Long-read assembly and annotation of rat genomes that are important models of complex genetic disease

项目总结： 大鼠通常被用作研究多种不同的生物过程的实验模型。 医学上的相关性。这些领域包括神经科学和脑功能、行为研究和药物依赖。 还有毒瘾。类似地，在大鼠身上更容易研究心血管和肾功能的各个方面 这些系统内的液体体积比较小的啮齿动物的体量更容易管理。 用于研究的大鼠模型的使用导致了近亲交配大鼠品系的发展，这些品系在医学上具有 相关表型。这些模型利用先前存在的自然遗传变异来确定基因组多样性。 这就产生了疾病易感性等特征。这些模型的存在刺激了基因 旨在发现导致疾病易感性特征的基因变异的研究 利用这些知识来揭示疾病发病机制的各个方面。 然而，现有大鼠基因组资源的低质量可能会阻碍大鼠的研究。例如，Rate 与人类和小鼠的基因组参考序列相比，基因组参考序列非常不发达。的邻接性 基因组组装减少了一个数量级，基因注释也大大减少了。此外，参考文献 基因组是从棕色挪威近亲交配的老鼠品系中产生的。这种菌株在生物学上与许多大鼠分离 用于研究的菌株。 老鼠被认为是一种适应能力很强的物种。进化生物学家已经认识到一种基本的 适应因素产生于基因组中的结构变异事件。例如，改编的 人类在引入以谷物为主的农业后对高淀粉饮食的结构变化是相关的 在淀粉酶基因中。这种结构性变异是由基因复制事件引起的，这种复制事件是适应性的 增加碳水化合物的消化。这些重复和其他大规模事件不能被观察到和 简单地通过将短读取基因组序列与参考基因组比对来理解。长时间阅读是 捕捉结构性变化事件所需的。 我们项目的目标是促进大鼠基因组学资源的发展，以增加它们对正在进行的 这个动物模型。为此，我们将使用PacBio长读测序来捕获所有基因组变异(SNP和 结构)。我们将重新组装9个广泛使用的大鼠品系的基因组。我们还将推出额外的 对大鼠基因组的注释以增加与大鼠相关的转录本和蛋白质的数量 参考基因组采用长读RNA测序。我们的工作结果将通过RAT公布 基因组数据库和EnSembl，并将向许多实验室提供必要的研究信息，这些实验室 在他们的研究中使用老鼠模型。

Project Summary: The rat is commonly used as an experimental model to investigate a wide diversity of biological processes of medical relevance. These include neuroscience and brain function, behavioral research, and drug dependency and addiction. Similarly, aspects of cardiovascular and renal function are more readily investigated in the rat where the volumes of fluid within these systems are on a much more manageable scale than in smaller rodents. The utility of rat models for investigation has led to the development of inbred rat strains that harbor medically relevant phenotypes. Such models have drawn on pre-existing, natural genetic variation to fix genomic diversity that creates traits such as disease susceptibility. The existence of such models has spurred genetic investigations that have sought to uncover genetic variation responsible for disease susceptibility traits and to utilize such knowledge to reveal mechanistic aspects of disease pathogenesis. However, rat studies can be impeded by the poor quality of existing rat genomic resources. For example, the rat genome reference sequence is very underdeveloped compared to that of human and mouse. Contiguity of the genome assembly is an order of magnitude smaller and gene annotation is much reduced. Further, the reference genome was generated from the Brown Norway inbred rat strain. This strain is biologically remote from many rat strains used in research. The rat is recognized as a highly adaptable species. Evolutionary biologists have recognized that an essential element of adaptation arises from structural variation events in the genome. For example, the adaptation of humans to high starch diets after the introduction of grain-based agriculture is associated with structural variation in the amylase gene. This structural variation results from gene duplication events that are adaptive in permitting increased carbohydrate digestion. These duplication and other large-scale events cannot be observed and understood simply by alignment of short read genome sequence to the reference genome. Long reads are required to capture structural variation events. The objective of our project is to advance rat genomics resources to increase their utility to ongoing studies of this animal model. To do so, we will use PacBio long read sequencing to capture all genomic variation (SNP and structural). We will assemble de novo the genomes of 9 widely used rat strains. We will also introduce additional annotation of the rat genome to increase the numbers of transcripts and proteins associated with the rat reference genome using long read RNA sequencing. The result of our work will be made available via the Rat Genome Database and by Ensembl and will provide essential research information to the many laboratories that employ rat models in their research.