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

Abstract

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.

Length variation and repetitive sequences of Internal Transcribed Spacer of ribosomal RNA gene, diagnostics and relationships of populations of potato rot nematode, Ditylenchus destructor Thorne, 1945 (Tylenchida: Anguinidae)

“…Slight differences in structures proposed in our study from those by Marek et al (2010) can be explained by the different methods and folding parameters used and may also reflect the dynamic nature of the ITS2 structure flexing between alternative folding patterns (Ma et al, 2008). The ITS1 transcript of D. destructor proposed in our study represents three domain structures.…”

Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia

“…Several recent studies have proved that ITS2 molecular morphometric analysis could be effectively used to resolve eukaryotic organisms at the genus and species level. Ma et al [33] reported that the application of secondary structure information provides a realistic picture of relationships within Heterodera . Chen et al [100] and Han et al [34] demonstrated the potential use of the ITS2 region as a standard DNA barcode to identify medicinal plants and their closely related species.…”

ITS2 Secondary Structure Improves Discrimination between Medicinal “Mu Tong” Species when Using DNA Barcoding

“…We followed the 28-symbol method of Subbotin [ 27 , 38 ] and considered each of the four bases in helixes as six states (e.g., AA, AC, AG, AU, A-,-A), together with each of the four base states in loops as additional symbols [ 27 ]. After each state was designated as separate character a new structure information matrix was produced through RNAstat software [ 27 ].…”