Gene trees
Gene trees are phylogenies that reflect the relationship between genes within and among species. They can provide insight into evolutionary history.
Steven Cannon at Iowa State University has created phylogenetic trees using data sets from Chamaecrista, Medicago truncatula, Gycine max (soybean), and Vitis(grape). Here is a link to a compressed folder with the trees he constructed from the Solexa assembly (Zip Archive 289kB Jan19 09). Here is a link to a compressed folder with the trees he constructed from the 454 assembly (gzip Archive 464kB Jan19 09).
There are a number of ways to use these trees after you have downloaded and uncompressed them.
- Do you see any patterns when you compare different trees that tell you about the evolution of the genomes of the legumes? For example, you might want to hypothesize about the origins whole genome duplications over evolutionary time. Many of the flowering genes are MADS box genes which have duplicated individually as well as through whole genome duplications. If you could sort out the whole genome duplications, it might be easier to identifiy single gene duplications in the MADS box family.
- How do the trees obtained from the Solexa data alone compare with the 454/Solexa assembly-based trees? What does this tell you?
- You might want to look for candidate genes on these trees.
- Be sure to check out the candidate gene strategy page for ideas.
- To make life a little easier for you, here is a link to a file with candidate genes (Excel 99kB Jan19 09) based on Arabidopsis and soy sequences that map to the Solexa assembly reads. For the curious, the Panther annotations are algorithmically assigned gene functions.
