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

鲑鱼多样性和健康进化中的基因和基因组复制

• 批准号: 138282-2012
• 负责人: Koop, Ben
• 金额: $ 2.91万
• 依托单位: University of Victoria
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2013
• 资助国家: 加拿大
• 起止时间: 2013-01-01 至 2014-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=522393
• 关键词: Gene; genome; duplication; evolution; diversity

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.

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对鲑鱼适应、健康和疾病的作用，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化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) 或片段重复产生的单个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去倍体化的多倍体脊椎动物的第一个代表。 这将为 67 种密切相关的不同鲑鱼物种提供共同参考。 2) 开发最接近的、非鲑鱼、非多倍体的 Esox 基因组（北方白斑狗鱼）。它是尚未经历 WGD 的鲑鱼的最近亲缘关系，因此提供了记录 WGD 在 i）物种进化、ii）分子功能专业化、iii）新功能出现和 iv）系统冗余生成中的作用所需的比较视角。 3) 检查基因重复保留/丢失的水平和机制、重复基因进化的速率、WGD重二倍化反应中基因组组织变化的广泛性、WGD后重复在重二倍化中的作用，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常见的疾病。 我们将解决基本的生物学问题，例如基因组如何重组自身以应对最近全基因组复制产生的复制染色体，以及基因复制对于进化、多样性和适应的重要性。 我们还将为整个经济和文化重要物种的疾病、抵抗力、繁殖、生长和环境变化耐受性等非常实际的问题提供新的方法。