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YIA-PGR: Tools for Plant Comparative Genomics

YIA-PGR：植物比较基因组学工具

基本信息

批准号：
0227314
负责人：
Todd Vision
金额：
$ 101.08万
依托单位：
University of North Carolina at Chapel Hill
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2002
资助国家：
美国
起止时间：
2002-09-01 至 2008-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=0227314&HistoricalAwards=false
关键词：
YIA PGR Tools Plant Comparative

项目摘要

The diversity of model systems presents both challenges and opportunities for applying comparative and phylogenetic approaches to questions in plant functional genomics. New methodologies are needed in order to describe features of biological sequences and maps across multiple organisms that are related by a known phylogeny, as opposed to making either simple pair-wise comparisons or 'flat' comparisons among multiple organisms that ignore the presence of phylogenetic structure. This research focuses on two test applications of phylogenomics: (1) identifying conserved motifs and residues that define particular lineages within a gene family and (2) reconstructing genome rearrangement events along a phylogeny in such a way as to be able to predict gene content and order in sparsely sampled genomes. Because some of the methodology proposed is computationally intensive and requires the integration of data from a variety of public sources, this work is complemented by the development of an online plant phylogenomics database called Phytome. In collaboration with the Partnership for Minority Advancement in the Biosciences, an inquiry-based K-12 educational module is developed and delivered to targeted public schools in North Carolina through a mobile science teaching laboratory. Information regarding all the deliverables for our Plant Genome Project willbe posted at the following URL:http://www.phytome.org

模式系统的多样性为将比较和系统发育方法应用于植物功能基因组学问题提供了挑战和机遇。需要新的方法来描述由已知系统发育相关的多个生物体的生物序列和图谱的特征，而不是在忽视系统发育结构存在的多个生物体之间进行简单的配对比较或‘扁平’比较。这项研究集中在系统基因组学的两个测试应用上：(1)识别定义基因家族中特定谱系的保守基序和残基；(2)沿系统发育重建基因组重排事件，以便能够预测稀疏样本基因组中的基因含量和顺序。由于所提出的一些方法是计算密集型的，需要整合来自各种公共来源的数据，这项工作通过开发名为Phytome的在线植物系统学数据库来补充。与生物科学少数群体促进伙伴关系合作，开发了以探究为基础的K-12教育模块，并通过一个流动科学教学实验室向北卡罗来纳州的目标公立学校提供。有关我们的植物基因组计划的所有交付成果的信息将发布在以下网址：http://www.phytome.org