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

总体目标是：1)阐明基因组和基因重复/缺失以及基因家族在脊椎动物进化和多样性中的作用；2)了解遗传变异和突变在鲑鱼适应、健康和疾病中的作用；3)探索新技术和分析策略，以梳理复杂的鲑鱼遗传系统，并将其与生物化学和生理功能联系起来。未来5年的具体目标是：1)确定由全基因组（WGD）或片段复制产生的单基因和重复基因的精确数量，并帮助开发高质量的大西洋鲑鱼基因组和成功重新部署的多倍体脊椎动物的第一个代表。这将为67种不同的近亲鲑科提供共同的参考。2)开发最接近的，非鲑科，非多倍体，Esox基因组（北梭鱼）。它是没有经历过WGD的鲑科最接近的现存近亲，因此提供了记录WGD在i)物种进化，ii)分子功能专业化，iii)新功能出现以及iv)系统冗余产生中的作用所需的比较视角。3)研究基因重复保留/丢失的水平和机制、重复基因进化的速率、WGD对重倍化反应中基因组组织变化的广泛性、重复序列在WGD后重倍化中的作用，以及基因重复导致的基因和通路表达的变化。4)使用新的和现有的鲑鱼和海虱基因组工具来检查环境和化学参数，改善鱼类健康和海虱控制。海虱是野生和养殖鲑鱼中最主要的疾病。我们将讨论一些基本的生物学问题，如基因组如何自我重组以应对最近全基因组复制引起的重复染色体，以及基因复制对进化、多样性和适应的重要性。我们还将为一群经济和文化上重要的物种的疾病、抗性、繁殖、生长和对环境变化的耐受性等非常实际的问题提供新的方法。

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.