Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids

Parveen, Iffat; Singh, Hemant Kumar; Malik, S.L.; Raghuvanshi, Saurabh; Babbar, Shashi B.

doi:10.1139/gen-2016-0215

Cited by 23 publications

(17 citation statements)

References 37 publications

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“…Although matK was proposed as the best barcode, with 100% resolution in two previous Paphiopedilum studies [28,41], our study agreed with Parveen et al (2017), who found that denser sampling decreased the resolution of matK [42]. However, the combination of matK with another locus was recommended as well.…”

Section: Genetic Diversity and Identification Of The Paphiopedilum Posupporting

confidence: 81%

Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences

Nguyen

et al. 2019

Biology

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Paphiopedilum is among the most popular ornamental orchid genera due to its unique slipper flowers and attractive leaf coloration. Most of the Paphiopedilum species are in critical danger due to over-exploitation. They were listed in Appendix I of the Convention on International Trade in Endangered Species of Wild Fauna and Flora, which prevents their being traded across borders. While most Paphiopedilum species are distinctive, owing to their respective flowers, their vegetative features are more similar and undistinguished. Hence, the conservation of these species is challenging, as most traded specimins are immature and non-flowered. An urgent need exists for effective identification methods to prevent further illegal trading of Paphiopedilum species. DNA barcoding is a rapid and sensitive method for species identification, at any developmental stage, using short DNA sequences. In this study, eight loci, i.e., ITS, LEAFY, ACO, matK, trnL, rpoB, rpoC1, and trnH-psbA, were screened for potential barcode sequences on the Vietnamese Paphiopedilum species. In total, 17 out of 22 Paphiopedilum species were well identified. The studied DNA sequences were deposited to GenBank, in which Paphiopedilum dalatense accessions were introduced for the first time. ACO, LEAFY, and trnH-psbA were limited in amplification rate for Paphiopedilum. ITS was the best single barcode. Single ITS could be used along with nucleotide polymorphism characteristics for species discrimination. The combination of ITS + matK was the most efficient identification barcode for Vietnamese Paphiopedilum species. This barcode also succeeded in recognizing misidentified or wrongly-named traded samples. Different bioinformatics programs and algorithms for establishing phylogenetic trees were also compared in the study to propose quick, simple, and effective tools for practical use. It was proved that both the Bayesian Inference method in the MRBAYES program and the neighbor-joining method in the MEGA software met the criteria. Our study provides a barcoding database of Vietnamese Paphiopedilum which may significantly contribute to the control and conservation of these valuable species.

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Section: Genetic Diversity and Identification Of The Paphiopedilum Posupporting

confidence: 81%

Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences

Nguyen

et al. 2019

Biology

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“…The reason for this seemingly ambiguity could be that for the unknown sample, the sequence being tested is not species-specific as it has been revealed that none of the barcode loci provides 100% species discrimination across the plant kingdom, (Kress et al 2005;Rubinoff et al 2006). Therefore, the need for a multi-locus barcode was realized by many authors (Chase et al 2007;Kress et al 2005;Kress and Erickson 2007;Mishra et al 2017;Parveen et al 2017). Though the revealed identities of the samples which were not authentic are tentative, the alarming trend emerging from the results is that substitutions are not according to the well known Ayurvedic principle for rational substitution of drugs known as ''Abhava Pratinidhi Dravyas'', propounded by Bhavmishra in sixteenth century A.D (Joshi et al 2012;Giri 2013).…”

Section: Discussionmentioning

confidence: 99%

“…(Singh et al 2012) and psbA-trnH spacer for Myristica spp. (Swetha et al 2017), generally, a combination of loci are required for the best species discrimination (Parveen et al 2017;Mishra et al 2017). Thus, in a number of studies, ITS, ITS2, matK and rbcL, along with a few others, such as rpoC1 and trnH-psbA spacer, have been used for the identification of medicinal plants and their herbal samples available in the markets (Song et al 2009, Kool et al 2012, Yuan et al 2015.…”

Section: Introductionmentioning

confidence: 99%

Employing barcoding markers to authenticate selected endangered medicinal plants traded in Indian markets

