1
|
Balaji R, Parani M. Development of an allele-specific PCR (AS-PCR) method for identifying high-methyl eugenol-containing purple Tulsi (Ocimum tenuiflorum L.) in market samples. Mol Biol Rep 2024; 51:439. [PMID: 38520476 DOI: 10.1007/s11033-024-09365-0] [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: 01/14/2024] [Accepted: 02/19/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Ocimum tenuiflorum L. is a highly traded medicinal with several therapeutic values. Green Tulsi and purple Tulsi are two subtypes in O. tenuiflorum and both have the same medicinal properties. Recent reports have revealed that purple Tulsi contains higher quantities of methyl eugenol (ME), which is moderately toxic and potentially carcinogenic. Therefore, we developed an allele-specific PCR (AS-PCR) method to distinguish the green and purple Tulsi. METHODS AND RESULT Using the green Tulsi as a reference, 12 single nucleotide polymorphisms (SNPs) and 10 insertions/deletions (InDels) were identified in the chloroplast genome of the purple Tulsi. The C > T SNP at the 1,26,029 position in the ycf1 gene was selected for the development of the AS-PCR method. The primers were designed to amplify 521 bp and 291 bp fragments specific to green and purple Tulsi, respectively. This AS-PCR method was validated in 10 accessions from each subtype and subsequently verified using Sanger sequencing. Subsequently, 30 Tulsi powder samples collected from the market were subjected to molecular identification by AS-PCR. The results showed that 80% of the samples were purple Tulsi, and only 3.5% were green Tulsi. About 10% of the samples were a mixture of both green and purple Tulsi. Two samples (6.5%) did not contain O. tenuiflorum and were identified as O. gratissimum. CONCLUSION The market samples of Tulsi were predominantly derived from purple Tulsi. The AS-PCR method will be helpful for quality control and market surveillance of Tulsi herbal powders.
Collapse
Affiliation(s)
- Raju Balaji
- Department of Genetic Engineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, TN, 603203, India
| | - Madasamy Parani
- Department of Genetic Engineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Kanchipuram, Chennai, TN, 603203, India.
| |
Collapse
|
2
|
Paschalidis K, Fanourakis D, Tsaniklidis G, Tsichlas I, Tzanakakis VA, Bilias F, Samara E, Ipsilantis I, Grigoriadou K, Samartza I, Matsi T, Tsoktouridis G, Krigas N. DNA Barcoding and Fertilization Strategies in Sideritis syriaca subsp. syriaca, a Local Endemic Plant of Crete with High Medicinal Value. Int J Mol Sci 2024; 25:1891. [PMID: 38339166 PMCID: PMC10856587 DOI: 10.3390/ijms25031891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Herein, we applied DNA barcoding for the genetic characterization of Sideritis syriaca subsp. syriaca (Lamiaceae; threatened local Cretan endemic plant) using seven molecular markers of cpDNA. Five fertilization schemes were evaluated comparatively in a pilot cultivation in Crete. Conventional inorganic fertilizers (ChFs), integrated nutrient management (INM) fertilizers, and two biostimulants were utilized (foliar and soil application). Plant growth, leaf chlorophyll fluorescence, and color were assessed and leaf content of chlorophyll, key antioxidants (carotenoids, flavonoids, phenols), and nutrients were evaluated. Fertilization schemes induced distinct differences in leaf shape, altering quality characteristics. INM-foliar and ChF-soil application promoted yield, without affecting tissue water content or biomass partitioning to inflorescences. ChF-foliar application was the most stimulatory treatment when the primary target was enhanced antioxidant contents while INM-biostimulant was the least effective one. However, when the primary target is yield, INM, especially by foliar application, and ChF, by soil application, ought to be employed. New DNA sequence datasets for the plastid regions of petB/petD, rpoC1, psbK-psbI, and atpF/atpH were deposited in the GenBank for S. syriaca subsp. syriaca while the molecular markers rbcL, trnL/trnF, and psbA/trnH were compared to those of another 15 Sideritis species retrieved from the GenBank, constructing a phylogenetic tree to show their genetic relatedness.
Collapse
Affiliation(s)
- Konstantinos Paschalidis
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, 71410 Heraklion, Greece; (D.F.); (I.T.); (V.A.T.)
| | - Dimitrios Fanourakis
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, 71410 Heraklion, Greece; (D.F.); (I.T.); (V.A.T.)
| | - Georgios Tsaniklidis
- Hellenic Agricultural Organization (ELGO-DIMITRA), Institute of Olive Tree, Subtropical Crops and Viticulture, 73134 Chania, Greece;
| | - Ioannis Tsichlas
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, 71410 Heraklion, Greece; (D.F.); (I.T.); (V.A.T.)
| | - Vasileios A. Tzanakakis
- Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, 71410 Heraklion, Greece; (D.F.); (I.T.); (V.A.T.)
