Plant Phylogenomics: Defining Synergies Between Plant Systematics and Genome Biology
Cannon, Steven .
Using phylogenomics to investigate patterns of genome duplication in the legume family.
Determining the timing and nature of ancient evolutionary genomic events is complicated by relatively high rates of gene losses and duplications, rearrangements, and general degradation of signal relative to noise. Use of large numbers of phylogenetic trees offers a way to identify meaningful signals of ancient events, for example, helping distinguish theĀ timings of early whole genome duplications (WGD) relative to the origins of the Fabaceae (legumes) and Salicaceae (poplar) in the Rosid I clade, and Brassicaceae (Arabidopsis) in the Rosid II clade. In effect, phylogenetic forests may be mined for information that is generally not present in single trees. A complementary analysis compares rates of changes in synonymous sites from orthologous genes separated by speciation and paralogous genes separated through genomic duplications. However, synonymous-site analysis is complicated by lineage-specific rate changes, and distinguishing orthologous and paralogous duplications requires additional information such as genomic position. Analyzing synonymous sites within a phylogenetic context, and incorporating genomic positional information, helps extract more information than can be gleaned from any of the single analyses, and offers a method of accounting for lineage-specific rate changes. These combined methods require large numbers of genes and positional information, so should be increasingly useful with the completion of more genome sequences.
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1 - USDA-ARS and Iowa State University, Agronomy, G401 Agronomy Hall, Ames, IA, 50011, USA
Presentation Type: Symposium or Colloquium Presentation
Location: Stevens 2/Hilton
Date: Monday, July 9th, 2007
Time: 9:00 AM