JOURNAL BROWSE
Search
Advanced SearchSearch Tips
Phylogenetic Analysis of 680 Prokaryotes by Gene Content
facebook(new window)  Pirnt(new window) E-mail(new window) Excel Download
  • Journal title : Journal of Life Science
  • Volume 26, Issue 6,  2016, pp.711-720
  • Publisher : Korean Society of Life Science
  • DOI : 10.5352/JLS.2016.26.6.711
 Title & Authors
Phylogenetic Analysis of 680 Prokaryotes by Gene Content
Lee, Dong-Geun; Lee, Sang-Hyeon;
  PDF(new window)
 Abstract
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.
 Keywords
COG (Clusters of Orthologous Groups of protein);gene content tree;maximum likelihood;neighbor-joining;
 Language
Korean
 Cited by
 References
1.
Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. and Doolittle, W. F. 2000. A kingdom level phylogeny of eukaryotes based on combined protein data. Science 290, 972-977. crossref(new window)

2.
Baum, D. 2008. Reading a phylogenetic tree: The meaning of monophyletic groups. Nat. Edu. 1, 190.

3.
Bennett, G. M. and Moran, N. A. 2013. Small, smaller, smallest: the origins and evolution of ancient dual symbioses in a Phloem-feeding insect. Genome Biol. Evol. 5, 1675-1688. crossref(new window)

4.
Boeckmann, B., Marcet-Houben, M., Rees, J. A., Forslund, K., Huerta-Cepas, J., Muffato, M., Yilmaz, P., Xenarios, I., Bork, P., Lewis, S. E. and Gabaldón, T. 2015. Quest for orthologs entails quest for tree of life: In search of the gene stream. Genome Biol. Evol. 7, 1988-1999. crossref(new window)

5.
Bos, D. H. and Posada, D. 2005. Using models of nucleotide evolution to build phylogenetic trees. Dev. Comp. Immunol. 29, 211-227. crossref(new window)

6.
Chaffron, S., Rehrauer, H., Pernthaler, J. and von Mering, C. 2010. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20, 947-959. crossref(new window)

7.
Chung, Y. and Ané, C. 2011. Comparing two Bayesian methods for gene tree/species tree reconstruction: simulations with incomplete lineage sorting and horizontal gene transfer. Syst. Biol. 60, 261-275. crossref(new window)

8.
Dutilh, B. E., Huynen, M. A., Bruno, W. J. and Snel, B. 2004. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J. Mol. Evol. 58, 527-539. crossref(new window)

9.
ftp://ftp.ncbi.nih.gov/pub/COG/COG2014/data

10.
Galperin, M. Y., Makarova, K. S., Wolf, Y. I. and Koonin, E. V. 2015. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43, D261-D269. crossref(new window)

11.
Guo, J., Ran, H., Zeng, J., Liu, D. and Xin, Z. 2016. Tafuketide, a phylogeny-guided discovery of a new polyketide from Talaromyces funiculosus Salicorn 58. Appl. Microbiol. Biotechnol. in press.

12.
Horz, H. P. and Conrads, G. 2010. The discussion goes on: What is the role of euryarchaeota in humans? Archaea 2010, 967271

13.
http://microbes.ucsc.edu/cgi-bin/hgGateway?db=methJann1

14.
http://www.ncbi.nlm.nih.gov/taxonomy/?term=Bacteroidetes/ Chlorobi%20group

15.
Jahn, U., Huber, H., Eisenreich, W., Hugler, M. and Fuchs, G. 2007. Insights into the autotrophic CO2 fixation pathway of the archaeon Ignicoccus hospitalis: comprehensive analysis of the central carbon metabolism. J. Bacteriol. 189, 4108-4119. crossref(new window)

16.
Klockgether, J., Munder, A., Neugebauer, J., Davenport, C. F., Stanke, F., Larbig, K. D., Heeb, S., Schöck, U., Pohl, T. M., Wiehlmann, L. and Tümmler, B. 2010. Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains. J. Bacteriol. 192, 1113-1121. crossref(new window)

17.
Lang, J. M., Darling, A. E. and Eisen, J. A. 2013. Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One 8, e62510. crossref(new window)