| | - Fotis Bilias
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.B.); (I.I.); (T.M.)
| | - Eftihia Samara
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.B.); (I.I.); (T.M.)
| | - Ioannis Ipsilantis
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.B.); (I.I.); (T.M.)
| | - Katerina Grigoriadou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, 57001 Thessaloniki, Greece; (K.G.); (I.S.); (N.K.)
| | - Ioulietta Samartza
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, 57001 Thessaloniki, Greece; (K.G.); (I.S.); (N.K.)
| | - Theodora Matsi
- Soil Science Laboratory, School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (F.B.); (I.I.); (T.M.)
| | - Georgios Tsoktouridis
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, 57001 Thessaloniki, Greece; (K.G.); (I.S.); (N.K.)
- Theofrastos Fertilizers, Industrial Area of Korinthos, Irinis & Filias, Ikismos Arion, Examilia, 20100 Korinthos, Greece
| | - Nikos Krigas
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, 57001 Thessaloniki, Greece; (K.G.); (I.S.); (N.K.)
| |
Collapse
|
3
|
Jiang Z, Zhang M, Kong L, Bao Y, Ren W, Li H, Liu X, Wang Z, Ma W. Identification of Apiaceae using ITS, ITS2 and psba-trnH barcodes. Mol Biol Rep 2023; 50:245-253. [PMID: 36329337 DOI: 10.1007/s11033-022-07909-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/19/2022] [Accepted: 08/31/2022] [Indexed: 11/06/2022]
Abstract
Apiaceae plants are used as medicinal herbs, pesticides, spices, and vegetables; thus, accurately identifying Apiaceae species is important. The grassland ecosystem of Heilongjiang Province in northern China has huge reserves of wild Apiaceae plants, but few reports have systematically documented their diversity. In this study, 275 Apiaceae plants of 23 species in 18 genera were collected from this area. We identified Apiaceae species by using nuclear internal transcribed spacer (ITS/ITS2) and psbA-trnH (chloroplast non-coding region) sequences based on experimental data. The identification efficiency of ITS, ITS2 and psbA-trnH sequences was determined and evaluated by sequence alignment and analysis, intraspecific and interspecific genetic distance analyses, and phylogenetic tree construction. ITS, ITS2 could distinguish 21 species from 17 genera of Apiaceae with good identification effect. When identifying species in the Apiaceae family, ITS2 can be used as the core barcode and psbA-trnH can be used as the supplementary barcode. These results can enrich the reference Apiaceae DNA barcode database.
Collapse
Affiliation(s)
- Zhehui Jiang
- School of forestry, Northeast Forestry University, 150040, Harbin, China
| | - Meiqi Zhang
- School of forestry, Northeast Forestry University, 150040, Harbin, China
| | - Lingyang Kong
- Pharmacy of College, Heilongjiang University of Chinese Medicine, 150040, Harbin, China
| | - Yihong Bao
- School of forestry, Northeast Forestry University, 150040, Harbin, China
| | - Weichao Ren
- Pharmacy of College, Heilongjiang University of Chinese Medicine, 150040, Harbin, China
| | - Hongyuan Li
- Pharmacy of College, Heilongjiang University of Chinese Medicine, 150040, Harbin, China
| | - Xiubo Liu
- College of Jiamusi, Heilongjiang University of Chinese Medicine, 154007, Jiamusi, China
| | - Zhen Wang
- Pharmacy of College, Heilongjiang University of Chinese Medicine, 150040, Harbin, China.
| | - Wei Ma
- School of forestry, Northeast Forestry University, 150040, Harbin, China. .,Pharmacy of College, Heilongjiang University of Chinese Medicine, 150040, Harbin, China.
| |
Collapse
|
4
|
Aneva I, Zhelev P, Bonchev G. Sideritis elica, a New Species of Lamiaceae from Bulgaria, Revealed by Morphology and Molecular Phylogeny. PLANTS (BASEL, SWITZERLAND) 2022; 11:2900. [PMID: 36365353 PMCID: PMC9654456 DOI: 10.3390/plants11212900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/22/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
Sideritis elica, from the Rhodope Mountains, is described as a species new to science. Results of a detailed morphological analysis were combined with the data of molecular analyses using DNA barcoding as an efficient tool for the genetic, taxonomic identification of plants. The combination of morphological features distinguishes the new species well: Its first three uppermost leaf pairs are significantly shorter and wider, the branchiness of the stems is much more frequent, the whole plant is much more lanate, and it looks almost white, as opposed to the other closed species of section Empedoclia, which look grayish green. The molecular analysis, based on the rbcL and trnH-psbA regions, supports the morphological data about the divergence of Sideritis scardica and Sideritis elica. The studied populations of the two taxa were found to be genetically distant (up to 6.8% polymorphism for trnH-psbA) with distinct population-specific nucleotide patterns, while no polymorphism in the DNA barcodes was detected within the Sideritis elica population. The results confirm the existence of a new species called Sideritis elica, which occurs in the nature reserve Chervenata Stena, located in the northern part of the Central Rhodope Mountains. There were only 12 individuals found in the locality, which underlines the necessity of conservation measures.
