Ribosomal DNA analyses reveal greater sequence variation in Polymyxa species than previously thought and indicate the possibility of new ribotype-host-virus associations
Article first published online: 13 JAN 2013
© 2012 Society for Applied Microbiology and Blackwell Publishing Ltd
Environmental Microbiology Reports
Thematic Issue on Environmental Ecology of Pathogens and Resistances
Volume 5, Issue 1, pages 143–150, February 2013
How to Cite
Smith, M. J., Adams, M. J. and Ward, E. (2013), Ribosomal DNA analyses reveal greater sequence variation in Polymyxa species than previously thought and indicate the possibility of new ribotype-host-virus associations. Environmental Microbiology Reports, 5: 143–150. doi: 10.1111/1758-2229.12026
- Issue published online: 3 FEB 2013
- Article first published online: 13 JAN 2013
- Accepted manuscript online: 19 DEC 2012 10:09PM EST
- Manuscript Accepted: 4 DEC 2012
- Manuscript Received: 28 JUN 2012
- Biotechnology and Biological Sciences Research Council of the UK
Fig. S1. Secondary structures of the ITS2 regions of P. graminis and P. betae isolates generated using the mfold web interface (http://mfold.rna.albany.edu/). The ITS2 region boundaries were determined from the annotations of the sequences in GenBank and by reference to the sequence alignments of Coleman (2003). DNA sequences were converted to rRNA sequences (positive strand) prior to analysis. Natural angles were used to draw the structures. The most thermodynamically stable secondary structures were retained for comparison between isolates and species. Structures shown are those which were diagnostic for a group, except for C and G which were anomalous for their groups A. PgF1(I), B. PgF51(II), C. PgGar (IIb), D. 108Sum18 (III), E. PgI9 (IV), F. PgMeta (V), G. PgJap (V), H. PbF67. Pg = Polymyxa graminis, Pb = Polymyxa betae. Group I were clearly represented by the structure shown in A. There were other structures which were common to some type I sequences, but not to all. Group II had five predicted structures with similar free energy (dG) values. The one structure predicted for PgGar (IIb) was different from any of the other type II structures. Group III (a and b) shared one common structure. Five structures were shared between groups IVa and IVb with dG values ranging between −46 and −49. Three structures were common between group V sequences PgAfr1, PgAfr2 and Meta, but the other group V sequence PgJap did not share any of these structures. Three entirely different structures were predicted for PgJap.
Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.