Whole‐Genome Sequencing and Resequencing of <i>Hucho bleekeri</i> Provides Insights into Genetic Mechanisms of Environmental Adaptation

Salmonidae represents an important family in the study of genome evolution following genome duplication. Hucho bleekeri has the lowest latitude distribution among all salmonid fish and is an excellent model for studying the relationships among biogeography, evolution, and environmental change. In this study, we constructed a high-quality reference genome for H. bleekeri, with a 3,700,945,220 bp length of the scaffold and a scaffold N50 of 75,100,808 bp. The final genome size of H. bleekeri was 3.7 G, and the genome was anchored to 44 chromosomes on the basis of Hi-C scaffolding. We confirmed the existence of Ss4R in the H. bleekeri genome, revealing that Ss4R occurred before the differentiation of salmonid species. Comparative genome analysis revealed that genes involved in transmembrane transport, metabolism, and stress were significantly expanded and may play important roles in the environmental adaptation of H. bleekeri. To further reveal the genetic structure of Salmonidae at the genome level, we conducted whole-genome resequencing of all Hucho species in China. Significant genetic differences were detected between different Hucho species and between different populations of same species. A genome-wide selective sweep test was conducted to analyze the different populations of H. bleekeri with significant body size variation. We predicted several candidate genes potentially subjected to selection, such as MYH, mAChR, SDH, and acyl-CoA dehydrogenase, which might be associated with the growth and environmental adaptation of H. bleekeri. Our study has profound significance in characterizing the evolution of salmonid fish and the population structure of Hucho species.