Non-contiguous finished genome sequence of the opportunistic oral pathogen Prevotella multisaccharivorax type strain (PPPA20T)

Prevotella multisaccharivorax Sakamoto et al. 2005 is a species of the large genus Prevotella, which belongs to the family Prevotellaceae. The species is of medical interest because its members are able to cause diseases in the human oral cavity such as periodontitis, root caries and others. Although 77 Prevotella genomes have already been sequenced or are targeted for sequencing, this is only the second completed genome sequence of a type strain of a species within the genus Prevotella to be published. The 3,388,644 bp long genome is assembled in three non-contiguous contigs, harbors 2,876 protein-coding and 75 RNA genes and is a part of the GenomicEncyclopedia ofBacteria andArchaea project.

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

[2]  K. Nelson,et al.  Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche , 2010, Microbial Ecology.

[3]  H. Klenk,et al.  En route to a genome-based classification of Archaea and Bacteria? , 2010, Systematic and applied microbiology.

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

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

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

[7]  I. N. Rôças,et al.  Prevalence of new candidate pathogens Prevotella baroniae, Prevotella multisaccharivorax and as-yet-uncultivated Bacteroidetes clone X083 in primary endodontic infections. , 2009, Journal of endodontics.

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

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

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

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

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

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

[14]  J. A. Aas,et al.  Bacterial Profiles of Root Caries in Elderly Patients , 2008, Journal of Clinical Microbiology.

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

[16]  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..

[17]  Eoin L. Brodie,et al.  Greengenes: Chimera-checked 16S rRNA gene database and workbench compatible in ARB , 2006 .

[18]  M. Sakamoto,et al.  Prevotella multisaccharivorax sp. nov., isolated from human subgingival plaque. , 2005, International journal of systematic and evolutionary microbiology.

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

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

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

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

[25]  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.

[26]  H. Shah,et al.  Prevotella, a new genus to include Bacteroides melaninogenicus and related species formerly classified in the genus Bacteroides. , 1990, International journal of systematic bacteriology.

[27]  I. N. Rôças,et al.  The oral microbiota: general overview, taxonomy, and nucleic acid techniques. , 2010, Methods in molecular biology.

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

[29]  G. Garrity Bergey's Manual of systematic bacteriology , 2001 .

[30]  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 .