SGER Grant: Plant Evolutionary Genomics: Develop and Test Bioinformatic Tools to Automate Ortholog Identification for Phylogenomics and Functional Genomic Studies

SGER 资助：植物进化基因组学：开发和测试生物信息工具，以自动进行系统发育和功能基因组研究的直系同源鉴定

• 批准号: 0346436
• 负责人: Gloria Coruzzi
• 金额: $ 8.32万
• 依托单位: New York University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-01 至 2004-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0346436&HistoricalAwards=false
• 关键词: SGER; Grant; Plant; Evolutionary; Genomics

One of the critical issues in comparative genomic studies is to distinguish genes derived from a common ancestral locus (orthologs), from paralogs, which are similar genes that arose as a result of duplication in one or both lineages, subsequent to an evolutionary split between species. Determining true orthology on a genome scale level is essential to enable researchers to understand species relationships using genome scale data (phylogenomics), and also to enable scientists to understand gene functions. New informatic tools will be further developed and tested to enable high throughput and accurate ortholog identification, using known genes from rice and Arabidopsis as fully-sequenced model organisms. The testing and refinement of these tools will involve three major steps. In step 1, putative orthologs will be identified using ViCoGenta (Viewer for Comparing Genomes to Arabidopsis) to scan a set of ESTs (Expressed Sequence Tags) spanning key Gymnosperm species. This will identify a set of ESTs that are each "top matches" to the same gene in the rice and/or Arabidopsis genomes. In Step 2, the orthology of these genes will be further verified using CAOS (Character Attribute Organization System) a new, rapid parsimony-based ortholog identification tool. In Step 3, orthology defined by CAOS analysis, will be compared to that determined by three other traditional phylogenetic methods. Validated orthologs will be used to generate phylogenetic hypotheses for the Gymnosperms, based on genome-wide test cases in rice and Arabidopsis, in order to understand how seeds evolved. The informatic tools developed, tested, and validated in this proof-of-principle project to determine gene orthology among diverse species, will be made available in a web-based form to enable a range of phylogenomic and functional genomic studies in the scientific community, spanning important crop and other plant genomes.

比较基因组学研究中的一个关键问题是区分来自共同祖先基因座（直系同源物）的基因和旁系同源物，旁系同源物是在物种之间进化分裂后，由于一个或两个谱系中的重复而产生的相似基因。 在基因组规模水平上确定真正的同源性对于使研究人员能够使用基因组规模数据（同源基因组学）理解物种关系以及使科学家能够理解基因功能至关重要。将进一步开发和测试新的信息学工具，以实现高通量和准确的直系同源物鉴定，使用水稻和拟南芥的已知基因作为完全测序的模式生物。这些工具的测试和改进将涉及三个主要步骤。在步骤1中，将使用ViCoGenta（用于将基因组与拟南芥进行比较的查看器）扫描一组跨越关键裸子植物物种的EST（表达序列标签）来鉴定推定的直系同源物。这将确定一组EST，每个EST都与水稻和/或拟南芥基因组中的相同基因“最匹配”。 在步骤2中，这些基因的直系同源性将进一步验证使用CAOS（字符属性组织系统），一个新的，快速简约为基础的直系同源物识别工具。在第三步，由CAOS分析定义的直系关系，将与其他三种传统的系统发育方法确定的直系关系进行比较。基于水稻和拟南芥的全基因组测试案例，验证的直系同源物将用于产生裸子植物的系统发育假设，以了解种子是如何进化的。 在这个原理验证项目中开发、测试和验证的信息学工具，以确定不同物种之间的基因同源性，将以基于网络的形式提供，以使科学界能够进行一系列跨重要作物和其他植物基因组的基因组和功能基因组研究。