Collapse
Affiliation(s)
- Ina Aneva
- Bulgarian Academy of Sciences, 1, 15 November Str., 1040 Sofia, Bulgaria
| | - Petar Zhelev
- Department of Dendrology, University of Forestry, 10 Kliment Ohridski Blvd., 1797 Sofia, Bulgaria
| | - Georgi Bonchev
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 21, 1113 Sofia, Bulgaria
| |
Collapse
|
5
|
Petrova D, Gašić U, Yocheva L, Hinkov A, Yordanova Z, Chaneva G, Mantovska D, Paunov M, Ivanova L, Rogova M, Shishkova K, Todorov D, Tosheva A, Kapchina-Toteva V, Vassileva V, Atanassov A, Mišić D, Bonchev G, Zhiponova M. Catmint ( Nepeta nuda L.) Phylogenetics and Metabolic Responses in Variable Growth Conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:866777. [PMID: 35651766 PMCID: PMC9150856 DOI: 10.3389/fpls.2022.866777] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Nepeta nuda (catmint; Lamiaceae) is a perennial medicinal plant with a wide geographic distribution in Europe and Asia. This study first characterized the taxonomic position of N. nuda using DNA barcoding technology. Since medicinal plants are rich in secondary metabolites contributing to their adaptive immune response, we explored the N. nuda metabolic adjustment operating under variable environments. Through comparative analysis of wild-grown and in vitro cultivated plants, we assessed the change in phenolic and iridoid compounds, and the associated immune activities. The wild-grown plants from different Bulgarian locations contained variable amounts of phenolic compounds manifested by a general increase in flowers, as compared to leaves, while a strong reduction was observed in the in vitro plants. A similar trend was noted for the antioxidant and anti-herpesvirus activity of the extracts. The antimicrobial potential, however, was very similar, regardless the growth conditions. Analysis of the N. nuda extracts led to identification of 63 compounds including phenolic acids and derivatives, flavonoids, and iridoids. Quantification of the content of 21 target compounds indicated their general reduction in the extracts from in vitro plants, and only the ferulic acid (FA) was specifically increased. Cultivation of in vitro plants under different light quality and intensity indicated that these variable light conditions altered the content of bioactive compounds, such as aesculin, FA, rosmarinic acid, cirsimaritin, naringenin, rutin, isoquercetin, epideoxyloganic acid, chlorogenic acid. Thus, this study generated novel information on the regulation of N. nuda productivity using light and other cultivation conditions, which could be exploited for biotechnological purposes.
Collapse
Affiliation(s)
- Detelina Petrova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Uroš Gašić
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Lyubomira Yocheva
- Department of Biology, Medical Genetics and Microbiology, Faculty of Medicine, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Anton Hinkov
- Laboratory of Virology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Zhenya Yordanova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Ganka Chaneva
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Desislava Mantovska
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Momchil Paunov
- Department of Biophysics and Radiobiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Lyubomira Ivanova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Mariya Rogova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Kalina Shishkova
- Laboratory of Virology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Daniel Todorov
- Laboratory of Virology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Anita Tosheva
- Department of Botany, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Veneta Kapchina-Toteva
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Danijela Mišić
- Department of Plant Physiology, Institute for Biological Research “Siniša Stanković”—National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Georgi Bonchev
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Miroslava Zhiponova
- Department of Plant Physiology, Faculty of Biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| |
Collapse
|
6
|
DNA Barcodes for Accurate Identification of Selected Medicinal Plants (Caryophyllales): Toward Barcoding Flowering Plants of the United Arab Emirates. DIVERSITY 2022. [DOI: 10.3390/d14040262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The need for herbal medicinal plants is steadily increasing. Hence, the accurate identification of plant material has become vital for safe usage, avoiding adulteration, and medicinal plant trading. DNA barcoding has shown to be a valuable molecular identification tool for medicinal plants, ensuring the safety and efficacy of plant materials of therapeutic significance. Using morphological characters in genera with closely related species, species delimitation is often difficult. Here, we evaluated the capability of the nuclear barcode ITS2 and plastid DNA barcodes rbcL and matK to identify 20 medicinally important plant species of Caryophyllales. In our analysis, we applied an integrative approach for species discrimination using pairwise distance-based unsupervised operational taxonomic unit “OTU picking” methods, viz., ABGD (Automated Barcode Gap Analysis) and ASAP (Assemble Species by Automatic Partitioning). Along with the unsupervised OTU picking methods, Supervised Machine Learning methods (SML) were also implemented to recognize divergent taxa. Our results indicated that ITS2 was more successful in distinguishing between examined species, implying that it could be used to detect the contamination and adulteration of these medicinally important plants. Moreover, this study suggests that the combination of more than one method could assist in the resolution of morphologically similar or closely related taxa.
