Salmonid Genome Duplication Drives Specialization and Adaptation

全基因组复制(WGD)很可能在进化创新中发挥着更重要的作用。在植物、动物、基本脊椎动物(~500MYA)、鱼类(~300MYA)以及最近在祖先鲑鱼(~90MYA)中都发现了这种广泛的复制。这些主要的基因组扩张使与各种环境的全新适应相关的遗传原料翻了一番，并可能在新物种和谱系的进化中发挥关键作用。WGDS和重大进化事件之间的联系似乎与进化史上的重大转变有关。我们在未来5年的具体目标是：1)在我们最近开发的高质量大西洋鲑鱼基因组参考序列的基础上，探索北极鲑鱼、Coho鲑鱼和Chinook鲑鱼的功能染色体结构和基因变化，并进一步注释大西洋鲑鱼中的重复基因；2)对鲑科外群Northern Pike基因组进行功能注释，并表征其染色体结构和一个新的性别决定系统。要探索的染色体结构特征包括DNA甲基化、组蛋白修饰和DNA开放，我们将把这些潜在的表观遗传特征与基因表达模式进行比较。表观遗传学的主题是有争议的，而且还在继续演变。染色质结构和DNA甲基化模式可以代代相传，环境因素可以改变这些模式。表观遗传变化可以引起非常迅速(和可逆)的表型变化，并适应快速变化的环境。这项建议在鲑鱼和梭鱼中探索这一主题，我们试图通过绘制这些位置并将它们与基因启动子和基因表达模式联系起来，来注释新开发的鲑鱼和梭子鱼基因组。我们还将探索在北美梭子鱼中发现的一种最近进化的新颖的、可能是环境修改的性别决定模式。

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.