Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil

Abstract

One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison and analysis of orthologous genes carried out between B. subtilis MJ01, reference strain B. subtilis subsp. subtilis str. 168, and close relative spizizenii TU-B-10 by microscope platform and various bioinformatics tools. More than 88% of 4269 predicted coding sequences in MJ01 had at least one similar sequence in genome of reference strain and spizizenii TU-B-10. Despite this high similarity, some differences were detected among encoding sequences of non-ribosome protein and bacteriocins in MJ01 and spizizenii TU-B-10. MJ01 has unique nucleotide sequences and a novel predicted lasso-peptide bacteriocin; it also has not any similar nucleotide sequence in non-redundant nucleotide data base.

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Acknowledgements

We thank to the LABGeM and the National Infrastructure « France Genomique », for their useful MicroScope platform tools and providing genome annotation and comparative analysis for MJ01 genome. We would also thanks to Mr. Moien Jahanbani Veshareh for providing MJ01 strain bacteria. This study was supported by Department of Biotechnology, Agriculture Faculty of Shiraz University.

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Correspondence to Ali Niazi or Esmaeil Ebrahimie.

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Rahimi, T., Niazi, A., Deihimi, T. et al. Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil. Funct Integr Genomics 18, 533–543 (2018). https://doi.org/10.1007/s10142-018-0604-1

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Keywords

  • Bacillus subtilis
  • Whole genome
  • Biodegradation
  • Genome interpretation
  • Genomics comparison
  • Biosurfactant
  • Micro scope platform