Evolution of Genome Organization
The Vision lab uses computational and molecular tools to study the evolution of genome organization, with a particular focus on flowering plants. Some of the questions they ask are:
1. What are the origins and consequences of differences in gene order both within populations and between species?
2. How do gene families diversify over time as new members come and
Their work has revealed surprising complexity in the genome of the model plant Arabidopsis thaliana. Despite having the most compact genome among flowering plants, the Vision lab has identified multiple, very ancient, large-scale genome duplications. They are developing computational tools that allow researchers to predict the gene content for chromosome regions of special interest in economically and scientifically important organisms that have not been completely mapped. The lab hosts an online comparative plant genomics database called Phytome that puts this information at the fingertips of scientists worldwide. They also put this information to use in their own work studying the genetic basis for complex traits in plants. As part of a collaborative project, they are identifying genes in tomato and rice that cause natural variation in photosynthetic efficiency. In another collaboration, they are applying population genetics tools to narrow down the search for genes related to reproductive isolation in the wild in the plant genus Mimulus. Much of their recent efforts have been geared toward understanding the genetic changes that underly crop domestication. Their primary focus is on the plant family Solanaceae, where an unexpected convergence of key domestication traits poses an evolutionary puzzle with profound practical consequences for agriculture.
Faddah DA, Ganko EW, McCoach C, Pickrell JK, Hanlon SE, Mann FG, Mieczkowska JO, Jones CD, Lieb JD, Vision TJ (2009) Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae. PLoS Genet. 5(6):e1000502.
Hartmann S, Vision TJ (2008) Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment? BMC Evol Biol. 8:95.
Ganko EW, Meyers BC, Vision TJ (2007) Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol. 24(10):2298-309.
Gaulton KJ, Mohlke KL, Vision TJ. (2007) A computational system to select candidate genes for complex human traits. Bioinformatics. Feb 21.
Xu Z, Zou F, Vision TJ. (2005) Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics 170:401-8.