Mining EST databases to resolve evolutionary events in major crop species

Genome. 2004 Oct;47(5):868-76. doi: 10.1139/g04-047.


Using plant EST collections, we obtained 1392 potential gene duplicates across 8 plant species: Zea mays, Oryza sativa, Sorghum bicolor, Hordeum vulgare, Solanum tuberosum, Lycopersicon esculentum, Medicago truncatula, and Glycine max. We estimated the synonymous and nonsynonymous distances between each gene pair and identified two to three mixtures of normal distributions corresponding to one to three rounds of genome duplication in each species. Within the Poaceae, we found a conserved duplication event among all four species that occurred approximately 50-60 million years ago (Mya); an event that probably occurred before the major radiation of the grasses. In the Solanaceae, we found evidence for a conserved duplication event approximately 50-52 Mya. A duplication in soybean occurred approximately 44 Mya and a duplication in Medicago about 58 Mya. Comparing synonymous and nonsynonymous distances allowed us to determine that most duplicate gene pairs are under purifying, negative selection. We calculated Pearson's correlation coefficients to provide us with a measure of how gene expression patterns have changed between duplicate pairs, and compared this across evolutionary distances. This analysis showed that some duplicates seemed to retain expression patterns between pairs, whereas others showed uncorrelated expression.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Databases, Nucleic Acid
  • Evolution, Molecular*
  • Expressed Sequence Tags*
  • Gene Duplication / radiation effects*
  • Gene Expression Regulation, Plant / genetics
  • Gene Expression Regulation, Plant / radiation effects
  • Genetic Variation / genetics
  • Medicago / genetics
  • Medicago / radiation effects
  • Poaceae / genetics*
  • Poaceae / radiation effects
  • Solanaceae / genetics*
  • Solanaceae / radiation effects
  • Soybeans / genetics
  • Soybeans / radiation effects