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KMID : 0613820160260060711
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Journal of Life Science
2016 Volume.26 No. 6 p.711 ~ p.720
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Phylogenetic Analysis of 680 Prokaryotes by Gene Content
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Lee Dong-Geun
Lee Sang-Hyeon
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Abstract
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To determine the degree of common genes and the phylogenetic relationships among genome-sequenced 680 prokaryotes, the similarities among 4,631 clusters of orthologous groups of protein (COGs)’ presence/absence and gene content trees were analyzed. The number of COGs was in the range of 103?2,199 (mean 1377.1) among 680 prokaryotes. Candidatus Nasuia deltocephalinicola str. NAS-ALF, an obligate symbiont with insects, showed the minimum COG, while Pseudomonas aeruginosa PAO1, an opportunistic pathogen, represented the maximum COG. The similarities between two prokaryotes were 49.30?99.78 % (mean 72.65%). Methanocaldococcus jannaschii DSM 2661 (hyperthermophilic and autotrophic, Euryarchaeota phylum) and Mesorhizobium loti MAFF303099 (mesophilic and symbiotic, alpha-Proteobacteria class) had the minimum amount of similarities. As gene content may represent the potential for an organism to adapt to each habitat, this may represent the history of prokaryotic evolution or the range of prokaryotic habitats at present on earth. COG content trees represented the following. First, two members of Chloroflexi phylum (Dehalogenimonas lykanthroporepellens BL-DC-9 and Dehalococcoides mccartyi 195) showed a greater relationship with Archaea than other Eubacteria. Second, members of the same phylum or class in the 16S rRNA gene were separated in the COG content tree. Finally, delta- and epsilon-Proteobacteria were in different lineages with other Proteobacteria classes in neighbor-joining (NJ) and maximum likelihood (ML) trees. The results of this study would be valuable to identifying the origins of organisms, functional relationships, and useful genes.
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KEYWORD
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COG (Clusters of Orthologous Groups of protein), gene content tree, maximum likelihood, neighbor-joining
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