Collapse
|
7
|
Philippe F, Dubrulle N, Marteaux B, Bonnet B, Choisy P, Berthon J, Garnier L, Leconte N, Milesi S, Morvan P, Saunois A, Sun J, Weber S, Giraud N. Combining DNA Barcoding and Chemical fingerprints to authenticate Lavender raw material. Int J Cosmet Sci 2022; 44:91-102. [PMID: 34860432 PMCID: PMC9305429 DOI: 10.1111/ics.12757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/19/2021] [Accepted: 12/01/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE This study was initiated and conducted by several laboratories, 3 of the main cosmetic ingredient suppliers and 4 brands of cosmetics in France. Its objective is to show the interest and robustness of coupling chemical and genetic analyses in the identification of plant species. In this study, the Lavandula genus was used. METHODS In this study, we used two analytical methods. Chemical analysis from UHPLC (ultra-high-performance liquid chromatography) and genetic analysis from barcoding with genetic markers. RESULTS Eleven lavender species were selected (botanically authenticated) and analysed. The results show that three chemical compounds (coumaric acid hexoside, ferulic acid hexoside and rosmarinic acid) and three genetic markers (RbcL, trnH-psbA and ITS) are of interest for the differentiation of species of the genus lavandula. CONCLUSION The results show that the combination of complementary analytical methods is a relevant system to prove the botanical identification of lavender species. This first study, carried out on a plant of interest for cosmetics, demonstrates the need for authentication using a tool combining genetic and chemical analysis as an advance over traditional investigation methods used alone, in terms of identification and authentication reliability.
Collapse
Affiliation(s)
| | - Nelly Dubrulle
- DNA Gensee17 rue du lac saint andréLe Bourget du Lac73370France
| | | | | | | | | | | | | | | | | | | | - Jian‐Sheng Sun
- Structure et Instabilite des GénomesMuséum national d’Histoire naturelleCNRSINSERM43 rue CuvierParis75005France
| | | | - Nicole Giraud
- DNA Gensee17 rue du lac saint andréLe Bourget du Lac73370France
| |
Collapse
|
8
|
Facilitating Conservation and Bridging Gaps for the Sustainable Exploitation of the Tunisian Local Endemic Plant Marrubium aschersonii (Lamiaceae). SUSTAINABILITY 2022. [DOI: 10.3390/su14031637] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
In the frame of conservation and sustainable utilization of neglected and underutilized phytogenetic resources, this study produced for the first time a detailed ecological profiling for the local Tunisian endemic Marrubium ascheronii (Lamiaceae) using Geographical Information Systems and open-source data. This profile was used to illustrate the abiotic environmental conditions of its wild habitats; the profile facilitated the examination of the effect of temperature on its seed germination and may inform species-specific guidelines for its cultivation in man-made environments. With effective seed propagation firstly reported herein (68.75% at 20 °C), species-specific in situ conservation efforts and ex situ conservation or sustainable exploitation strategies were enabled for M. aschersonii. The first-reported molecular authentication (DNA barcoding) of M. aschersonii may facilitate its traceability, allowing for product design. This study also reports for the first time the effects of chemical and integrated nutrient management (INM) fertilizers on the growth and pilot cultivation of M. aschersonii seedlings, with the latter being advantageous. This multidisciplinary approach has bridged important research gaps that hindered the conservation efforts and/or the sustainable exploitation for this local endemic plant of Tunisia. Based on all the above, we re-evaluated and updated the feasibility and readiness timescale for sustainable exploitation of M. aschersonii in the medicinal-cosmetic, agro-alimentary and ornamental-horticultural sectors.
Collapse
|
9
|
DNA Barcoding Study of Representative Thymus Species in Bulgaria. PLANTS 2022; 11:plants11030270. [PMID: 35161250 PMCID: PMC8840554 DOI: 10.3390/plants11030270] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/11/2022] [Accepted: 01/15/2022] [Indexed: 11/28/2022]
Abstract
We present a study on the taxonomy of eleven Thymus species, belonging to two sections and occurring naturally in Bulgaria. Four DNA barcoding markers—matK, rbcL, trnH-psbA and ITS—were applied to discriminate the species and to reveal their phylogenetic relationships. The results showed that rbcL has the lowest discriminating power regarding the studied species, while the other markers yielded results fitting better to the existing taxonomic schemes based on morphological traits. However, even in the case of better performing markers, the results were not straightforward—morphologically distinct species belonging to different sections were grouped together, and closely related species appeared genetically distinct. The results are typical for taxonomically complex groups, such as the genus Thymus, characterized in Bulgaria with great diversity, high percentage of endemism and still requiring a full and comprehensive taxonomic study. The results are discussed in the light of unresolved taxonomic problems and application of DNA barcoding methods.
