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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

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 t...

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Autores principales: Acharya, Gobinda Chandra, Mohanty, Sansuta, Dasgupta, Madhumita, Sahu, Supriya, Singh, Satyapriya, Koundinya, Ayyagari V. V., Kumari, Meenu, Naresh, Ponnam, Sahoo, Manas Ranjan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9498504/
https://www.ncbi.nlm.nih.gov/pubmed/36140845
http://dx.doi.org/10.3390/genes13091678
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author Acharya, Gobinda Chandra
Mohanty, Sansuta
Dasgupta, Madhumita
Sahu, Supriya
Singh, Satyapriya
Koundinya, Ayyagari V. V.
Kumari, Meenu
Naresh, Ponnam
Sahoo, Manas Ranjan
author_facet Acharya, Gobinda Chandra
Mohanty, Sansuta
Dasgupta, Madhumita
Sahu, Supriya
Singh, Satyapriya
Koundinya, Ayyagari V. V.
Kumari, Meenu
Naresh, Ponnam
Sahoo, Manas Ranjan
author_sort Acharya, Gobinda Chandra
collection PubMed
description 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.
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spelling pubmed-94985042022-09-23 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 Genes (Basel) Article 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. MDPI 2022-09-19 /pmc/articles/PMC9498504/ /pubmed/36140845 http://dx.doi.org/10.3390/genes13091678 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Acharya, Gobinda Chandra
Mohanty, Sansuta
Dasgupta, Madhumita
Sahu, Supriya
Singh, Satyapriya
Koundinya, Ayyagari V. V.
Kumari, Meenu
Naresh, Ponnam
Sahoo, Manas Ranjan
Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India
title Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India
title_full Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India
title_fullStr Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India
title_full_unstemmed Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India
title_short Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India
title_sort molecular phylogeny, dna barcoding, and its2 secondary structure predictions in the medicinally important eryngium genotypes of east coast region of india
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9498504/
https://www.ncbi.nlm.nih.gov/pubmed/36140845
http://dx.doi.org/10.3390/genes13091678
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