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First report on the whole genome sequence of Pseudomonas cichorii strain JBC 1 and comparison with other Pseudomonas species
Author(s) -
Ramkumar G.,
Lee S. W.,
Weon H.Y.,
Kim B.Y.,
Lee Y. H.
Publication year - 2015
Publication title -
plant pathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.928
H-Index - 85
eISSN - 1365-3059
pISSN - 0032-0862
DOI - 10.1111/ppa.12259
Subject(s) - biology , genome , genetics , whole genome sequencing , virulence , pseudomonas , genbank , prophage , gene , microbiology and biotechnology , bacteria , escherichia coli , bacteriophage
Pseudomonas cichorii , a plant pathogen that infects a wide range of host plants worldwide, causes several diseases in economically important vegetable crops. Availability of the genome sequences of pathogens can greatly enhance research necessary for the advancement of disease management programmes. Despite the significance of P. cichorii , its whole genome sequence has not been reported previously. The genome sequence of P. cichorii JBC 1, described for the first time in this study, is 5 986 012 bp with an average GC content of 58·1% and has 5174 coding sequences ( CDS ). The genes related to virulence, transport mechanisms, phytotoxic compounds, and secondary metabolite products were analysed and the genome was compared to eight other Pseudomonas species to understand the diversity at species level. Despite the high similarity (up to 80·85%), significant diversity was found among the different Pseudomonas species at the genome level. A comparison of JBC 1 pathogenicity island ( PAI ) regions indicated that the P. viridiflava UASWS 0038 PAI has more similarity than the P. syringae PAI region, and the analysis revealed significant divergence at PAI regions among the Pseudomonas species, providing an insight into the differences in host specificity and degree of virulence. In addition, JBC 1 encodes antibiotic resistance and tolerance to heavy metals, and two different prophage segments were inserted at three different regions. The genome sequence of JBC 1, which was deposited into the NCBI GenBank (accession no. CP007039 ), will be a reference sequence for other P. cichorii strains and a useful resource for further research.