Complete genome sequence of Dyadobacter fermentans type strain (NS114T)

Dyadobacter fermentans (Chelius and Triplett, 2000) is the type species of the genus Dyadobacter. It is of phylogenetic interest because of its location in the Cytophagaceae, a very diverse family within the order ‘Sphingobacteriales’. D. fermentans has a mainly respiratory metabolism, stains Gram-negative, is non-motile and oxidase and catalase positive. It is characterized by the production of cell filaments in aging cultures, a flexirubin-like pigment and its ability to ferment glucose, which is almost unique in the aerobically living members of this taxonomically difficult family. Here we describe the features of this organism, together with the complete genome sequence, and its annotation. This is the first complete genome sequence of the sphingobacterial genus Dyadobacter, and this 6,967,790 bp long single replicon genome with its 5804 protein-coding and 50 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project.

[1]  Natalia N. Ivanova,et al.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea , 2009, Nature.

[2]  I-Min A. Chen,et al.  IMG ER: a system for microbial genome annotation expert review and curation , 2009, Bioinform..

[3]  Lei Zhang,et al.  Dyadobacter alkalitolerans sp. nov., isolated from desert sand. , 2009, International journal of systematic and evolutionary microbiology.

[4]  Chris F. Taylor,et al.  The minimum information about a genome sequence (MIGS) specification , 2008, Nature Biotechnology.

[5]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[6]  I-Min A. Chen,et al.  The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions , 2007, Nucleic Acids Res..

[7]  Yoon-Dong Park,et al.  Pedobacter koreensis sp. nov., isolated from fresh water. , 2007, International journal of systematic and evolutionary microbiology.

[8]  Mi Sun Kim,et al.  Dyadobacter koreensis sp. nov., isolated from fresh water. , 2007, International journal of systematic and evolutionary microbiology.

[9]  H. Gong,et al.  Dyadobacter beijingensis sp. nov., isolated from the rhizosphere of turf grasses in China. , 2007, International journal of systematic and evolutionary microbiology.

[10]  James R. Cole,et al.  Taxonomic Outline of the Bacteria and Archaea: Formerly the Taxonomic Outline of the Prokaryotes , 2007 .

[11]  James R. Cole,et al.  Taxonomic Outline of the Bacteria and Archaea , Release 7 . 7 March 6 , 2007 . Part 9 – The Bacteria : Phylum “ Firmicutes ” : Class “ Bacilli ” , 2007 .

[12]  Deok-Chun Yang,et al.  Dyadobacter ginsengisoli sp. nov., isolated from soil of a ginseng field. , 2006, International journal of systematic and evolutionary microbiology.

[13]  S. Shivaji,et al.  Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India. , 2005, International journal of systematic and evolutionary microbiology.

[14]  F. Garcia-Pichel,et al.  Dyadobacter crusticola sp. nov., from biological soil crusts in the Colorado Plateau, USA, and an emended description of the genus Dyadobacter Chelius and Triplett 2000. , 2005, International journal of systematic and evolutionary microbiology.

[15]  U. Karlson,et al.  Isolation and taxonomic affiliation of N-heterocyclic aromatic hydrocarbon-transforming bacteria , 2005, Applied Microbiology and Biotechnology.

[16]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[17]  Ryuichi Hosoya,et al.  Distribution of two triamines, spermidine and homospermidine, and an aromatic amine, 2-phenylethylamine, within the phylum Bacteroidetes. , 2004, The Journal of general and applied microbiology.

[18]  E. Topp,et al.  Bacteria Associated with Cysts of the Soybean Cyst Nematode (Heterodera glycines) , 2003, Applied and Environmental Microbiology.

[19]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[20]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[21]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[22]  Wei Qian,et al.  Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. , 2000, Molecular biology and evolution.

[23]  M. Chelius,et al.  Dyadobacter fermentans gen. nov., sp. nov., a novel gram-negative bacterium isolated from surface-sterilized Zea mays stems. , 2000, International journal of systematic and evolutionary microbiology.

[24]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[25]  P. Green,et al.  Consed: a graphical tool for sequence finishing. , 1998, Genome research.

[26]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[27]  P. Sneath,et al.  Approved lists of bacterial names. , 1980, The Medical journal of Australia.