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

比较基因组学研究中的关键问题之一是区分源自共同祖先座位(直系物)的基因和平行基因，后者是物种之间进化分裂后，由于一个或两个谱系复制而产生的相似基因。在基因组水平上确定真正的正交学对于使研究人员能够使用基因组规模数据(系统基因组学)来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同源基因识别，使用来自水稻和拟南芥的已知基因作为全序列模式生物。这些工具的测试和改进将涉及三个主要步骤。在第一步中，将使用ViCoGenta(用于将基因组与拟南芥进行比较的查看器)来扫描一组跨越主要裸子植物物种的EST(表达序列标签)，以确定假定的同源基因。这将识别出一组EST，每个EST都与水稻和/或拟南芥基因组中的同一基因“最匹配”。在步骤2中，将使用基于简约的新的快速同源同源识别工具CAOS(字符属性组织系统)来进一步验证这些基因的同源同源性。在步骤3中，将CAOS分析所定义的正词学与其他三种传统系统发育方法所确定的正词学进行比较。经过验证的同源基因将被用来根据水稻和拟南芥的全基因组测试案例，为裸子植物生成系统发育假说，以了解种子是如何进化的。在这一原则验证项目中开发、测试和验证的信息工具将以基于网络的形式提供，以确定不同物种之间的基因正交学，以使科学界能够进行一系列系统基因组和功能基因组研究，涵盖重要的作物和其他植物基因组。

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.