Abstract
Phylogenetic analysis of photosynthetic prokaryotes contributes to our understanding not only of their phylogenetic relationship, but also of the origin of chloroplast. Current progress of the phylogenetic analysis of these organisms is achieved by using the conserved genes such as rDNA and rpoC1. However, the different branching patterns are obtained depending on the genes. This problem is reasonable because evolution is not reflected by a single or limited numbers of genes, but by whole genome sequences. Recently, a growing number of complete genome sequences are available and several methods for the phylogenetic analysis based on the whole genome sequences have been proposed. We developed a new method for the phylogenetic analysis based on the comparison of whole genome sequences and this method was applied to the analysis of the evolution of photosynthetic prokaryote and to the identification of the gene encoding chlorophyllide a oxygenase from Prochlorococcus genomes.
