated to support the development of scientifically robust programmes for the sustainable conservation of marine fishery resources.