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Oscillibacter valericigenes Sjm18-20T (= NBRC 101213T)

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close this sectionAbout this Microorganism


Photo by Dr. Iino (NBRC, NITE)
Oscillibacter valericigenes Sjm18-20T (= NBRC 101213T) is a mesophilic, strictly anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam (Corbicula japonica) in Shimane Prefecture. Based on 16S rRNA gene sequences, the strain was revealed belonging to the clostridial cluster IV, one of the 19 clusters of clostridial bacteria. Clostridial cluster IV is known to contain phenotypically heterogeneous bacteria. O. valericigenes was shown to be distant from any other species of clostridial cluster IV in 16S rRNA sequence analysis. Instead, it was most similar to the large cells mechanically enriched from sheep rumen contents and thought to represent "Oscillospira guilliermondii", which was originally reported in as early as 1913. The genome sequence of strain Sjm18-20 revealed one circular chromosome (4,410,036 bp, 53.32 % G+C, 4,656 ORFs, 3 rRNA operons, 58 tRNA genes) and one circular plasmid (60,586 bp, 43.33% G+C, 67 ORFs). The genome sequence of the strain would provide clues about the lifestyle and the isolation of related and uncultivated bacteria.

close this sectionProject history

close this date 2012-05-14 ..... 1
2012-05-14 Release of the Oscillibacter valericigenes Sjm18-20T(= NBRC 101213T) genomic data
imageWe published the genomic data of Oscillibacter valericigenes Sjm18-20T(= NBRC 101213T).

close this sectionSummary of the genomic data

OV1
Genomic size 4,470,622 bp
G+C content 53.19 %
Number of ORFs assigned 4,723
Percentage of the coding regions 85.87 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 9
5S16S23S
333
Number of tRNA genes 58
AlaArgAsnAspCysGln
641212
GluGlyHisIleLeuLys
441364
MetPheProSerThrTrp
413431
TyrVal
13
Number of other features
(misc_RNA,misc_feature,repeat)
2
misc_RNA
2

close this sectionGeneral Procedure

The nucleotide sequence of the Oscillibacter valericigenes Sjm18-20T genome was determined by the whole genome shotgun sequencing method as in the case of other organisms analyzed at NITE Biotechnology Center.


General Procedure
  • DNA shotgun libraries
    DNA shotgun libraries with inserts of 1.7 and 4.6 kb in pUC18 vector (TAKARA) was constructed.

  • Fosmid library
    A Fosmid library with inserts of 40 kb in the pCC1FOS fosmid vector was constructed using the CopyControl Fosmid Library Production Kit (Epicentre).

  • Nucleotide sequencing
    Plasmid and Fosmid clones were end-sequenced using dye-terminator chemistry on an ABI Prism 3730 sequencer (ABI).
    Sequence reads were trimmed at a threshold quality value of 20 by Phred and assembled using PHRAP/CONSED software (http://www.phrap.org).

  • Gap closing
    Fosmid end sequences were mapped onto the assembled sequence.
    Fosmid clones that link two contigs were selected and sequenced by primer walking to close any gaps.
    In some cases, gaps were subcloned to Entransposon using Template Generation System II Kit (Finnzymes) or amplified by PCR following construction of shot-gun libraries and sequenced.
    Resulting chromosome sequence was composed of 2 contigs; the last 2 contigs were concatenated by repetitive primer walking using DNA Walking SpeedUp Premix Kit 2 (Funakoshi).

  • Validation of the assembled sequence data
    In construction of final nucleotide sequence, low-quality regions with a Phrap quality score of less than 40 were re-sequenced and verified. Finally, each base of genome was successfully ensured to be sequenced from Phrap quality value more than 40.


Gene identification and annotation
  • Putative non-translated genes were identified using the Rfam, tRNAscan-SE and ARAGORN programs.

  • The prediction of open reading frames (ORFs) was performed using Glimmer3. The initial set of ORFs was manually selected from the prediction result in combination with BLASTP results.

  • For functional annotation, ORFs were searched against the UniProt database and protein signature database, InterPro, and these results were manually examined.

  • The KEGG database was used for pathway reconstruction.

  • Signal peptides in proteins were predicted using SignalP and transmembrane helices were predicted using TMHMM.


close this sectionRelated links to external databases