Salmonid Genome Duplication Drives Specialization and Adaptation

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Whole genome duplications (WGD) very likely play one of the more significant roles in evolutionary innovation. Such expansive duplications are found in plants, animals, in basal vertebrates (~500MYA), fishes (~300MYA), and more recently in ancestral salmonids (~90MYA). These major genome expansions double the genetic raw material that has been associated with radically new adaptations to various environments and likely play a key role in the evolution of novel species and lineages. A connection between WGDs and major evolutionary events appears to be linked to seminal shifts in evolutionary history. Our specific objectives over the next 5 years are to: 1) build on our recent development of a high quality Atlantic salmon genome reference sequence to explore functional chromosomal structural and gene changes in Arctic charr, Coho and Chinook salmon, and further annotate duplicate genes within the Atlantic salmon, and 2) develop functional annotation for the salmonid outgroup Northern Pike genome and characterize its chromosome structure and a novel sex-determining system. Chromosome structural characteristics to be explored include DNA methylation, histone modification, and DNA openness and we will compare these potential epigenetic features with gene expression patterns. The subject of epigenetics is controversial and continues to evolve. Chromatin structure and DNA methylation patterns can be passed from one generation to the next and environmental factors can modify such patterns. Epigenetic changes can cause very rapid (and reversible) phenotypic changes and adaptation to a rapidly changing environment. This proposal explores this subject in salmonids and pike where we seek to annotate newly developed salmonid and pike genomes by mapping these sites and linking them to gene promoter and gene expression patterns. We will also explore a very recently evolved novel and possibly environmentally modified sex-determining pattern found in North American pike.