Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)

Saccharomonospora azurea Runmao et al. 1987 is a member of the genus Saccharomonospora, which is in the family Pseudonocardiaceae and thus far poorly characterized genomically. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, the surface of peat, and moist and over-heated grain, and may play a role in the primary degradation of plant material by attacking hemicellulose. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for which a completely sequenced type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence with project status ‘Improved high quality draft’, and the annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

[1]  Olga,et al.  Complete genome sequence of Actinosynnema mirum type strain (101) , 2014 .

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

[3]  H. Klenk,et al.  Actinopolyspora alba sp. nov. and Actinopolyspora erythraea sp. nov., isolated from a salt field, and reclassification of Actinopolyspora iraqiensis Ruan et al. 1994 as a heterotypic synonym of Saccharomonospora halophila. , 2011, International journal of systematic and evolutionary microbiology.

[4]  J. Chun,et al.  Reassessment of the systematics of the suborder Pseudonocardineae: transfer of the genera within the family Actinosynnemataceae Labeda and Kroppenstedt 2000 emend. Zhi et al. 2009 into an emended family Pseudonocardiaceae Embley et al. 1989 emend. Zhi et al. 2009. , 2011, International journal of systematic and evolutionary microbiology.

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

[6]  Wenjun Li,et al.  Saccharomonospora marina sp. nov., isolated from an ocean sediment of the East China Sea. , 2010, International journal of systematic and evolutionary microbiology.

[7]  N. Kyrpides,et al.  Complete genome sequence of Thermobispora bispora type strain (R51T) , 2010, Standards in genomic sciences.

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

[9]  George M. Garrity,et al.  NamesforLife BrowserTool takes expertise out of the database and puts it right in the browser , 2010 .

[10]  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..

[11]  Krishna,et al.  Complete genome sequence of Thermobispora bispora type strain (R51 T ) , 2010 .

[12]  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 .

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

[14]  P. D’haeseleer,et al.  Complete genome sequence of Saccharomonospora viridis type strain (P101T) , 2009, Standards in genomic sciences.

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

[16]  N. Kyrpides,et al.  Complete genome sequence of Actinosynnema mirum type strain (101T) , 2009, Standards in genomic sciences.

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

[18]  E. Stackebrandt,et al.  An update of the structure and 16S rRNA gene sequence-based definition of higher ranks of the class Actinobacteria, with the proposal of two new suborders and four new families and emended descriptions of the existing higher taxa. , 2009, International journal of systematic and evolutionary microbiology.

[19]  Manfred,et al.  Complete genome sequence of Saccharomonospora viridis type strain ( P 101 T ) , 2009 .

[20]  Olga,et al.  Complete genome sequence of Actinosynnema mirum type strain ( 101 T ) , 2009 .

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

[22]  Alla Lapidus,et al.  POLISHER: a Tool for Using Ultra Short Reads in Microbial Genome Finishing , 2008 .

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

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

[25]  Saccharomonospora saliphila sp. nov., a halophilic actinomycete from an Indian soil. , 2008, International journal of systematic and evolutionary microbiology.

[26]  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..

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

[28]  Peter F. Hallin,et al.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes , 2007, Nucleic acids research.

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

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

[31]  S. Brunak,et al.  Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.

[32]  E. Stackebrandt,et al.  Saccharomonospora paurometabolica sp. nov., a moderately halophilic actinomycete isolated from soil in China. , 2003, International journal of systematic and evolutionary microbiology.

[33]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[34]  E. Stackebrandt,et al.  Saccharomonospora halophila sp. nov., a novel halophilic actinomycete isolated from marsh soil in Kuwait. , 2002, International journal of systematic and evolutionary microbiology.

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

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

[37]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

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

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

[40]  J. Yoon,et al.  NOTE: DNA-DNA relatedness between Saccharomonospora species: 'Saccharomonospora caesia' as a synonym of Saccharomonospora azurea , 1999 .

[41]  C. Jiang,et al.  Description of Saccharomonospora xinjiangensis sp. nov. based on chemical and molecular classification. , 1998, International journal of systematic bacteriology.

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

[43]  E. Stackebrandt,et al.  Proposal for a New Hierarchic Classification System, Actinobacteria classis nov. , 1997 .

[44]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[45]  M. Aguirre,et al.  Validation of the publication of new names and new combinations previously effectively published outside the IJSB. , 1996, International journal of systematic bacteriology.

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

[47]  O. Kandler,et al.  Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[48]  E. Stackebrandt,et al.  The Phylogeny of Mycolate-less Wall Chemotype IV Actinomycetes and Description of Pseudonocardiaceae fam. nov. , 1988 .

[49]  H. Runmao Saccharomonospora azurea sp. nov., a New Species from Soil , 1987 .

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

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

[52]  R. E. Buchanan STUDIES IN THE NOMENCLATURE AND CLASSIFICATION OF THE BACTERIA II. THE PRIMARY SUBDIVISIONS OF THE SCHIZOMYCETES , 1917, Journal of bacteriology.