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Sutula M, Kakanay A, Tussipkan D, Dzhumanov S, Manabayeva S. Phylogenetic Analysis of Rare and Endangered Tulipa Species ( Liliaceae) of Kazakhstan Based on Universal Barcoding Markers. BIOLOGY 2024; 13:365. [PMID: 38927245 PMCID: PMC11200791 DOI: 10.3390/biology13060365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024]
Abstract
In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.
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Affiliation(s)
- Maxim Sutula
- National Center for Biotechnology, Astana 010000, Kazakhstan; (M.S.); (A.K.); (D.T.)
| | - Ayan Kakanay
- National Center for Biotechnology, Astana 010000, Kazakhstan; (M.S.); (A.K.); (D.T.)
| | - Dilnur Tussipkan
- National Center for Biotechnology, Astana 010000, Kazakhstan; (M.S.); (A.K.); (D.T.)
| | | | - Shuga Manabayeva
- National Center for Biotechnology, Astana 010000, Kazakhstan; (M.S.); (A.K.); (D.T.)
- Faculty of Natural Sciences, L.N. Gumilyov Eurasian National University, Astana 010008, Kazakhstan
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Nakkaew A, Masjon T, Voravuthikunchai SP. Genomic and Transcriptional Profiling Analysis and Insights into Rhodomyrtone Yield in Rhodomyrtus tomentosa (Aiton) Hassk. PLANTS (BASEL, SWITZERLAND) 2023; 12:3156. [PMID: 37687402 PMCID: PMC10490526 DOI: 10.3390/plants12173156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023]
Abstract
Rhodomyrtus tomentosa is a source of a novel antibiotic, rhodomyrtone. Because of the increasing industrial demand for this compound, germplasm with a high rhodomyrtone content is the key to sustainable future cultivation. In this study, rhodomyrtone genotypes were verified using the plastid genomic region marker matK and nuclear ribosomal internal transcribed spacer ITS. These two DNA barcodes proved to be useful tools for identifying different rhodomyrtone contents via the SNP haplotypes C569T and A561G, respectively. The results were correlated with rhodomyrtone content determined via HPLC. Subsequently, R. tomentosa samples with high- and low-rhodomyrtone genotypes were collected for de novo transcriptome and gene expression analyses. A total of 83,402 unigenes were classified into 25 KOG classifications, and 74,102 annotated unigenes were obtained. Analysis of differential gene expression between samples or groups using DESeq2 revealed highly expressed levels related to rhodomyrtone content in two genotypes. semiquantitative RT-PCR further revealed that the high rhodomyrtone content in these two genotypes correlated with expression of zinc transporter protein (RtZnT). In addition, we found that expression of RtZnT resulted in increased sensitivity of R. tomentosa under ZnSO4 stress. The findings provide useful information for selection of cultivation sites to achieve high rhodomyrtone yields in R. tomentosa.
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Affiliation(s)
- Alisa Nakkaew
- Center for Genomic and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand;
- Division of Biological Science, Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Thipphanet Masjon
- Center for Genomic and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand;
- Division of Biological Science, Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Supayang Piyawan Voravuthikunchai
- Center of Antimicrobial Biomaterial Innovation-Southeast Asia, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand;
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Shah AP, Travadi T, Sharma S, Pandit R, Joshi C, Joshi M. Comprehensive analysis using DNA metabarcoding, SCAR marker based PCR assay, and HPLC unveils the adulteration in Brahmi herbal products. Mol Biol Rep 2023; 50:7605-7618. [PMID: 37532919 DOI: 10.1007/s11033-023-08653-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Brahmi is one of the important nootropic botanicals, widely sold in the market, with the name "Brahmi'' being used to describe both Bacopa monnieri and Centella asiatica species. The Brahmi herbal products market is expanding; hence, economically motivated adulteration is highly prevalent. METHODS AND RESULTS This study aimed to develop DNA-based methods, including SCAR marker-based PCR and metabarcoding, to authenticate Brahmi herbal products and compare these methods with HPLC. These methods have been validated using mock controls (in-house blended formulations). All targeted plant species in mock controls were detected successfully with all three methods, whereas, in market samples, only 22.2%, 55.6%, and 50.0% were found positive for Brahmi by PCR assay, DNA metabarcoding, and HPLC, respectively. Metabarcoding can detect the presence of non-labeled plants together with targeted species, which is an advantage over PCR assay or HPLC. CONCLUSION SCAR marker-based PCR is a rapid and cost-effective method for detecting the presence of B. monnieri and C. asiatica. However, in this study, the success rate of PCR amplification was relatively low because the primers targeted either RAPD or ITS-based SCAR markers. HPLC assay, although an alternative, was unable to detect the presence of other botanicals, just like the SCAR marker-based PCR assay. On the other hand, metabarcoding can be utilized to identify the target plants, even in very small quantities, while also providing simulated identification of other botanicals. This study successfully addressed the need for quality control of Brahmi herbal products and provided the first-time report of DNA metabarcoding for such products.
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Affiliation(s)
- Abhi P Shah
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Tasnim Travadi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Sonal Sharma
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Ramesh Pandit
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Chaitanya Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Madhvi Joshi
- Gujarat Biotechnology Research Centre (GBRC), Department of Science and Technology, Government of Gujarat, Gandhinagar, India.
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Techen N, Parveen I, Khan IA. Deoxyribonucleic Acid Barcoding for the Identification of Botanicals. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2023; 122:261-288. [PMID: 37392314 DOI: 10.1007/978-3-031-26768-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2023]
Abstract
The Natural Herbal Products industry uses botanicals or herbs as raw materials for production of herbal products or dietary supplements. Recently, the demand for natural herbal products has increased tremendously and this has led to adulteration and to counterfeit herbal products. The present chapter deals with currently used molecular methods from "simple" single genomic regions to high-throughput whole genome or transcriptome sequencing methods used in the identification of botanicals.
