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

比较基因组研究的关键问题之一是区分来自共同祖先位点的基因（同源基因）和同源基因，同源基因是由于一个或两个谱系中的复制而产生的类似基因，随后在物种之间进化分裂。在基因组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尺度数据（系统基因组学）理解物种关系以及使科学家能够理解基因功能至关重要。新的信息工具将进一步开发和测试，以实现高通量和准确的同源鉴定，使用来自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（比较拟南芥基因组的查看器）扫描一组est（表达序列标签）来识别假定的同源物，这些est（表达序列标签）跨越关键的裸子植物物种。这将确定一组与水稻和/或拟南芥基因组中的同一基因“顶级匹配”的est。在第二步，这些基因的同源性将使用CAOS（字符属性组织系统）进一步验证，这是一种新的，快速的基于简约的同源性识别工具。在步骤3中，由CAOS分析定义的同源性将与其他三种传统系统发育方法确定的同源性进行比较。基于水稻和拟南芥的全基因组测试案例，经过验证的同源物将用于为裸子植物产生系统发育假设，以了解种子是如何进化的。在这个原理验证项目中开发、测试和验证的信息工具将以网络形式提供，以确定不同物种之间的基因同源性，从而使科学界能够开展一系列系统基因组学和功能基因组学研究，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.