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The internal transcribed spacer 2 (ITS2) of the ribosomal RNA gene is a double-edged tool for eukaryote evolutionary comparison. In this paper, we re-evaluate the putative ITS2 secondary structures proposed for 29 species of cyst-forming nematodes in the genus Heterodera and present optimized variants. The models are organized in four main helices emerging from a central core. Helix III is always the longest and has two branches exhibited as a Y-shaped structure near the apex. In most species, helices III and IV have merged to form a segment of the central core. Two conservative motifs, GAUCR and UURC, were found in helices II and III, respectively. Using the MARNA program taking into consideration both the primary sequence and the secondary structure, we generated an optimal alignment for Heterodera sequences. The alignment was analyzed by Bayesian inference under a general-time-reversible model and the complex models, and by a maximum parsimony approach using original data and sequence data converted according to secondary-structure information. The consensus ITS2 secondary structure model for Heteroderidae can serve as a useful guide for reconstruction of optimal alignment and can be used as an additional source of data incorporating structural parameters of molecules for the study of nematode phylogeny. Application of the secondary ITS2 structure data allows a more resolved and realistic picture of relationships within Heteroderidae

ITS2 secondary structure and phylogeny of cyst-forming nematodes of the genus Heterodera (Tylenchida: Heteroderidae)