Advances in Plant Systematics and Population Genomics: Applications of Next Generation Techniques
Egan, Ashley N , Schlueter, Jessica , Doyle, Jeff .
Comparative genomics of phaseoloid legumes: what 454 transcriptomics can tell us about phylogeny.
The legume family (Leguminosae; Fabaceae) is one of the most diverse plant families on earth, having ~18,000 species. The phaseoloid group contains many economically important species such as the cultivated soybean (Glycine max; a polyploid) and Kudzu (Pueraria montana; a highly invasive species in the U.S.). Polyploidy (whole genome duplication) has played an important role in the diversification of legumes, both anciently and in the more recent evolutionary past. Polyploidy events are easily inferred from doubled (or multiplicative) base chromosome numbers of species relative to related evolutionary lineages. However, ancient polyploidy may go unnoticed due to reduction in chromosome number (diploidization), making ancient polyploidy cryptic. To assess the prevalence of polyploidy in phaseoloid legume evolution, we sequenced the transcriptomes of several species using Roche 454 pyrosequencing. We examined signatures of polyploidy by creating a distribution of synonymous substitutions across duplicated gene pairs within each genome. Using the soybean genome and cDNA database as a reference, we compare ancient signatures of polyploidy across species to obtain a robust estimate of the time of ancient polyploidization within legumes. We discuss the pros and cons of using next-gen sequencing for Ks estimation and compare outcomes with other estimates of polyploidy in the soybean genome using Expressed Sequence Tags (ESTs). In addition, we present a phylogenomic hypothesis of phaseoloid relationships using orthologous genes culled from transcriptome data.
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1 - East Carolina University, Biology, Howell Science Complex N303a, Mailstop 551, Greenville, NC, 27858, USA
2 - University of North Carolina - Charlotte, Bioinformatics and Genomics, 9201 University City Blvd , Bioinformatics Building 261 , Charlotte, NC, 28223, USA
3 - Cornell Univeristy, 412 Mann Library Building, ITHACA, NY, 14853-4301, USA
Next Generation Sequencing.
Presentation Type: Symposium or Colloquium Presentation
Location: Lenox Room/Chase Park Plaza
Date: Monday, July 11th, 2011
Time: 4:15 PM