Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India

Abstract

Commercial interest in the culinary herb, <i>Eryngium foetidum</i> L., has increased worldwide due to its typical pungency, similar to coriander or cilantro, with immense pharmaceutical components. The molecular delimitation and taxonomic classification of this lesser-known medicinal plant are restricted to conventional phenotyping and DNA-based marker evaluation, which hinders accurate identification, genetic conservation, and safe utilization. This study focused on species discrimination using DNA sequencing with chloroplast-plastid genes (<i>matK</i>, <i>Kim matK</i>, and <i>rbcL</i>) and the nuclear <i>ITS2</i> gene in two <i>Eryngium</i> genotypes collected from the east coast region of India. The results revealed that <i>matK</i> discriminated between two genotypes, however, <i>Kim matK</i>, <i>rbcL</i>, and <i>ITS2</i> identified these genotypes as <i>E. foetidum</i>. The ribosomal nuclear <i>ITS2</i> region exhibited significant inter- and intra-specific divergence, depicted in the DNA barcodes and the secondary structures derived based on the minimum free energy. Although the efficiency of <i>matK</i> genes is better in species discrimination, <i>ITS2</i> demonstrated polyphyletic phylogeny, and could be used as a reliable marker for genetic divergence studies understanding the mechanisms of RNA molecules. The results of this study provide insights into the scientific basis of species identification, genetic conservation, and safe utilization of this important medicinal plant species.