The Ciona savignyi Genetic Map

玻璃海鞘遗传图谱

• 批准号: 7162134
• 负责人: AREND SIDOW
• 金额: $ 20.35万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-01-01 至 2008-12-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7162134
• 关键词: Algorithms; Alleles; Anchored Polymerase Chain Reaction; Animal Model; Chordata; Chromosome Mapping; Chromosomes; Ciona intestinalis; Cloning; Communities; Data; Databases; Development; Drosophila genus; Embryonic Development; Exhibits; Exons; Fracture; Gene Expression Regulation; Gene Order; Generations; Genetic; Genetic Polymorphism; Genome; Genomics; Genotype; Goals; Grant; Human; Individual; Internet; Link; Maps; Modeling; Molecular; Mutagenesis; Mutation; NIH Program Announcements; Organism; Parents; Physical Map of the Human Genome; Polymorphic Microsatellite Marker; Population; Positioning Attribute; Process; Protocols documentation; Range; Regulation; Research Personnel; Resolution; Resources; Running; Scientist; Shotguns; Sister; Site; Spiders; Standards of Weights and Measures; Vertebrates; ascidian; base; desire; genome sequencing; genome wide association study; improved; insight; mutant; physical mapping; programs; response; size; tool

DESCRIPTION (provided by applicant): This grant is submitted in response to the Program Announcement Tools for Genetic and Genomic Studies in Emerging Model Organisms. I propose to construct a 300-marker linkage map in the ascidian, Ciona savignyi, that is fully integrated with what will become the annotated high quality genome reference sequence. This map will not only aid in the cloning of mutations, but also in achieving the long range contiguity in the C. savignyi reference sequence that will be needed to efficiently perform whole genome scans for induced or naturally occurring mutations. In addition to the genome-wide map, high-resolution fine- scale mapping in regions of uncertain sequence assembly will be performed to resolve ambiguities in the C. savignyi genome reference sequence. The map, along with a database of thousands of potentially polymorphic markers distributed across the genome, will be made available to the community. Ascidians are among the simplest chordates, yet their fundamental developmental mechanisms are structurally and molecularly conserved with those of vertebrates. Despite the high level of conservation, ascidian genomes are comparable in size to Drosophila's (about 180 Mb), thus exhibiting experimentally advantageous genomic simplicity. Further, ascidians have many attractive embryological and experimental features that facilitate studies of gene regulation during development. Over the past few years, C. savignyi has been developed as a genetic model organism, with mutants readily obtainable from wild populations or by mutagenesis. The genetic map, the markers, and the long-range contiguity of the genome assembly are the missing, critically important, resources to establish C. savignyi as a full-fledged genetic and genomic model organism. Ciona savignyi and its sister species, Ciona intestinalis, are uniquely informative with regards to the mechanisms of chordate embryonic development. Fundamental as well as specific features of embryonic development and gene regulation are conserved between humans and these chordates. Insights into the molecular mechanisms of regulation and development using Ciona as a model are highly effective and relevant to the homologous processes in human.

描述(由申请人提供)：这项资助是为了响应新兴模式生物遗传和基因组研究的计划公告工具而提交的。我建议在海鞘中构建一个300个标记的连锁图谱，它与将成为注释的高质量基因组参考序列完全整合。这一图谱不仅有助于突变的克隆，而且还有助于实现萨维尼弧菌参考序列的长距离邻接，这将是有效地进行全基因组扫描以寻找诱导或自然发生的突变所必需的。除了全基因组图谱外，还将在不确定序列组装区域进行高分辨率精细图谱绘制，以解决萨维尼弧菌基因组参考序列中的歧义。该图谱以及分布在基因组中的数千个潜在多态标记的数据库将向社区提供。海鞘动物是最简单的脊索动物之一，但它们的基本发育机制在结构和分子上与脊椎动物的机制是保守的。尽管高度保守，海鞘动物的基因组在大小上与果蝇的相当(约180Mb)，因此显示出实验上有利的基因组简单性。此外，海鞘具有许多诱人的胚胎学和实验特征，有助于研究发育过程中的基因调控。在过去的几年里，萨维尼弧菌已经发展成为一种遗传模式生物，突变株很容易从野生种群中获得或通过突变获得。遗传图谱、标记和基因组组装的远程邻接性是将萨维尼弧菌建立为成熟的遗传和基因组模式生物所缺少的、至关重要的资源。关于脊索胚胎发育的机制，Ciona savignyi和它的姊妹物种Ciona enterinalis是独一无二的信息源。胚胎发育和基因调控的基本和特殊特征在人类和这些脊索动物之间是保守的。以Ciona为模型对调节和发育的分子机制的洞察是非常有效的，并且与人类的同源过程相关。