Additional file 4.

ITS2 sequence and secondary structure phylogenetic analyses of three strains of Heterococcus group D (H. leptosiroides). (A) ProfDistS [27] sequence-structure NJ tree (unrooted) as derived from the multiple sequence-structure alignment of ITS2 helices I-IV recovered for strains of group D, H. leptosiroides. Bootstrap values based on 100 pseudo-replicates are mapped to the appropriate internodes. Branch lengths are drawn proportional to inferred changes. The template ITS2 variant used in B) is highlighted in bold. Scale bar, substitutions per site. (B) ITS2 secondary structure of ITS2 variant EIF 423/A790-5_cl65 used for homology modeling of secondary structures for all strains of group D (H. leptosiroides). The secondary structure was visualized with VARNA [28]. Helices are numbered I–IV. Four strains indicated by an asterisk are devoid of the apical part of helix III. An arrowhead indicates the highly conserved GGU motif 5’ to the apex of helix III. A cloud highlights the segment of helix III conserved across all studied strains. Open arrowheads mark positions of two CBCs that distinguish groups D and E.

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Rybalka et al. BMC Evolutionary Biology 2013 13:39   doi:10.1186/1471-2148-13-39