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

Acharya, Gobinda Chandra; Mohanty, Sansuta; Dasgupta, Madhumita; Sahu, Supriya; Singh, Satyapriya; Koundinya, Ayyagari V. V.; Kumari, Meenu; Naresh, Ponnam; Sahoo, Manas Ranjan

doi:10.3390/genes13091678

Open AccessArticle

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

by

Gobinda Chandra Acharya

^1,†,

Sansuta Mohanty

^1,†,

Madhumita Dasgupta

²,

Supriya Sahu

^1,3,

Satyapriya Singh

¹,

Ayyagari V. V. Koundinya

¹,

Meenu Kumari

⁴,

Ponnam Naresh

⁵ and

Manas Ranjan Sahoo

^1,*

¹

Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India

²

ICAR Research Complex for Northeastern Hill Region, Manipur Centre, Imphal 795004, Manipur, India

³

All India Institute of Medical Sciences, Bhubaneswar 751019, Odisha, India

⁴

ICAR Research Complex for Eastern Region, Research Centre, Ranchi 834010, Jharkhand, India

⁵

ICAR–Indian Institute of Horticultural Research, Bengaluru 560089, Karnataka, India

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Genes 2022, 13(9), 1678; https://doi.org/10.3390/genes13091678

Submission received: 7 September 2022 / Revised: 15 September 2022 / Accepted: 15 September 2022 / Published: 19 September 2022

(This article belongs to the Special Issue Phylogenetics, Genetics, and Breeding of Medicinal Plants)

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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.

Keywords: DNA barcoding; ITS2 secondary structure; medicinal herbs; species discrimination; spiny coriander

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MDPI and ACS Style

Acharya, G.C.; Mohanty, S.; Dasgupta, M.; Sahu, S.; Singh, S.; Koundinya, A.V.V.; Kumari, M.; Naresh, P.; Sahoo, M.R. Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India. Genes 2022, 13, 1678. https://doi.org/10.3390/genes13091678

AMA Style

Acharya GC, Mohanty S, Dasgupta M, Sahu S, Singh S, Koundinya AVV, Kumari M, Naresh P, Sahoo MR. Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India. Genes. 2022; 13(9):1678. https://doi.org/10.3390/genes13091678

Chicago/Turabian Style

Acharya, Gobinda Chandra, Sansuta Mohanty, Madhumita Dasgupta, Supriya Sahu, Satyapriya Singh, Ayyagari V. V. Koundinya, Meenu Kumari, Ponnam Naresh, and Manas Ranjan Sahoo. 2022. "Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India" Genes 13, no. 9: 1678. https://doi.org/10.3390/genes13091678

APA Style

Acharya, G. C., Mohanty, S., Dasgupta, M., Sahu, S., Singh, S., Koundinya, A. V. V., Kumari, M., Naresh, P., & Sahoo, M. R. (2022). Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India. Genes, 13(9), 1678. https://doi.org/10.3390/genes13091678

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

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