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Affiliation(s)
- Natascha Techen
- School of Pharmacy, National Center for Natural Product Research, The University of Mississippi, P.O. Box 1848, University, MS, 38677-1848, USA.
| | - Iffat Parveen
- School of Pharmacy, National Center for Natural Product Research, The University of Mississippi, P.O. Box 1848, University, MS, 38677-1848, USA
| | - Ikhlas A Khan
- School of Pharmacy, National Center for Natural Product Research, The University of Mississippi, P.O. Box 1848, University, MS, 38677-1848, USA
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Mahima K, Sunil Kumar KN, Rakhesh KV, Rajeswaran PS, Sharma A, Sathishkumar R. Advancements and future prospective of DNA barcodes in the herbal drug industry. Front Pharmacol 2022; 13:947512. [PMID: 36339543 PMCID: PMC9635000 DOI: 10.3389/fphar.2022.947512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/10/2022] [Indexed: 08/04/2023] Open
Abstract
Ethnopharmacological relevance: The past couple of decades have witnessed the global resurgence of medicinal plants in the field of herbal-based health care. Increased consumption of medicinal plants and their derivative products is the major cause of the adulteration issues in herbal industries. As a result, the quality of herbal products is affected by spurious and unauthorized raw materials. Recent development in molecular plant identification using DNA barcodes has become a robust methodology to identify and authenticate the adulterants in herbal samples. Hence, rapid and accurate identification of medicinal plants is the key to success for the herbal industry. Aim of the study: This paper provides a comprehensive review of the application of DNA barcoding and advanced technologies that have emerged over the past 10 years related to medicinal plant identification and authentication and the future prospects of this technology. Materials and methods: Information on DNA barcodes was compiled from scientific databases (Google Scholar, Web of Science, SciFinder and PubMed). Additional information was obtained from books, Ph.D. thesis and MSc. Dissertations. Results: Working out an appropriate DNA barcode for plants is challenging; the single locus-based DNA barcodes (rbcL, ITS, ITS2, matK, rpoB, rpoC, trnH-psbA) to multi-locus DNA barcodes have become the successful species-level identification among herbal plants. Additionally, multi-loci have become efficient in the authentication of herbal products. Emerging advances in DNA barcoding and related technologies such as next-generation sequencing, high-resolution melting curve analysis, meta barcodes and mini barcodes have paved the way for successful herbal plant/samples identification. Conclusion: DNA barcoding needs to be employed together with other techniques to check and rationally and effectively quality control the herbal drugs. It is suggested that DNA barcoding techniques combined with metabolomics, transcriptomics, and proteomics could authenticate the herbal products. The invention of simple, cost-effective and improved DNA barcoding techniques to identify herbal drugs and their associated products of medicinal value in a fool-proof manner will be the future thrust of Pharmacopoeial monograph development for herbal drugs.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
- Department of Pharmacognosy, Siddha Central Research Institute, Chennai, Tamil Nadu, India
| | | | | | | | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Santiago de Queretaro, Queretaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu, India
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Cai Y, Gao Y, Zhang Z, Liu H, Wang Y, Ma Y, Li Y, Feng S, Wang H. Development and Application of a Cultivar-Specific Sequence-Characterized Amplified Region (SCAR) Marker for the Detection of Chrysanthemum morifolium Ramat. 'Daboju'. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050604. [PMID: 35270074 PMCID: PMC8912837 DOI: 10.3390/plants11050604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 05/13/2023]
Abstract
Chrysanthemummorifolium Ramat. 'Daboju' is a C. morifolium cultivar with important ornamental and medicinal values, and is often used in the treatment of colds, blurred vision, dizziness, and itchy skin. As the morphological characteristics of C. morifolium 'Daboju' are very similar to those of other C. morifolium cultivars, they are often confused in practice. However, the medicinal value and practical use of C. morifolium depends on using the correct rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, morphologically similar C. × morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific DNA marker was developed with the aim of the rapid and accurate identification of C. morifolium 'Daboju' and its differentiation from other, similar C. morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct C. morifolium cultivars. One cultivar-specific 385-bp amplicon (named SCoT36-385), amplified only in C. morifolium 'Daboju' (and in all samples of this cultivar), was identified, cloned, and sequenced. Subsequently, a sequence-characterized amplified region (SCAR) marker (named DBJF/DBJR), generating a 360-bp amplicon, was developed from SCoT36-385 and tested for amplification in all 21 C. morifolium cultivars, ten C. morifolium 'Daboju' populations, and different simulated adulterations of 'Daboju' with other cultivars. The primers amplified the specific 360-bp-long DNA fragment in all the tested C. morifolium 'Daboju' samples but failed in the absence of 'Daboju'. The detection limit of the SCAR primer pair (DBJF/DBJR) was 100 pg of DNA extracted from C. morifolium 'Daboju'. Hence, this SCAR marker has a very high detection sensitivity, and can be used for accurate and rapid identification of C. morifolium 'Daboju'. It can play an important role in ensuring the quality of medicinal preparations and protecting C. morifolium 'Daboju' germplasm resources in breeding programs and in identifying lines generated from this cultivar.
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Affiliation(s)
- Yuchen Cai
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Yadi Gao
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhenhao Zhang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
| | - Huijie Liu
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yifan Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yuxin Ma
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Yixin Li
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
| | - Shangguo Feng
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
- Correspondence: (S.F.); (H.W.)
| | - Huizhong Wang
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou 310036, China; (Y.C.); (Y.G.); (Z.Z.); (H.L.); (Y.W.); (Y.M.); (Y.L.)
- Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou 310036, China
- Correspondence: (S.F.); (H.W.)
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