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

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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.