2013 Volume 41 Issue 2 Pages 14-19
Archaea was established according to difference of 16S rRNA nucleotide sequences, and is thought to be the ancestral organism for eukaryote. Now many entire nucleotide sequences of Archaeal genomes are available. By comparing among Archaeal genomic data, information for their evolution can be extracted. In this work, the evolutional features are extracted from genomic information of three Archaeal species, Pyrococcus horikoshii, Aeropyrum pernix and Sulfolobus tokodaii. 1. From the comparison of the overall positioning of the similar genes, it is shown that two Pyrococcus species, P. abyssi and P. horikoshii, conserve their overall gene ordering with a few times grovel genomic recombination, revealing that these two species were separated recently. Conversely, species in genus Sulfolobus did not show any structural similarity of genome, predicting that species in genus Sulfolobus were developed independently. 2. Among Pyrococcus species, the gene ordering within the mannosylglycerate biosynthesis gene cluster is completely retained with high sequence similarity of each gene, revealing that this cluster is thought to be important for genus Pyrococcus. 3. From comparison of gene ordering within the UDP-GlcNAc biosynthesis gene cluster, it is shown that phylogenetic distance between P. horikoshii and A. pernix is closer than that between P. horikoshii and S. tokodaii. 4. When compared the amino acid sequences of the gene family, functionally similar genes are consisting a phylogenetic cluster. But when compared the nucleotide sequences, genes from same species are consisting a phylogenetic cluster. These results indicate that nucleotide sequences were developed with retaining features of the host species, but the translated amino acid sequences were developed under pressure of the function. 5. Other features, like presence or absence of plasmid, transposable elements, duplication and recombination, also provide the important information on evolution. These analyses shown above indicate detail analysis is necessary for recognition of the recent history of genomic evolution.