Collapse
|
10
|
Nazar N, Howard C, Slater A, Sgamma T. Challenges in Medicinal and Aromatic Plants DNA Barcoding-Lessons from the Lamiaceae. PLANTS (BASEL, SWITZERLAND) 2022; 11:137. [PMID: 35009140 PMCID: PMC8747715 DOI: 10.3390/plants11010137] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
The potential value of DNA barcoding for the identification of medicinal plants and authentication of traded plant materials has been widely recognized; however, a number of challenges remain before DNA methods are fully accepted as an essential quality control method by industry and regulatory authorities. The successes and limitations of conventional DNA barcoding are considered in relation to important members of the Lamiaceae. The mint family (Lamiaceae) contains over one thousand species recorded as having a medicinal use, with many more exploited in food and cosmetics for their aromatic properties. The family is characterized by a diversity of secondary products, most notably the essential oils (EOs) produced in external glandular structures on the aerial parts of the plant that typify well-known plants of the basil (Ocimum), lavender (Lavandula), mint (Mentha), thyme (Thymus), sage (Salvia) and related genera. This complex, species-rich family includes widely cultivated commercial hybrids and endangered wild-harvested traditional medicines, and examples of potential toxic adulterants within the family are explored in detail. The opportunities provided by next generation sequencing technologies to whole plastome barcoding and nuclear genome sequencing are also discussed with relevant examples.
Collapse
Affiliation(s)
- Nazia Nazar
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
| | - Caroline Howard
- Tree of Life Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK;
| | - Adrian Slater
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
| | - Tiziana Sgamma
- Biomolecular Technology Group, Leicester School of Allied Health Science, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK;
| |
Collapse
|
11
|
Pyrka I, Stefanaki A, Vlachonasios KE. DNA Barcoding of St. John's wort (Hypericum spp.) Growing Wild in North-Eastern Greece. PLANTA MEDICA 2021; 87:528-537. [PMID: 33618378 DOI: 10.1055/a-1379-3249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plants of the genus Hypericum, commonly known as "St. John's wort" ("spathohorto" or "valsamo" in Greek), have been used since antiquity for their therapeutic properties. Wild-harvested Hypericum plants are still popular today in herbal medicines, commercially exploited due to their bioactive compounds, hypericin and hyperforin, which have antidepressant, antimicrobial and antiviral activity. Species identification of commercial products is therefore important and DNA barcoding, a molecular method that uses small sequences of organisms' genome as barcodes, can be useful in this direction. In this study, we collected plants of the genus Hypericum that grow wild in North-Eastern Greece and explored the efficiency of matK, and trnH-psbA regions as DNA barcodes for their identification. We focused on 5 taxa, namely H. aucheri, H. montbretii, H. olympicum, H. perforatum subsp. perforatum, and H. thasium, the latter a rare Balkan endemic species collected for the first time from mainland Greece. matK (using the genus-specific primers designed herein), trnH-psbA, and their combination were effectively used for the identification of the 5 Hypericum taxa and the discrimination of different H. perforatum subsp. perforatum populations. These barcodes were also able to discriminate Greek populations of H. perforatum, H. aucheri, H. montbretii, and H. olympicum from populations of the same species growing in other countries.
Collapse
Affiliation(s)
- Ioanna Pyrka
- Postgraduate Studies Program, Conservation of Biodiversity and Sustainable Exploitation of Native Plants (BNP), School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Konstantinos E Vlachonasios
- Postgraduate Studies Program, Conservation of Biodiversity and Sustainable Exploitation of Native Plants (BNP), School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Botany, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Natural Products Research Centre of Excellence (NatPro-AUTh), Center of Interdisciplinary Research and Innovation of Aristotle University of Thessaloniki (CIRI-AUTh), Thessaloniki, Greece
| |
Collapse
|
12
|
Thakur VV, Tripathi N, Tiwari S. DNA barcoding of some medicinally important plant species of Lamiaceae family in India. Mol Biol Rep 2021; 48:3097-3106. [PMID: 33913093 DOI: 10.1007/s11033-021-06356-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/16/2021] [Indexed: 11/24/2022]
Abstract
Several species of the Lamiaceae family are the primary source of bioactive aromatic oils and secondary metabolites, having broader applications in the cosmetics, pharmaceuticals, food, confectionery and liquor industries. Due to the scarcity of raw materials and high costs of this family's economically vital species, its products often adulterated to cater to the market's high demand. The present study provides a DNA based approach for identifying different species of this family. Henceforth, the performance of three already proposed barcode loci (matK, trnH-psbA and trnL) was examined for their PCR amplification and species recognition efficacy on various Lamiaceae species and cultivars using three different approaches such as pairwise genetic distance method, BLASTn and phylogenetic tree based on maximum likelihood (ML) analysis. Results illustrate that among all the DNA barcoding loci, matK locus can accurately and efficiently distinguish all the studied species followed by trnH-psbA and trnL. Present investigation may help diminish the illegal trade and events of adulteration of medicinally important plants species in genus Mentha, Ocimum and Plectranthus. This investigation will also help fulfil the scarcity of sequences of barcode loci of these species in the NCBI database. Apart from providing a molecular level reference for identifying processed herbal products, this technique also offers a convenient method for species identification and germplasm conservation of the Lamiaceae family.
