Systematic Identification of Genome Structural Variation in Mimulus

酸浆菌基因组结构变异的系统鉴定

• 批准号: 0743939
• 负责人: Todd Vision
• 金额: $ 13.52万
• 依托单位: University of North Carolina at Chapel Hill
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-15 至 2008-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0743939&HistoricalAwards=false
• 关键词: Systematic; Identification; Genome; Structural; Variation

Genome sequencing projects typically produce a single reference genome. While tremendously useful, this glosses over potentially important variation in the sequence or structure of the genome within that species. Until recently, it has not even been possible to systematically survey sub-microscopic genome structural variations after the fact, due to the lack of suitable methodology. The investigators will apply a novel method for the genome-wide identification of structural variants in which the chromosomal location of one or more genes differs among individuals. This will be achieved by combining a particular genetic cross with massively-parallel DNA hybridization technology. The study will be done using closely related species of the model evolutionary plant, Mimulus. The specific goal of this work is to identify the frequency, position, size and gene content of chromosomal regions that are variable in position. The availability of genomic resources in Mimulus, its amenability to field studies in natural populations, and the tremendous diversity of the genus, make it an excellent model in which to study the ecological and evolutionary consequences of naturally-occurring genome structural variation. Recent findings suggest that gene content routinely differs among individuals within a species. For example, pairs of humans have been found to differ from each other in the copy number of approximately a dozen chromosomal regions of nearly half a million base pairs each. These regions contain genes of neurological, developmental, and metabolic importance. Though studies such as this suggest that structural variation may be common, and despite the potential contribution of structural variation to adaptation and speciation, almost nothing is currently known about the abundance of gene copy number and gene location variation in natural populations. Thus, this work sets the stage for understanding the functional, ecological and evolutionary consequences of a class of molecular variation that has been hitherto largely neglected.

基因组测序项目通常产生单个参考基因组。 虽然非常有用，但这掩盖了该物种内基因组序列或结构的潜在重要变异。 直到最近，由于缺乏合适的方法，甚至不可能在事后系统地调查亚微观基因组结构变异。 研究人员将应用一种新的方法来全基因组鉴定结构变异，其中一个或多个基因的染色体位置在个体之间不同。 这将通过将特定的遗传杂交与大规模平行DNA杂交技术相结合来实现。 这项研究将使用与模式进化植物Mimulus密切相关的物种进行。这项工作的具体目标是确定频率，位置，大小和染色体区域的基因内容是可变的位置。 在Mimulus基因组资源的可用性，其顺从自然种群的实地研究，以及属的巨大多样性，使其成为一个很好的模型，研究自然发生的基因组结构变异的生态和进化后果。最近的研究结果表明，基因内容通常在一个物种内的个体之间存在差异。 例如，已经发现成对的人类在大约12个染色体区域的拷贝数上彼此不同，每个区域近50万个碱基对。这些区域包含神经、发育和代谢重要性的基因。 虽然像这样的研究表明，结构变异可能是常见的，尽管结构变异的适应和物种形成的潜在贡献，目前几乎没有什么是已知的丰富的基因拷贝数和基因位置的变化在自然种群。 因此，这项工作为理解迄今为止在很大程度上被忽视的一类分子变异的功能，生态和进化后果奠定了基础。