The Ciona savignyi Genetic Map

玻璃海鞘遗传图谱

基本信息

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
项目类别：
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

项目摘要

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）：这笔赠款是为了响应新兴模式生物遗传和基因组研究计划公告工具而提交的。我建议在海鞘 (Ciona savignyi) 中构建一个包含 300 个标记的连锁图谱，该图谱与将成为带注释的高质量基因组参考序列完全整合。该图谱不仅有助于克隆突变，而且有助于实现萨维尼参考序列的长范围连续性，这是有效执行诱导或自然发生突变的全基因组扫描所必需的。除了全基因组图谱之外，还将在不确定序列组装区域进行高分辨率精细绘图，以解决萨维尼基因组参考序列中的歧义。该图谱以及分布在整个基因组中的数千个潜在多态性标记的数据库将向社区开放。海鞘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相似。尽管高度保守，海鞘基因组的大小与果蝇基因组相当（约 180 Mb），因此表现出实验上有利的基因组简单性。此外，海鞘具有许多有吸引力的胚胎学和实验特征，有助于研究发育过程中的基因调控。在过去的几年中，萨维尼梭菌已被开发为一种遗传模式生物，其突变体很容易从野生种群或通过诱变获得。遗传图谱、标记和基因组组装的远程连续性是将萨维尼隐孢子虫建立为成熟的遗传和基因组模型生物所缺少的、至关重要的资源。 Ciona savignyi 及其姊妹物种 Ciona Enteris 在脊索动物胚胎发育机制方面具有独特的信息。胚胎发育和基因调控的基本特征和具体特征在人类和这些脊索动物之间是保守的。以 Ciona 作为模型来深入了解调控和发育的分子机制是非常有效的，并且与人类的同源过程相关。