Computational Identification of Terpene Synthase Genes and Their Evolutionary Analysis

Terpenoids, the largest and most structurally and functionally diverse class of natural compounds on earth, are mostly synthesized by plants to be involved in various plant environment interactions. Some terpenoids are classified as primary metabolites essential for plant growth and development. Terpene synthases (TPSs), the key enzymes for terpenoid biosynthesis, are the major determinant of the tremendous diversity of terpenoid carbon skeletons. The TPS genes represent a mid-size family of about 30-100 functional genes in almost all major sequenced plant genomes. TPSs are also found in fungi and bacteria, but microbial TPS genes share low levels of sequence similarity and different patterns of gene structure with their plant counterparts. Although one common ancestor theory has been suggested and supported by studies from model species, the evolution of plant terpene synthase genes and the evolutionary relationships among terpene synthase genes in plants, bacteria and fungi are still unclear. The recent discovery of microbial-type TPS genes in Selaginella muellendorffii makes it even more confusing. The goal of this dissertation project is to study the mechanisms that govern the dynamic evolution of terpene synthase genes using comparative genomics methods. Here, we carried out a large-scale screen to identify terpene synthases in plants (transcriptomes for over 1000 plant species sequenced by the OneKP project and selected genomes from non- seed plants), fungi and bacteria species (sequenced genomes in JGI). Several important discoveries were made by analyzing the data: (1) the microbial-type TPS genes are widely and specifically distributed in non-seed land plants; (2) HGT from bacterial to fungi in TPS gene family is identified; (3) a new subfamily x is identified and new insights into the subfamily classification of TPSs are reported by including TPSs identified from large-scale non-seed plant species; (4) the distribution and genomic organization of four types of TPSs in fungi are characterized. These important findings will help us better understand the evolution of plant secondary metabolism, especially for basal land plants.