Additional file 6.

ITS2 sequence and secondary structure phylogenetic analyses of Heterococcus fuornensis strain SAG 835–5. (A) ProfDistS [27] sequence-structure NJ tree (unrooted) of ITS2 variants recovered from strain H. fuornensis SAG 835–5 as derived from the multiple sequence-structure alignment of ITS2 helices I-IV. 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 SAG 835-5_46 used for homology modeling of secondary structures for all ITS2 variants of the same strain. 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