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.
References
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 311:1283–1287
Dandekar T, Snel B, Huynen M, Bork P (1998) Conservation of gene order: a finger print of proteins that physically interact. Trends Biochem Sci 23:324–328
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 59:972–980
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 465–471
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 York
Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol Mol Biol Rev 62:1435–1491
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 160–183
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 429:59–64
Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774
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 59:1028–1035
Kunisawa T (2003) Gene arrangements and branching orders of gram-positive bacteria. J Theor Biol 222:495–503
Kunisawa T (2006) Dichotomy of bacterial major phyla inferred from gene arrangement comparisons. J Theor Biol 239:367–375
Kunisawa T (2007) Gene arrangements characteristic of the phylum Actinobacteria. Antonie van Leeuwenhoek 92:359–365
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 60:1090–1102
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 NCBI
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 50:1611–1619
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 89:6575–6579
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 53:839–846
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 17:123–137
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 29:22–28
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 75:2046–2056
Wu M, Eisen JA (2008) A simple, fast, and accurate method of phylogenomic inference. Genome Biol 9:R151
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Kunisawa, T. Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison. Antonie van Leeuwenhoek 99, 417–422 (2011). https://doi.org/10.1007/s10482-010-9492-7
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DOI: https://doi.org/10.1007/s10482-010-9492-7