Unveiling the evolutionary and functional impact of genomic structural variants of Atlantic salmon

Project Summary: This project aimed to explore how genomic variants influence the diversity and evolution of Atlantic salmon by integrating large-scale computational genomics and advanced gene-editing techniques. We sought to develop a pipeline to analyze genomic variants across populations, breeds and species, with applications in aquaculture, and conservation. Key findings so far: Domestication of Atlantic Salmon: The study uncovered the important role of salmonid-specific whole genome duplication (WGD) in Atlantic salmon's rapid domestication, akin to plant domestication. By analyzing to pairs of genomic data from aquaculture and wild populations in the Eastern and Western Atlantic, we identified selective sweeps on specific variants in major histocompatibility complex (MHC) genes. These findings suggest that both long-term balancing selection and human-induced selection have shaped the evolution of MHC genes, crucial for adapting to aquaculture environments. Evolution of Circadian Genes: Our second major discovery involved the evolutionary history and functional diversification of Period genes across vertebrates. We identified multiple lineage-specific gains and losses of Per genes, with particular emphasis on salmonid species, many of which lost per3 gene, except for Atlantic salmon. We identified key adaptive changes in the CRY-binding regions of Per1 and Per3, critical for circadian rhythm regulation. These results contribute to understanding genomic mechanisms in domestication and adaptive evolution in aquaculture species, suggesting the importance of maintaining genetic diversity for sustainable aquaculture practices.

Genomic structural variants contribute largely to phenotypic diversity, including disease susceptibility, metabolism, morphology and growth traits. However, due to their complex nature, which and how structural variants have contributed to adaptive evolution with functional advantage are yet to be clarified. To identify adaptive structural variants and clarify their phenotypic advantage at the molecular scale, I propose (1) cutting-edge bioinformatics approaches that integrate multiple omics data sets (population genomics, gene expression during development, and aquaculture traits) and (2) functional investigation with gene-editing technology at the cellular and organismal levels. This project will link how genomic structural variants contribute to the phenotypic diversity including aquacultural traits and adaptive evolution in domesticated Atlantic salmon populations. On a broader scale, this study will establish a pipeline to investigate the phenotypic and evolutionary effect of structural variants in non-model organisms, including aqua- and agricultural species and endangered species. Understanding genetic diversity also contributes to the sustainable maintaining of both wild and farmed Atlantic salmons.