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 go?

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.

Selected Publications:
Bouck A, Vision T. (2007) The molecular ecologist's guide to expressed sequence tags. Mol Ecol. 16(5):907-24.

Gaulton KJ, Mohlke KL, Vision TJ. (2007) A computational system to select candidate genes for complex human traits. Bioinformatics. Feb 21.

Leebens-Mack J, Vision T, Brenner E, Bowers JE, Cannon S, Clement MJ, Cunningham CW, dePamphilis C, deSalle R, Doyle JJ, Eisen JA, Gu X, Harshman J, Jansen RK, Kellogg EA, Koonin EV, Mishler BD, Philippe H, Pires JC, Qiu YL, Rhee SY, Sjolander K, Soltis DE, Soltis PS, Stevenson DW, Wall K, Warnow T, Zmasek C. (2006) Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). OMICS. 10(2):231-7.

Zou F, Xu Z, Vision T. (2006) Assessing the significance of quantitative trait loci in replicable mapping populations. Genetics. 174(2):1063-8.

Hartmann S, Lu D, Phillips J, Vision TJ. (2006) Phytome: a platform for plant comparative genomics. Nucleic Acids Res. 34(Database issue):D724-30.

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.

contact information:

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