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Arthrospira platensis NIES-39

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close this sectionAbout this Microorganism

Photo by Dr. Ohmori in Saitama University

Arthrospira (Spirulina) plantensis is a filamentous non-N2-fixing cyanobacterium and known to be an important organism for industrial application and as a food supply. The strain NIES-39 was originally isolated from a saline lake in Africa and grows under severe conditions such as high salt and alkaline pH. Despite the importance in industrial applications, little is known about the biology and genetic system of A. platensis and related cyanobacterial species because of, at least in part, the difficulty in genetic transformation.

Almost complete genome sequence of A. platensis NIES-39 was determined. Optical mapping analysis revealed that the genome consists of a single circular chromosome of 6.8Mb. A total of 6,630 protein-coding genes, two sets of rRNA genes and 40 tRNA genes were predicted and annotated. Of the protein-coding genes, 78% are similar to those of other organisms and the remaining 22% are currently unknown.

Comparative genome analysis with other sequenced cyanobacterial genomes highlighted genes specific to filamentous cyanobacteria. Surprisingly, almost 10% of the genome (612 kb) is composed of group II introns, phage-like sequences, insertion elements and other types of repetitive sequences. In addition, the genome harbors many pseudogenes, suggesting that the genome is undergoing rapid evolution to adapt to environmental conditions. The genome was found to contain a number of restriction-modification systems for protecting the genome from exogenous DNA elements. These results may provide important clues for post-genome studies, including the development of genetic transformation system, and for further industrial utilization.

close this sectionProject history

close this date 2012-05-15 ..... 1
2012-05-15 Release of proteome analysis result of Arthrospira platensis NIES-39
imageWe have analyzed the proteome of Arthrospira platensis NIES-39 by using the following method; 2D-PAGE followed by N-terminal amino acid sequencing.
Changed ORFs
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close this sectionSummary of the genomic data

Genomic size 6,788,435 bp
G+C content 43.65 %
Number of ORFs assigned 6,630
Percentage of the coding regions 81.25 %
Percentage of the intronic regions 0.00 %
Number of rRNA genes 6
Number of tRNA genes 40
Number of other features

close this sectionGeneral Procedure

The nucleotide sequence of the A. platensis NIES-39 genome was determined by the whole genome shotgun sequencing method as in the case of other organisms analyzed at NITE-DOB.

General Procedure
  • DNA shotgun libraries
    DNA shotgun libraries with inserts of 1.5 and 5 kb in pUC118 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).
    Raw sequencing data corresponding to 11-fold coverage were assembled using PHRED/PHRAP/CONSED software (

  • 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.
    Contig sequences generated by Roche 454 FLX sequencer were also used to fill some gaps.

  • Validation of the assembled sequence data
    Optical maps and sequence contigs were compared according to their restriction fragment pattern.

Gene identification and annotation
  • Putative non-translated genes were identified using the Rfam, tRNAscan-SE programs and rRNA genes using the RNAmmer and BLASTN 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, the non-redundant UniProt database and protein signature database, InterPro, were searched to assign the predicted protein sequences based on sequence similarities.

  • Ortholog genes among cyanobacteria were manually curated using Gclust and CYORF.

  • 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