18.
Langille, M. G., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., Beiko, R. G. and Huttenhower, C. 2013. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat. Biotechnol. 31, 814-821. crossref(new window)

19.
Lee, D. G., Kang, H. Y., Kim, S. H., Lee, S. H., Kim, C. M., Kim, S. J. and Lee, J. H. 2003. Classification of archaebacteria and bacteria using a gene content tree approach. KSBB J. 18, 39-44

20.
Lee, D. G., Lee, J. H., Lee, S. H., Ha, B. J., Kim, C. M., Shim, D. H., Park, E. K., Kim, J. W., Li, H. Y., Nam, C. S., Kim, N. Y., Lee, E. J., Back, J. W. and Ha, J. M. 2005. Investigation of conserved genes in microorganism. J. Life Sci. 15, 261-266. crossref(new window)

21.
Lee, D. G. and Lee, S. H. 2015. Investigation of conservative genes in 711 prokaryotes. J. Life Sci. 25, 1007-1013. crossref(new window)

22.
Lienau, E. K., DeSalle, R., Rosenfeld, J. A. and Planet, P. J. 2006. Reciprocal illumination in the gene content tree of life. Syst. Biol. 55, 441-453. crossref(new window)

23.
Löffler, F. E., Yan, J., Ritalahti, K. M., Adrian, L., Edwards, E. A., Konstantinidis, K. T., Müller, J. A., Fullerton, H., Zinder, S. H. and Spormann, A. M. 2013. Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int. J. Syst. Evol. Microbiol. 63, 625-635. crossref(new window)

24.
Ludwig, W. and Klenk, H. P. 2000. Overview: A phylogenetic backbone and taxonomic framework for procaryotic systematics. pp. 49-65. In Boone, D. R., Castenholz, R. W. and Garrity, G. M. (eds.) Bergey's Manual of Systematic Bacteriology Volume 1. 2nd edition. Springer-Verlag , NY.

25.
Mukherjee, K., Bowman, K. S., Rainey, F. A., Siddaramappa, S., Challacombe, J. F. and Moe, W. M. 2014. Dehalogenimonas lykanthroporepellens BL-DC-9T simultaneously transcribes many rdhA genes during organohalide respiration with 1,2-DCA, 1,2-DCP, and 1,2,3-TCP as electron acceptors. FEMS Microbiol. Lett. 354, 111-118. crossref(new window)

26.
Rajendhran, J. and Gunasekaran, P. 2011. Microbial phylogeny and diversity: Small subunit ribosomal RNA sequence analysis and beyond. Microbiol. Res. 166, 99-110. crossref(new window)

27.
Salichos, L. and Rokas, A. 2013. Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497, 327-331. crossref(new window)

28.
Shi T. 2016. Impact of gene family evolutionary histories on phylogenetic species tree inference by gene tree parsimony. Mol. Phylogenet. Evol. 96, 9-16. crossref(new window)

29.
Szöllősi, G. J., Tannier, E., Daubin, V. and Boussau, B. 2015. The inference of gene trees with species trees. Syst. Biol. 64, e42-e62. crossref(new window)

30.
Tank, M. and Bryant, D. A. 2015. Chloracidobacterium thermophilum gen. nov., sp. nov.: an anoxygenic microaerophilic chlorophotoheterotrophic acidobacterium. Int. J. Syst. Evol. Microbiol. 65, 1426-1430. crossref(new window)

31.
Tian, J., Chen, H., Guo, Z., Liu, N., Li, J., Huang, Y., Xiang, W. and Chen, Y. 2016. Discovery of pentangular polyphenols hexaricins A-C from marine Streptosporangium sp. CGMCC 4.7309 by genome mining. Appl. Microbiol. Biotechnol. in press.

32.
Wagner, M. and Horn, M. 2006. The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr. Opin. Biotechnol. 17, 241-249. crossref(new window)

33.
Walter, J. and Ley, R. 2011. The human gut microbiome: Ecology and recent evolutionary changes. Annu. Rev. Microbiol. 65, 411-429. crossref(new window)

34.
Zheng, J., Zhao, X., Lin, X. B. and Gänzle, M. 2015. Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations. Sci. Rep. 5, 18234. crossref(new window)