Phylogenetic tree based on complete genomes using fractal and correlation analyses without sequence alignment
The complete genomes of living organisms have provi ded much information on their phylogenetic relationship s. Similarly, the complete genomes of chloroplasts hav e helped resolve the evolution of this organelle in photosyn thetic eukaryotes. In this review, we describe two algorit hms to construct phylogenetic trees based on the theories f fractals and dynamic language using complete genomes. These algorithms were developed by our research group in the past few years. Our distance-based phylogenetic tree of 109 prokaryotes and eukaryotes agrees with the biologis ts’ “tree of life” based on the 16S-like rRNA genes in a majorit y of basic branchings and most lower taxa. Our phylogenetic a nalysis also shows that the chloroplast genomes are separat d into two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understan ding on chloroplast evolution.