Collapse
Affiliation(s)
- Vishwa V Thakur
- Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, 482004, India.,Lac Production Division, ICAR-Indian Institute of Natural Resins and Gums, Namkum, Ranchi, Jharkhand, 834010, India
| | - Niraj Tripathi
- Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, 482004, India
| | - Sharad Tiwari
- Biotechnology Centre, Jawaharlal Nehru Agriculture University, Jabalpur, 482004, India.
| |
Collapse
|
13
|
Heylen OCG, Debortoli N, Marescaux J, Olofsson JK. A Revised Phylogeny of the Mentha spicata Clade Reveals Cryptic Species. PLANTS (BASEL, SWITZERLAND) 2021; 10:819. [PMID: 33924227 PMCID: PMC8074783 DOI: 10.3390/plants10040819] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/30/2021] [Accepted: 04/18/2021] [Indexed: 05/29/2023]
Abstract
The genus Mentha is taxonomically and phylogenetically challenging due to complex genomes, polyploidization and an extensive historical nomenclature, potentially hiding cryptic taxa. A straightforward interpretation of phylogenetic relationships within the section Mentha is further hindered by dominant but outdated concepts on historically identified hybrid taxa. Mentha spicata is traditionally considered to be of hybrid origin, but the evidence for this is weak. Here, we aim to understand the phylogenetic relationships within the section Mentha using large sample sizes and to revisit the hybrid status and identity of M. spicata. We show that two of three traditional species in the subsection Spicatae are polyphyletic, as is the subsection as a whole, while the real number of cryptic species was underestimated. Compared to previous studies we present a fundamentally different phylogeny, with a basal split between M. spicata s.s. and M. longifolia s.s. Cluster analyses of morphological and genotypic data demonstrate that there is a dissociation between morphologically and genotypically defined groups of samples. We did not find any evidence that M. spicata is of hybrid origin, and we conclude its taxonomic status should be revised. The combination of genetic and phenotypic information is essential when evaluating hyperdiverse taxonomic groups.
Collapse
Affiliation(s)
| | | | | | - Jill K. Olofsson
- Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, bygning 7, DK-1353 Copenhagen, Denmark;
| |
Collapse
|
14
|
Junren C, Xiaofang X, Mengting L, Qiuyun X, Gangmin L, Huiqiong Z, Guanru C, Xin X, Yanpeng Y, Fu P, Cheng P. Pharmacological activities and mechanisms of action of Pogostemon cablin Benth: a review. Chin Med 2021; 16:5. [PMID: 33413544 PMCID: PMC7791836 DOI: 10.1186/s13020-020-00413-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/18/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
Patchouli ("Guanghuoxiang") or scientifically known as Pogostemon cablin Benth, belonging to the family Lamiaceae, has been used in traditional Chinse medicine (TCM) since the time of the Eastern Han dynasty. In TCM theory, patchouli can treat colds, nausea, fever, headache, and diarrhea. Various bioactive compounds have been identified in patchouli, including terpenoids, phytosterols, flavonoids, organic acids, lignins, glycosides, alcohols, pyrone, and aldehydes. Among the numerous compounds, patchouli alcohol, β-patchoulene, patchoulene epoxide, pogostone, and pachypodol are of great importance. The pharmacological impacts of these compounds include anti-peptic ulcer effect, antimicrobial effect, anti-oxidative effect, anti-inflammatory effect, effect on ischemia/reperfusion injury, analgesic effect, antitumor effect, antidiabetic effect, anti-hypertensive effect, immunoregulatory effect, and others.For this review, we examined publications from the previous five years collected from PubMed, Web of Science, Springer, and the Chinese National Knowledge Infrastructure databases. This review summarizes the recent progress in phytochemistry, pharmacology, and mechanisms of action and provides a reference for future studies focused on clinical applications of this important plant extract.
Collapse
Affiliation(s)
- Chen Junren
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Xie Xiaofang
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Li Mengting
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Xiong Qiuyun
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Li Gangmin
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Zhang Huiqiong
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Chen Guanru
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Xu Xin
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Yin Yanpeng
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China
| | - Peng Fu
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China.
