Evolutionary, developmental, and physiological genomics of salmonid fishes

鲑鱼的进化、发育和生理基因组学

• 批准号: RGPIN-2017-04017
• 负责人: Danzmann, Roy
• 金额: $ 2.91万
• 依托单位: University of Guelph
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2022
• 资助国家: 加拿大
• 起止时间: 2022-01-01 至 2023-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=757622
• 关键词: Evolutionary; developmental; physiological; genomics; salmonid

Whole genome duplication (WGD) events where all the chromosomes in each cell undergo a complete doubling to give rise to a completely identical set of genes are now recognized as being potential accelerators of evolutionary change in animals and plants. The fates of new genes that arise from WGD are varied, but most duplicated copies appear destined to become nonfunctional (silenced). We still do not understand why some genes are retained as duplicates for long periods of time as essentially identical copies of one another, while other duplicate genes diverge from one another and acquire new expression patterns and potentially new functions. I use salmonid fishes (trout, salmon, charr) to study the distribution and retention of duplicate genes because they are the most recent vertebrate group to have undergone a WGD event in their ancestry. I contrast the patterns of duplicate gene expression in Arctic charr (Salvelinus alpinus), a species whose chromosomes are more representative of the diploid fish ancestor with rainbow trout (Oncorhynchus mykiss) where some evolutionarily unrelated chromosome arms have fused. My research will examine the relationships between variation in pairing among duplicated chromosomes, DNA sequence similarity, and the relative proportion of nucleotide types, and how this variation may influence the expression of duplicate gene pairs from different functional categories. I will also determine if environmental change has different effects on the expression of duplicate genes involved with extracellular functions (e.g., stress-related genes) versus intracellular functional classes (e.g., development-regulating) and if mild stress experienced when the fish are young will influence gene expression responses to more severe stress later in life. If I find that different kinds of duplicate genes show varied responses to stress brought on by environmental change, I will test if one kind of change in DNA structure (methylation) explains the patterns observed. This research will fundamentally enhance our knowledge of polyploidy as a force shaping evolution and speciation.

全基因组复制（WGD）事件，即每个细胞中的所有染色体经历完全加倍，产生一组完全相同的基因，现在被认为是动物和植物进化变化的潜在加速器。 WGD 产生的新基因的命运各不相同，但大多数重复拷贝似乎注定会失去功能（沉默）。 我们仍然不明白为什么有些基因会在很长一段时间内保留为重复基因，彼此基本相同，而其他重复基因却彼此不同，并获得新的表达模式和潜在的新功能。 我使用鲑鱼（鳟鱼、鲑鱼、红点鲑）来研究重复基因的分布和保留，因为它们是最近经历了祖先 WGD 事件的脊椎动物群体。 我对比了北极红点鲑（Salvelinus alpinus）的重复基因表达模式，该物种的染色体更能代表虹鳟鱼（Oncorhynchus mykiss）的二倍体鱼类祖先，其中一些进化上不相关的染色体臂融合在一起。 我的研究将研究重复染色体配对变异、DNA 序列相似性和核苷酸类型相对比例之间的关系，以及这种变异如何影响不同功能类别的重复基因对的表达。 我还将确定环境变化是否对涉及细胞外功能（例如，应激相关基因）和细胞内功能类别（例如，发育调节）的重复基因的表达有不同的影响，以及鱼年轻时经历的轻微应激是否会影响基因表达对以后生活中更严重应激的反应。 如果我发现不同种类的重复基因对环境变化带来的压力表现出不同的反应，我将测试 DNA 结构（甲基化）的一种变化是否可以解释观察到的模式。这项研究将从根本上增强我们对多倍体作为塑造进化和物种形成的力量的认识。