Germline sequence resources & analyses in a vertebrate model that undergoes PGR

描述（由申请人提供）：海七鳃鳗，Petromyzon marinus，是一种新兴的非哺乳动物模式生物，令人满意地满足PA-07-457标准。基因组已测序到9.1X覆盖范围，汇编是公开的。提出这一建议的动力是基于我们对海七鳃鳗基因组动态性质的观察。我们最近的研究表明，P. marinus经历了大量的染色质减少，多达20%的体细胞基因组在早期胚胎发生时被丢弃。本提案中提供的大量初步数据证实了这些损失，并重要地证实了我们之前的观察，即大量蛋白质编码序列也在发育中被消除。这些发现揭示了可用的七鳃鳗基因组序列组装的严重缺陷。在这个应用程序中，我们提出从P. marinus种系中生成和组装DNA序列，这将为该物种提供一个全面改进的基因组组装。提出的工作填补了该生物序列知识的主要空白，因此对几乎每个利用七鳃鳗作为主要模型或作为理解脊椎动物发育、生理学或基因组生物学基本特征的参考的实验室都至关重要。通过开发未采样区域的种子组合，提高体细胞和种系基因组组合的亲和性，交叉告知现有克隆资源，并在基因组的固定和修饰区域中注释表达序列的位置，我们将显著提高现有七鳃鳗基因组资源对社区的利用，并在这个非哺乳动物模型系统中了解更多程序化基因组重排。

DESCRIPTION (provided by applicant): The sea lamprey, Petromyzon marinus, is an emerging nonmammalian model organism that satisfactorily meets the criteria for PA-07-457. The genome has been sequenced to 9.1X coverage and an assembly is publicly available. The impetus for this proposal is based on our observations concerning the dynamic nature of the sea lamprey genome. We have recently shown that P. marinus undergoes substantial chromatin diminution with as much as 20% of its somatic genome being discarded during early embryogenesis. Extensive preliminary data presented in this proposal confirm these losses and importantly corroborate our prior observations that large swaths of protein-coding sequences are also being developmentally eliminated. These findings uncover a severe deficiency in the available lamprey genome sequence assembly. In this application we propose to generate and assemble DNA sequences from the P. marinus germline that will provide an overall improved genome assembly for this species. The proposed work fills a major gap in sequence knowledge for this organism and is therefore critical to nearly every lab that utilizes lamprey as a primary model or as a reference for understanding basal features of vertebrate development, physiology, or genome biology. By developing seeded assemblies of unsampled regions, improving contiguity of the somatic and germline genome assemblies, cross-informing existing clone resources, and annotating the location of expressed sequences within constant and modified regions of the genome, we stand to dramatically improve the utility of existing lamprey genome resources for the community and to learn much about programmed genome rearrangement in this nonmammalian model system. PUBLIC HEALTH RELEVANCE: The lamprey is an emerging nonmammalian model organism that has been utilized extensively to study many vertebrate-specific characteristics, including those of human health relevance. The inadequacy of the lamprey genome sequence, however, is highly problematic for researchers studying this organism. Development of an improved lamprey genome sequence is thus imperative for the community.