Complete genome sequence of the aquatic bacterium Runella slithyformis type strain (LSU 4 T )

Cytophagaceae , Cytophagia , GEBA Runella slithyformis Larkin and Williams 1978 is the type species of the genus Runella , which belongs to the Cytophagaceae , a family that was only recently classified to the order Cytophagales in the class Cytophagia . The species is of interest because it is able to grow at temperatures as low as 4°C. This is the first completed genome sequence of a member of the genus Runella and the sixth sequence from the family Cytophagaceae . The 6,919,729 bp long genome consists of a 6.6 Mbp circular genome and five circular plasmids of 38.8 to 107.0 kbp length, harboring a total of 5,974 protein-coding and 51 RNA genes and is a part of the G enomic E ncyclopedia of B acteria and A rchaea project.

[1]  J. Ruan.  [Bergey's Manual of Systematic Bacteriology (second edition) Volume 5 and the study of Actinomycetes systematic in China]. , 2013, Wei sheng wu xue bao = Acta microbiologica Sinica.

[2]  G. Garrity.  Bergey’s Manual® of Systematic Bacteriology , 2012, Springer New York.

[3]  Anton Güntsch,et al.  The DNA bank network: the start from a german initiative. , 2011, Biopreservation and biobanking.

[4]  Lynne A. Goodwin,et al.  Complete genome sequence of Leadbetterella byssophila type strain (4M15) , 2011 .

[5]  Nolan,et al.  Complete genome sequence of Leadbetterella byssophila type strain ( 4 M 15 T ) , 2011 .

[6]  Natalia N. Ivanova,et al.  GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes , 2010, Nature Methods.

[7]  I-Min A. Chen,et al.  The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata , 2007, Nucleic Acids Res..

[8]  Noel R. Krieg,et al.  Phylum XIV. Bacteroidetes phyl. nov. , 2010 .

[9]  Bristow,et al.  Complete genome sequence of Spirosoma linguale type strain ( 1 T ) , 2010 .

[10]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

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

[12]  Alexandros Stamatakis,et al.  How Many Bootstrap Replicates Are Necessary? , 2009, RECOMB.

[13]  Cynthia,et al.  Complete genome sequence of Dyadobacter fermentans type strain ( NS 114 T ) , 2009 .

[14]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[15]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

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

[17]  Pablo N. Hess,et al.  An empirical test of the midpoint rooting method , 2007, Biological journal of the Linnean Society. Linnean Society of London.

[18]  C. Jeon,et al.  Runella defluvii sp. nov., isolated from a domestic wastewater treatment plant. , 2007, International journal of systematic and evolutionary microbiology.

[19]  P. Richardson,et al.  Genome Sequence of the Cellulolytic Gliding Bacterium Cytophaga hutchinsonii , 2007, Applied and Environmental Microbiology.

[20]  Woojun Park,et al.  Runella limosa sp. nov., isolated from activated sludge. , 2006, International journal of systematic and evolutionary microbiology.

[21]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[22]  M. Chelius,et al.  Runella zeae sp. nov., a novel gram-negative bacterium from the stems of surface-sterilized Zea mays. , 2002, International journal of systematic and evolutionary microbiology.

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

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

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

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

[27]  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.

[28]  J. Euzéby.  List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. , 1997, International journal of systematic bacteriology.

[29]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[30]  Martin F. Porter,et al.  An algorithm for suffix stripping , 1997, Program.

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

[32]  J. Larkin,et al.  Runella slithyformis gen. nov., sp. nov., a Curved, Nonflexible, Pink Bacterium , 1978 .

[33]  A. Balows.  Bergey's Manual of Determinative Bacteriology. Eighth Edition , 1975 .

[34]  S. T. Cowan.  Bergey's Manual of Determinative Bacteriology , 1948, Nature.

[35]  R. Stanier.  Studies on the Cytophagas , 1940, Journal of bacteriology.