Gene and genome duplication in the evolution of diversity and health in salmonids

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The overall objectives are to 1) elucidate the role of genome and gene duplications/deletions and gene families in the evolution and diversity of vertebrates, 2) understand the role of genetic variation and mutation for salmonid adaptation, health, and disease, 3) explore new technologies, and analysis strategies to tease apart complex salmonid genetic systems and relate them to biochemical and physiological functions. Specific objectives over the next 5 years are to 1) Determine the precise number of single and duplicate genes resulting from a whole genome (WGD) or segmental duplications and help develop a high quality Atlantic salmon genome and the first representation of a successfully re-deploidized polyploidy vertebrate. This will provide a common reference for 67 different closely related salmonid species. 2) Develop the closest, non-salmonid, non-polyploid, Esox genome (Northern Pike). It is the closest living relative of salmonids that has not undergone a WGD and as such provides the comparative perspective needed for documenting of the role of WGD in the i) evolution of species, ii) specialization of molecular functions, iii) appearance of new functions, and iv) generation of system redundancy. 3) Examine levels and mechanisms of gene duplicate retension/loss, rates of duplicate gene evolution, extensiveness of genome organizational changes in rediploidization response to WGD, the role of repeats in rediploidization after a WGD, and the changes in gene and pathway expression as a result of gene duplications. 4) Improve fish health and sea lice control using new and existing salmon and sea lice genomic tools to examine environmental and chemical parameters. Sea lice is the most prominent disease in wild and cultured salmon. We will address basic biological questions such as how a genome reorganizes itself to cope with duplicated chromosomes arising from a recent whole-genome duplication and the importance of gene duplications for evolution, diversity and adaptation. We will also provide new approaches for very practical issues of disease, resistance, reproduction, growth, and tolerance to environmental change for a whole group of economically and culturally important species.