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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.

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