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, Eryngium foetidum 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 (matK, Kim matK, and rbcL) and the nuclear ITS2 gene in two Eryngium genotypes collected from the east coast region of India. The results revealed that matK discriminated between two genotypes , however, Kim matK, rbcL, and ITS2 identified these genotypes as E. foetidum. The ribosomal nuclear ITS2 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 matK genes is better in species discrimination, ITS2 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.

DNA Barcoding, Phylogenetic Analysis and Secondary Structure Predictions of Nepenthes ampullaria, Nepenthes gracilis and Nepenthes rafflesiana

“…The alignment of the primary nucleic acid sequences could be optimized and modified using the secondary ITS2 information, contributing to the accuracy and robustness of the phylogeny [ 45 ]. Previous research had shown that genetic structure uniqueness at the conserved nuclear region could be useful for developing species-specific primers, as reported in a previous study [ 18 ]. Meanwhile, little information was available on the function and secondary structure of ITS1, leaving a gap in the knowledge on whether ITS1 secondary structure prediction could enhance species identification.…”

“…According to the previous literature, trn L and ITS DNA barcodes can be used to distinguish between the Nepenthes species based on their geographical origin area [ 17 ]. Meanwhile, other studies concluded that RNA secondary structure prediction is an advanced tool for species discrimination [ 18 ], and the integration of secondary structure information in species identification can significantly improve its accuracy for other plant species [ 18 , 19 , 20 ]. However, there are not many reports on how ITS1 and ITS2 secondary structure predictions can be used together to differentiate between species.…”

Standardization of Euphorbia tithymaloides (L.) Poit. (Root) by Conventional and DNA Barcoding Methods

“…Since every plant has a different DNA sequence, it includes using a short, standardized DNA sequence as a “barcode” to identify a certain species of plant. The chloroplast gene rbcL, matK, and trnH-psbA are the most frequently used barcode region, but the ITS (Internal Transcribed Spacer) marker has been also used in recent studies. , In a study, the ITS marker was used for DNA barcoding of Euphorbiaspecies, and the researchers found that this marker was able to effectively distinguish between Euphorbia subgenus and closely related species. It was reported that the ITS marker might be used to identify Euphorbia species and to verify the authenticity of the plant material used in conventional medicine and the pharmaceutical industry .…”

Morphological, Genetic Characterization, and Chemical Analysis of Castor Bean ( Ricinus communis ) Growing in Riyadh Saudi Arabia

“…DNA barcoding -is a standard gene fragment1 for identification of species. It has been developing rapidly in recent yearsbecome a useful tool for biodiversity investigation and monitoring, and molecular phylogeny and evolution [16]. Both primers (matk+rbcl) -conserved DNA sequences-are used as barcode primers, and would be an accurate method for identification and differentiation of species [17].…”