Abstract
Megalobrama, a genus of cyprinid fish, is an economically important freshwater fish widely distributed in major waters of China. Here, we report the genome resequencing of 180 Megalobrama fish including M. amblycephala, M. skolkovii, M. hoffmanni, and M. pellegrini. Population structure indicated that geographically divergent Megalobrama populations were separated into six subgroups. A phylogenetic tree showed that M. skolkovii was more closely related to M. pellegrini than other species and M. hoffmanni was clustered apart from other Megalobrama species, showing a high nucleotide diversity in geographic groups. Treemix validated gene flow from M. amblycephala to M. skolkovii, suggesting that introgression may provide an important source of genetic variation in the M. skolkovii populations. According to the demographic history analysis, it is speculated that Megalobrama might have been originally distributed in the Pearl River with some spread to Hainan Island and northern China due to lower sea levels during the glacial period. Whole-genome selective sweeps analysis demonstrated that M. amblycephala likely developed an enhanced energy metabolism mostly through fatty acid degradation pathways whereas M. hoffmanni possibly regulate lipid absorption via the cholesterol metabolism pathway. Taken together, this study provides a valuable genomic resource for future genetic investigations aiming to improve genome-assisted breeding of Megalobrama species.