- West China School of Pharmacy, Sichuan University, 17 South Renmin Rd, 610065, Chengdu, China.
| | - Peng Cheng
- Chengdu University of Traditional Chinese Medicine, Chengdu, 610075, China.
- State Key Laboratory of Traditional Chinese Medicine Resources in Southwest China, Chengdu, 610075, China.
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, 37 Shierqiao Road, Jinniu District, Chengdu, 611137, China.
| |
Collapse
|
15
|
Kumar A, Rodrigues V, Baskaran K, Shukla AK, Sundaresan V. DNA barcode based species-specific marker for Ocimum tenuiflorum and its applicability in quantification of adulteration in herbal formulations using qPCR. J Herb Med 2020. [DOI: 10.1016/j.hermed.2020.100376] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
16
|
DNA barcodes for delineating Clerodendrum species of North East India. Sci Rep 2020; 10:13490. [PMID: 32778674 PMCID: PMC7417596 DOI: 10.1038/s41598-020-70405-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/06/2020] [Indexed: 01/06/2023] Open
Abstract
The diversified genus of Clerodendrum with its complex evolutionary history leads to taxonomic mystification. Unlike traditional taxonomic methods, DNA barcoding could be a promising tool for the identification and conservation of Clerodendrum species. This study was attempted to develop an efficient barcode locus in Clerodendrum species of North East India. We evaluated four barcode candidates (ITS2, matK, rbcL, ycf1) and its combinations in different Clerodendrum species. The reliability of barcodes to distinguish the species were calculated using genetic pairwise distances, intra- and inter-specific diversity, barcode gap, and phylogenetic tree-based methods. The results exemplify that matK posse’s maximum number of variables and parsimony-informative sites (103/100), intra- (0.021 ± 0.001) and inter- (0.086 ± 0.005) specific divergences and species resolution rate (89.1%) followed by ITS2, ycf1, and rbcL. Among the combinatorial locus, ITS2 + matK showed the best species discrimination with distinctive barcode gaps. Therefore, we tentatively suggest that the combination of ITS2 + matK as core barcode for Clerodendrum and converted into quick response (QR) code. Hence, this finding indicates that DNA barcoding could provide consistent resources for species discrimination and resolve taxonomic controversies of the genus as well as set a preliminary assessment toward its biodiversity.
Collapse
|
17
|
Li S, Qian X, Zheng Z, Shi M, Chang X, Li X, Liu J, Tu T, Zhang D. DNA barcoding the flowering plants from the tropical coral islands of Xisha (China). Ecol Evol 2018; 8:10587-10593. [PMID: 30464830 PMCID: PMC6238132 DOI: 10.1002/ece3.4545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/19/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
AIM DNA barcoding has been widely applied to species diversity assessment in various ecosystems, including temperate forests, subtropical forests, and tropical rain forests. However, tropical coral islands have never been barcoded before due to the difficulties in field exploring. This study aims at barcoding the flowering plants from a unique ecosystem of the tropical coral islands in the Pacific Ocean and supplying valuable evolutionary information for better understanding plant community assembly of those particular islands in the future. LOCATION Xisha Islands, China. METHODS This study built a DNA barcode database for 155 plant species from the Xisha Islands using three DNA markers (ITS, rbcL, and matK). We applied the sequence similarity method and a phylogenetic-based method to assess the barcoding resolution. RESULTS All the three DNA barcodes showed high levels of PCR success (96%-99%) and sequencing success (98%-100%). ITS performed the highest rate of species resolution (>95%) among the three markers, while plastid markers delivered a relatively poor species resolution (85%-90%). Our analyses obtained a marginal increase in species resolution when combining the three DNA barcodes. MAIN CONCLUSIONS This study provides the first plant DNA barcode data for the unique ecosystem of tropical coral islands and considerably supplements the DNA barcode library for the flowering plants on the oceanic islands. Based on the PCR and sequencing success rates, and the discriminatory power of the three DNA regions, we recommend ITS as the most successful DNA barcode to identify the flowering plants from Xisha Islands. Due to its high sequence variation and low fungal contamination, ITS could be a preferable candidate of DNA barcode for plants from other tropical coral islands as well. Our results also shed lights on the importance of biodiversity conservation of tropical coral islands.
