Branch Mutation Rates and Selection Give Insights on Gene Family Trees: N-methyltransferases, FAD2 Enzymes and Terpenes

Abstract

Gene trees enable the detailed study of the evolution of genes. These trees can be additive, based purely on mutational counts, or ultrametric, where the branches represent the time elapsed. The purpose of this thesis will be to relate evolutionary rate changes to gene function by examining the effects of a tree transformation on gene trees. The study will focus on the coffee genomes C. arabica, C. eugenioides and C. canephora. Three gene family trees will be studied: N-methyltransferases, FAD2 enzymes and terpenes. An additive tree can be transformed into an ultrametric tree using a transformation method. By taking each additive tree branch length and dividing the branch by the ultrametric branch length we can get a branch mutation rate. To quantify functional divergence, we compared aligned sequences of genes from groups of interest to calculate the ratio of non-synonymous mutations to synonymous mutations (Kn/Ks). Kn/Ks was found to correlate with the branch mutation rate in some but not all groups of interest. In groups in which correlation was present, there was also a correlation between Kn/Ks and branch length. The branch mutation rate can be used in some cases to further prove that functional divergence is present.