Phylogenetic analysis of aerobic anoxygenic phototrophic bacteria and their relatives based on farnesyl pyrophosphate synthase gene

The study aims to reveal phylogenetic and evolutionary relationship between aerobic anoxygenic phototrophic bacteria (AAnPB) and their relatives, anaerobic anoxygenic phototrophic bacteria (AnAnPB) and nonphototrophic bacteria (NPB, which had high homology of 16S rDNA gene with AAnPB and fell into the same genus), and validate reliability and usefulness of farnesyl pyrophosphate synthase (FPPS) gene for the phylogenetic determination. FPPS genes with our modified primers and 16S rDNA genes with general primers, were amplified and sequenced or retrieved from GenBank database. In contrast to 16S rDNA gene phylogenetic tree, AAnPB were grouped into two clusters and one branch alone with no intermingling with NPB and AnAnPB in the tree constructed on FPPS. One branch of AAnPB, in both trees, was located closer to outgroup species than AnAnPB, which implicated that some AAnPB would be diverged earlier in FPPS evolutionary history than AnAnPB and NPB. Some AAnPB and NPB were closer located in both trees and this suggested that they were the closer relatives than AnAnPB. Combination codon usage in FPPS with phylogenetic analysis, the results indicates that FPPS gene and 16S rRNA gene have similar evolutionary pattern but the former seems to be more reliable and useful in determining the phylogenic and evolutionary relationship between AAnPB and their relatives. This is the first attempt to use a molecular marker beside 16S rRNA gene for studying the phylogeny of AAnPB, and the study may also be helpful in understanding the evolutionary relationship among phototrophic microbes and the trends of photosynthetic genes transfer.