Malik

Priya

Babbar

2018

Physiol Mol Biol Plants

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The high demand of medicinal plants and their unrestricted collection have rendered many of these as rare or endangered. The restrictions imposed on their collection and trade are difficult to implement because of the inability to identify them in fragmented form. The rarity of these plants in nature and lack of their cultivation raise doubt about the authenticity of the herbals sold in markets. Therefore, in the present investigation, ITS/ITS2, matK, rbcL and rpoC1 sequences of fourteen species of important medicinal plants, some of which are endangered, were generated and checked for their species-specificity (sequences having maximum similarity only with their own) by BLAST1 and/or BOLD identifications. ITS sequences of 12 species were species-specific. However, ITS2 of only 10 of these 12 species were species-specific. As for the chloroplast loci, rbcL and rpoC1 sequences of all 14 species could be obtained, while matK sequences of only 10 of these could be generated. Of the retrieved sequences, rbcL, rpoC1 and matK sequences of 7, 11 and 7 species, respectively, were species-specific. The sequences of the targeted loci from the herbal samples of these species were difficult to retrieve because of failure in the amplification or sequencing. Nevertheless, based on ITS2 and/or one or more of the chloroplast loci targeted, the botanical identities of 22 herbal market samples were checked by phylogenetic tree, BLAST1 and BOLD identification methods. Of these 22 samples, only one of each of Rauvolfia serpentina and Picrorhiza kurroa were found to be authentic.

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“…The Department of Botany at the University of Delhi has pioneered DNA barcoding of orchids in India, focusing on several medicinal and threatened species. Research has ranged from checking the applicability of the recommended locus/loci for congeneric species (Parveen et al, 2012;Singh et al, 2012;Khasim & Ramadu, 2018) to diverse orchid taxa (Parveen et al, 2017;Kishor & Sharma, 2018). Several genetic barcoding markers such as ITS, matK, rbcL, and rpoB and rpoC1, amplified fragment length polymorphism (AFLPs), double-digested random amplified DNA (ddRAD), inter simple sequence repeat (ISSRs), random amplification of polymorphic DNA (RAPDs, single primer amplification reactions (SPAR), simple sequence repeats (SSRs) in various taxon-specific combinations aided in assessing genetic diversity in nature (Sreedhar et al, 2007;Sharma et al, 2011Sharma et al, , 2012aSharma et al, , 2013aChattopadhyay et al, 2012;Bhattacharyya et al, 2013Bhattacharyya et al, , 2017Manners et al, 2013;Thakur & Kaur, 2013;Bhattacharyya & Kumaria, 2015;Ramesh et al, 2016;Roy et al, 2017;Rao, 2020).…”

Section: Cytology and Molecular Biologymentioning

confidence: 99%

A conspectus of orchid studies in India

Adit¹,

Jalal²,

Koul³

et al. 2021

Rheedea

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Orchidaceae represents the largest family of flowering plants in India. The country has come a long way from an era of exploration phase, identification and preparation of inventories of orchids, yet it appears to be an unfinished endeavour. Besides documenting the ethnobotanical knowledge of various orchid species, in vitro tissue regeneration, micropropagation, and cell culture protocols have also been standardised for many orchid species. However, in contrast to the available diversity, ecological and molecular studies of orchids have not been conducted extensively in the country. Although above (pollinators) and below ground (fungal endophytes) mutualists have been recorded for few orchid taxa, the underlying functional mechanisms, which facilitate the processes, are unexplored. The present review offers insights into the major works that have been carried out on orchids in India, and also highlights several areas of potential research that are neglected or understudied. Most importantly, there is a need to broaden the objectives while training orchidologists. It appears that unification of subdisciplines is a priority in orchid biology in general, and conservation in particular.

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Evaluating five different loci (rbcL, rpoB, rpoC1, matK, and ITS) for DNA barcoding of Indian orchids

Cited by 23 publications

References 37 publications

Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences

Genetic Diversity and Identification of Vietnamese Paphiopedilum Species Using DNA Sequences

Employing barcoding markers to authenticate selected endangered medicinal plants traded in Indian markets

A conspectus of orchid studies in India

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