ITS2 sequence and secondary structure phylogenetic analyses of 28 strains of Heterococcus. (A) ProfDistS  sequence-structure NJ tree (unrooted) as derived from the multiple sequence-structure alignment of ITS2 helix II. Bootstrap values (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. (B) ITS2 secondary structure of ITS2 variant DB14-1-1_acl11 (group F, H. ramosissimus) used for homology modeling of helix II (shaded) for all strains of Heterococcus. The secondary structure was visualized with VARNA . Helices are numbered I–IV. Typical ITS2 motifs are highlighted by filled arrowheads. Open arrowheads mark positions of two CBCs that distinguish groups D (= H. leptosiroides) and E (= H. caespitosus). An additional conserved region throughout all strains of Heterococcus is indicated by a cloud (see text). In contrast to the template structure the region d1 is deleted in four strains (group D, see Additional file 4). The region d2 is deleted in all other strains not classified in group F. (C) Subtree as obtained by using the complete sequence-structure information from helices I-IV (template highlighted in bold). Further subtrees as derived using clade specific structural templates (helices I-IV) are provided as Additional files 4, 5, 6. (D) Visualization of the complete sequence-structure alignment used to generate the tree as shown in A). Consensus structure (51%) of helix II for all ITS2-sequences obtained from the complete multiple sequence-structure alignment without gaps. Sequence conservation is indicated from red (not conserved) to green (conserved). Nucleotides which are 100% conserved in all sequences are written as A, U, G or C. Nucleotide bonds which are 100% conserved throughout the alignment are marked in yellow. Note the U-U mismatch. The figure was generated with 4SALE .
Rybalka et al. BMC Evolutionary Biology 2013 13:39 doi:10.1186/1471-2148-13-39