Identification of novel chloroplast proteins of endosymbiotic origin by phylogenetic profiling using homolog groups

Chloroplasts are believed to be descendants of an ancestral endosymbiont related to cyanobacteria. Comparative genomics is expected to be useful in identifying the proteins that were transferred to chloroplasts from the endosymbiont. However, most of the present-day chloroplast proteins are encoded by the nuclear genome, and it was not until the nuclear genome of a land plant Arabidopsis thaliana was determined that such nuclear genes were estimated by comparative genomics. This year, the genome of a red alga Cyanidioschyzon merolae was also determined. By exploiting these two genomes, we tried to identify novel nuclear genes that encode chloroplast proteins, which might be involved in photosynthesis. Among various ways of comparing genomes, we tested, in the present study, phylogenetic profiling using homolog groups. In comparing diverse genomes such as prokaryotic and eukaryotic genomes, many genes are highly duplicated depending on organisms. To enable comparison of such diverse genomes, it is necessary that these paralogous genes be treated as a single homolog group. Phylogenetic profiling is useful in identifying genes, which are specific to certain pathways that are shared by certain groups of organisms. Photosynthesis is a good example of such shared pathways. However, no comprehensive study on whole genome comparison was attempted in photosynthetic organisms, except comparison between A. thaliana and some cyanobacteria including Synechocystis [1]. We present here initial results of phylogenetic profiling of photosynthetic genes based on eight cyanobacteria, a land plant and a red alga. Emphasis is laid on integration of computational and experimental approaches.