Antonie van Leeuwenhoek

, Volume 99, Issue 2, pp 417–422 | Cite as

Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison

Short Communication

Abstract

The phylogenetic placement of the phylum Deferribacteres was investigated on the basis of gene order comparisons of completely sequenced bacterial genomes. Two completely sequenced Deferribacteres species share five sets of gene arrangements with a group of phyla, Proteobacteria, Aquificae, Planctomycetes, Spirochaetes, Bacteroidetes, Chlorobi, Acidobacteria, Verrucomicrobia, Elusimicrobia and Nitrospirae, while the other group of phyla, Synergistetes, Firmicutes, Actinobacteria, Thermotogae, Chloroflexi and Deinococcus-Thermus, Fusobacteria, shares alternative sets of gene arrangements, suggesting that the Deferribacteres is classified in the former group of phyla. Gene transfers that are thought to have occurred in a common ancestor of the Deferribacteres, Deltaproteobacteria and Nitrospirae exclusive of virtually all other phyla were identified, which suggests that the Deferribacteres is phylogenetically proximal to the Proteobacteria and Nitrospirae.

Keywords

Phylogeny Deferribacteres Genome Gene order Gene transfer 

References

  1. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287CrossRefPubMedGoogle Scholar
  2. Dandekar T, Snel B, Huynen M, Bork P (1998) Conservation of gene order: a finger print of proteins that physically interact. Trends Biochem Sci 23:324–328CrossRefPubMedGoogle Scholar
  3. Downes J, Vartoukian SR, Dewhirst FE, Zard J, Chen T, Yu WH, Sutcliffe IC, Wade WD (2009) Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum ‘Synergistetes’ isolated from the human oral cavity. Int J Syst Evol Microbiol 59:972–980CrossRefPubMedGoogle Scholar
  4. Garrity GM, Holt JM (2001) Phylum BIX. Deferribacteres phy. nov. In: Boone DR, Castenholz RW (eds) Bergey’s Manual of Systematic Bacteriology, 2nd edn. Springer, New York, pp 465–471Google Scholar
  5. Garrity GM, Bell JA, Lilburn TG (2004) Taxonomic outline of the Prokaryotes. Bergey's Mannual of Systematic Bacteriology, 2nd edn, Release 5.0. Springer, New YorkGoogle Scholar
  6. Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol Mol Biol Rev 62:1435–1491PubMedGoogle Scholar
  7. Gupta RS (2005) Molecular sequences and the early history of life. In: Sapp J (ed) Microbial phylogeny and evolution: concepts and controversies. Oxford University Press, New York, pp 160–183Google Scholar
  8. Horiike T, Miyata D, Hamada K, Saruhashi S, Shinozawa T, Kumar S, Chakraborty R, Komiyama T, Tateno Y (2009) Phylogenetic construction of 17 bacterial phyla by new method and carefully selected orthologs. Gene 429:59–64CrossRefPubMedGoogle Scholar
  9. Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774PubMedGoogle Scholar
  10. Jumas-Bilak E, Roudière L, Marchandin H (2009) Description of ‘Synergistetes’ phyl. nov. and emended description of the phylum ‘Deferribacteres’ and of the family Syntrophomonadaceae, phylum ‘Firmicutes’. Int J Syst Evol Microbiol 59:1028–1035CrossRefPubMedGoogle Scholar
  11. Kunisawa T (2003) Gene arrangements and branching orders of gram-positive bacteria. J Theor Biol 222:495–503PubMedGoogle Scholar
  12. Kunisawa T (2006) Dichotomy of bacterial major phyla inferred from gene arrangement comparisons. J Theor Biol 239:367–375CrossRefPubMedGoogle Scholar
  13. Kunisawa T (2007) Gene arrangements characteristic of the phylum Actinobacteria. Antonie van Leeuwenhoek 92:359–365CrossRefPubMedGoogle Scholar
  14. Kunisawa T (2010) Evaluation of the phylogenetic position of the sulfate-reducing bacterium Thermodesulfovibrio yellowstonii (phylum Nitrospirae) by means of gene order data from completely sequenced genomes. Int J Syst Evol Microbiol 60:1090–1102CrossRefPubMedGoogle Scholar
  15. Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Dalin E, Tice H, Bruce D, Goodwin L, Pitluck S, Kyrpides N, Mavromatis K, Ivanova N, Mikhailova N, Kiss H, Brettin T, Detter JC, Han C, Larimer F, Land M, Hauser L, Markowitz V, Cheng J-F, Hugenholtz P, Woyke T, Wu D, Lang E, Spring S, Kopitz M, Schneider S, Klenk H-P, Eisen JA (2010) The complete genome of Denitrovibrio acetiphilus DSM 12809. Data prepared by the US DOE Joint Genome Institute. Direct submission to NCBIGoogle Scholar
  16. Myhr S, Torsvik T (2000) Denitrovibrio acetiphilus, a novel genus and species of dissimilatory nitrate-reducing bacterium isolated from an oil reservoir model column. Int J Syst Evol Microbiol 50:1611–1619PubMedGoogle Scholar
  17. Sankoff D, Leduc G, Antoine N, Paquin B, Lang BF, Cedergren R (1992) Gene order comparisons for phylogenetic inference: evolution of the mitochondrial genome. Proc Natl Acad Sci USA 89:6575–6579CrossRefPubMedGoogle Scholar
  18. Takai K, Kobayashi H, Nealson KH, Horikoshi K (2003) Deferribacter desulfuricans sp. nov., a novel sulfur-, nitrate- and arsenate-reducing thermophile isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 53:839–846CrossRefPubMedGoogle Scholar
  19. Takaki Y, Shimamura S, Nakagawa S, Fukuhara Y, Horikawa H, Ankai A, Harada T, Hosoyama A, Oguchi A, Fukui S, Fujita N, Takami H, Takai K (2010) Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1. DNA Res 17:123–137CrossRefPubMedGoogle Scholar
  20. Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22–28CrossRefPubMedGoogle Scholar
  21. Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, Sait M et al (2009) Three genomes from the phylum Acidobacteria provide insight into their lifestyles in soils. Appl Environ Microbiol 75:2046–2056CrossRefPubMedGoogle Scholar
  22. Wu M, Eisen JA (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9:R151CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Department of Applied Biological SciencesScience University of TokyoNodaJapan

Personalised recommendations