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

Rahimi, T ; Sharif University of Technology | 2018

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  1. Type of Document: Article
  2. DOI: 10.1007/s10142-018-0604-1
  3. Publisher: Springer Verlag , 2018
  4. Abstract:
  5. 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. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature
  6. Keywords:
  7. Bacillus subtilis ; Biodegradation ; Biosurfactant ; Genome interpretation ; Genomics comparison ; Micro scope platform ; Whole genome ; Bacteriocin ; Hydrocarbon ; Ribosome protein ; Surfactin ; Bacterial protein ; Cyclopeptide ; Lipopeptide ; Oil ; Surfactant ; Surfactin peptide ; Article ; Bacterial genome ; Bacterial strain ; Bacterium isolation ; Bioinformatics ; Bioremediation ; Comparative genomic analysis ; Gene sequence ; Gene structure ; Genomics ; Microscopy ; Nonhuman ; Oil spill ; Orthology ; Priority journal ; Protein structure ; Sequence homology ; Soil pollution ; Strain difference ; Biology ; Biosynthesis ; Chemistry ; Classification ; Contig mapping ; Gene expression regulation ; Genetics ; Metabolism ; Microbiology ; Molecular genetics ; Soil ; Soil pollutant ; Whole genome sequencing ; Bacterial Proteins ; Bacteriocins ; Biodegradation, Environmental ; Computational Biology ; Contig Mapping ; Gene Expression Regulation, Bacterial ; Gene Ontology ; Genome, Bacterial ; Industrial Oils ; Lipopeptides ; Molecular Sequence Annotation ; Peptides, Cyclic ; Phylogeny ; Soil Microbiology ; Soil Pollutants ; Surface-Active Agents ; Whole Genome Sequencing
  8. Source: Functional and Integrative Genomics ; Volume 18, Issue 5 , 2018 , Pages 533-543 ; 1438793X (ISSN)
  9. URL: https://link.springer.com/article/10.1007%2Fs10142-018-0604-1