Additional file 5.

ITS2 sequence and secondary structure phylogenetic analyses of twelve strains of Heterococcus groups A-C (H. viridis, H. conicus, H. virginis). (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 the H. viridis clade, i.e. groups A-C, H. viridis, H. conicus and H. virginis. 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) Secondary structure of ITS2 variant H. viridis EIF 430/A801-2_24 used for homology modeling of secondary structures for all strains of Heterococcus groups A-C. The secondary structure was visualized with VARNA [28]. Helices are numbered I–IV. 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.

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