Comparative genomics of thermophilic bacteria and archaea

Elucidation of the origin and the early evolution of life is fundamental to our understanding of ancient living systems and of the ancient global environment where early life evolved. A number of molecular phylogenetic trees have been constructed by comparing the homologous gene sequences. In this chapter, we have reviewed the universal trees constructed based on different types of genetic information. The tree topology was different depending on the type of the gene analyzed as well as the method used. The root of the universal tree is most likely placed between the bacterial branch and the common ancestor of Archaea and Eucarya. However, there are possibilities that the root may be within the bacterial branches. Monophyly of Archaea is rather controversial. Though the rRNA tree suggested the monophyly, other types of the tree are also reported. The conclusive result where the Eucarya originated within/outside of the branch of Archaea is yet to come. The growth temperature of the ancient organism has long been a topic that has interested many scientists. Theoretical works suggested mesophilic, thermophilic, and hyperthermophilic origin of life, depending on the report. Experimental test analyzing the effect of each or combination of ancestral amino acid residues suggested the hyperthermophilic origin of life. However, we cannot totally deny the possible artifact based on the method used for the estimation of ancestral sequences possessed by the ancestral organisms.