Secondary Structure Form of ITS2 Region: A Significant Labeling Tool at all Taxonomic Levels

Abstract

The general purpose of the molecular systematic studies is to illuminate the ITS2 structure of the target populations, to determine its phylogenetic boundaries, and to clarify intra-species and inter-species relationships. Particularly, the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA is used in molecular systematics because of availability of conserved regions with its highly repeated in number in plant genomes. Addition to the primary sequences of ITS2, also secondary structure form of the region became a valuable feature in species divergence and became to use like a morphological character. In the current study to indicate the secondary structure form of the ITS2 region as a useful tool in systematics, different taxa from 22 genera were used. The DNA samples were collected in the field studies in 2021 and sequences were aligned using ClustalW and Kimura-2 parameter to calculate the genetic distances. Phylogenetic tree was also constructed with Maximum Likelihood method with the best suitable model at MEGA X software. The secondary structure predictions of species and ΔG (Gibbs) free energy calculations, the tools of both the ITS2 database and mFOLD web server were used. The results indicated that ITS2 secondary structure estimations represented the genetic differences visibly with its helices and motifs like a morphological character. Consequently, even if primary structure of the ITS2 region revealed as valuable marker in molecular systematic studies, also, all tested secondary structure forms of the region will be used as an ideal marker for taxonomic and phylogenetic reconstructions at all taxonomic levels.