Egan, Ashley N. , Innes, Roger , Maroof, Saghai , Roe, Bruce , Young, Nevin , Doyle, Jeff J. .
Comparative Analysis of Legume Genome Evolution: Rates and Dates in Low-Copy Genes.
The legume genus, Glycine, underwent a recent polyploid event (~12 million years ago) (mya) and an older event shared with Medicago. We are sequencing a ~1 Mb region and its homoeologues in soybean (G. max) and G. tomentella, and the orthologous region in a diploid relative, Phaseolus vulgaris (http://www.bio.indiana.edu/~nsflegume/index.php). To address questions concerning the amount, variation and timing of divergence in these regions, we calculated synonymous substitution rates (Ks) for 15 linked genes. These range from 0.05-0.18 for comparisons between the two most similar Glycine homoeologues, suggesting the recent polyploid event happened 4.09-14.74 mya using standard mutation rates. Ks estimates between more ancient Glycine homoeologues based on 7 genes range from 0.35-0.60, suggesting dates for the older polyploid event of 28.66-49.3 mya. Ks suggests that G. max and G. tomentella diverged 2.17-8.05 mya. Penalized likelihood (PL) analyses suggest dates of 7.6-11 mya and 3.7-5.4 mya for the recent polyploid event and the G. max/tomentella split, respectively, based on 7 concatenated genes. PL based on one gene suggests dates of 28.07-40.57 mya for the older polyploid event. These dates are more recent than the 54.3 mya Medicago/Glycine split estimated by Lavin et al. (2005) from chloroplast regions. This is not unexpected given the nature of nuclear gene evolution and the methodology used. Both relaxed and molecular clock methods suggest rate heterogeneity between genes and among lineages, thus creating a spectrum of divergence dates. However, comparison of Ks among genes and lineages suggests that Ks variation is gene, not taxon, specific. The evidence for Ks variation among genes illustrates the importance of using multiple genes when estimating rates and dates of molecular evolution for a taxonomic group.
Log in to add this item to your schedule
Comparative Analysis of Legume Genome Evolution
1 - Cornell University, L. H. Bailey Hortorium, Dept. of Plant Biology, 228 Plant Science, Ithaca, NY, 14853, United States
2 - Indiana University, Biology
3 - Virginia Tech, Department: Crop & Soil Environmental Science, Virginia Polytechnic Institute, Blacksburg, VA, 24601, USA
4 - University of Oklahoma, Stephenson Research and Technology Center, Norman, OK, 73019, USA
5 - University of Minnesota, Department of Plant Pathology, St. Paul, MN, 55108, USA
6 - Cornell University, L.H. Bailey Hortorium, Department of Plant Biology, Ithaca, New York, 14853, USA
Presentation Type: Oral Paper:Papers for Sections
Location: 182/I K Barber
Date: Monday, July 28th, 2008
Time: 9:00 AM