2002 Volume 13 Pages 173-182
Chloroplast genome originates from the genome of ancestral cyanobacterial endosymbiont. The comparison of the genomes of cyanobacteria and plants has been made possible by the advance in genome sequencing. I report here current results of our computational efforts to compare the genomes of cyanobacteria and plants and to trace the process of evolution of cyanobacteria, chloroplasts and plants. Cyanobacteria form a clearly defined monophyletic clade with reasonable level of diversity and are ideal for testing various approaches of genome comparison. Analysis of short sequence features such as genome signature was found to be useful in characterizing cyanobacterial genomes. Comparison of genome contents was performed by homology grouping of predicted protein coding sequences, rather than orthologue-based comparison, to minimize effects of multidomain proteins and large protein families, both of which are important in cyanobacterial genomes. Comparison of the genomes of six species of cyanobacteria suggests that there are a number of species-specific additions of protein genes, and this information is useful in reconstructing phylogenetic relationship. The homology groups in cyanobacteria were used as a reference to compare plants and non-photosynthetic organisms. The results suggest that 238 groups that are common to all organisms analyzed may define a minimal set of gene groups. In addition, only 80 groups are identified as the gene groups that could not have been acquired by plants without cyanobacterial endosymbiosis. Further study is needed to identify plant genes of cyanobacterial origin.