Figure 11.

Evolution of the TPS11/CYP706A3 gene cluster in Brassicaceae.

TPS11 (A) and CYP706A (B) phylogeny in Brassicales. Protein sequences were retrieved using a homology search with Arabidopsis TPS11 or CYP706A3 sequences as a template, from the Phytozome website (http://phytozome.jgi.doe.gov/), the BrassicaDB page (http://brassicadb.org/brad), or David Nelson’s website (http://drnelson.uthsc.edu/CytochromeP450.html), and used to build the tree using PhyML on Gblocks sets defined on the multiple alignment of protein sequences using Seaview (http://doua.prabi.fr/software/seaview). Alignments and global trees used to generate the figure are available in Supplemental Data Sets 4 to 7.

(A) Phylogeny of TPS11. TPS sequences closest to TPS11 in Capsella and Arabidopsis are used as an outgroup.

(B) Phylogeny of the available sequences assigned to the CYP706A subfamily of Brassicales and some closest homologs were used as an outgroup. If not specifically named yet, sequences were referred to according to their position in the different branches of the tree. Bootstrap values for the different branches are available in Supplemental Data Sets 5 and 7.

(C) Structure of the TPS11/CYP706A3 locus. Species possessing a CYP706A3 homolog were aligned at the genome level to show potential gene clusters. TPS11 and homologs were given different names corresponding to their position in the phylogenetic tree below. Conserved features and neighboring genes were highlighted by similar box shape, color, or putative annotation. Shown are CYP706A3 and duplicates (magenta); TPS11 and duplicates (blue); SAMT (green): S-adenosyl methyltransferase domain; MCM6 (yellow): DNA replication licensing factor; DREPP (orange): PF05558 DREPP plasma membrane polypeptide; TuF (gray): elongation factor Tu; CH (gray): charged multivesicular body protein 2A; LSD1 (gray); NiR: unnamed nitrate dehydrogenase. Light gray boxes: no annotation available. Scale bar = substitutions per site.