Collapse
Affiliation(s)
- Shengchun Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zexin Zheng
- South China Agricultural UniversityGuangzhouChina
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Xiaoyu Chang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Xiaojuan Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Junfang Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tieyao Tu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| |
Collapse
|
18
|
Hind KR, Adal AM, Upson TM, Mahmoud SS. An assessment of plant DNA barcodes for the identification of cultivated Lavandula (Lamiaceae) taxa. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.09.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
19
|
Stefanaki A, Cook CM, Lanaras T, Kokkini S. Essential oil variation of Thymbra spicata L. (Lamiaceae), an East Mediterranean “oregano” herb. BIOCHEM SYST ECOL 2018. [DOI: 10.1016/j.bse.2018.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
20
|
Hosein FN, Austin N, Maharaj S, Johnson W, Rostant L, Ramdass AC, Rampersad SN. Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad. Ecol Evol 2017; 7:7311-7333. [PMID: 28944019 PMCID: PMC5606854 DOI: 10.1002/ece3.3220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 05/17/2017] [Accepted: 06/12/2017] [Indexed: 02/06/2023] Open
Abstract
The islands of the Caribbean are considered to be a "biodiversity hotspot." Collectively, a high level of endemism for several plant groups has been reported for this region. Biodiversity conservation should, in part, be informed by taxonomy, population status, and distribution of flora. One taxonomic impediment to species inventory and management is correct identification as conventional morphology-based assessment is subject to several caveats. DNA barcoding can be a useful tool to quickly and accurately identify species and has the potential to prompt the discovery of new species. In this study, the ability of DNA barcoding to confirm the identities of 14 endangered endemic vascular plant species in Trinidad was assessed using three DNA barcodes (matK, rbcL, and rpoC1). Herbarium identifications were previously made for all species under study. matK, rbcL, and rpoC1 markers were successful in amplifying target regions for seven of the 14 species. rpoC1 sequences required extensive editing and were unusable. rbcL primers resulted in cleanest reads, however, matK appeared to be superior to rbcL based on a number of parameters assessed including level of DNA polymorphism in the sequences, genetic distance, reference library coverage based on BLASTN statistics, direct sequence comparisons within "best match" and "best close match" criteria, and finally, degree of clustering with moderate to strong bootstrap support (>60%) in neighbor-joining tree-based comparisons. The performance of both markers seemed to be species-specific based on the parameters examined. Overall, the Trinidad sequences were accurately identified to the genus level for all endemic plant species successfully amplified and sequenced using both matK and rbcL markers. DNA barcoding can contribute to taxonomic and biodiversity research and will complement efforts to select taxa for various molecular ecology and population genetics studies.
Collapse
Affiliation(s)
- Fazeeda N. Hosein
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Nigel Austin
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Shobha Maharaj
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Winston Johnson
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Luke Rostant
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Amanda C. Ramdass
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| | - Sephra N. Rampersad
- Faculty of Science and TechnologyDepartment of Life SciencesThe University of the West IndiesSt. AugustineTrinidad and Tobago – West Indies
| |
Collapse
|
21
|
O. Elansary H, Ashfaq M, Ali HM, Yessoufou K. The first initiative of DNA barcoding of ornamental plants from Egypt and potential applications in horticulture industry. PLoS One 2017; 12:e0172170. [PMID: 28199378 PMCID: PMC5310869 DOI: 10.1371/journal.pone.0172170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 01/31/2017] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding relies on short and standardized gene regions to identify species. The agricultural and horticultural applications of barcoding such as for marketplace regulation and copyright protection remain poorly explored. This study examines the effectiveness of the standard plant barcode markers (matK and rbcL) for the identification of plant species in private and public nurseries in northern Egypt. These two markers were sequenced from 225 specimens of 161 species and 62 plant families of horticultural importance. The sequence recovery was similar for rbcL (96.4%) and matK (84%), but the number of specimens assigned correctly to the respective genera and species was lower for rbcL (75% and 29%) than matK (85% and 40%). The combination of rbcL and matK brought the number of correct generic and species assignments to 83.4% and 40%, respectively. Individually, the efficiency of both markers varied among different plant families; for example, all palm specimens (Arecaceae) were correctly assigned to species while only one individual of Asteraceae was correctly assigned to species. Further, barcodes reliably assigned ornamental horticultural and medicinal plants correctly to genus while they showed a lower or no success in assigning these plants to species and cultivars. For future, we recommend the combination of a complementary barcode (e.g. ITS or trnH-psbA) with rbcL + matK to increase the performance of taxa identification. By aiding species identification of horticultural crops and ornamental palms, the analysis of the barcode regions will have large impact on horticultural industry.
Collapse
Affiliation(s)
- Hosam O. Elansary
- Floriculture, Ornamental Horticulture and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
- * E-mail: ,
| | - Muhammad Ashfaq
- Biodiversity Institute of Ontario, University of Guelph, ON, Guelph, Canada
| | - Hayssam M. Ali
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Timber Trees Research Department, Sabahia Horticulture Research Station, Horticulture Research Institute, Agriculture Research Center, Alexandria, Egypt
| | - Kowiyou Yessoufou
- Department of Geography, Environmental Management and Energy Studies, University of Johannesburg, APK campus, Johannesburg, South Africa
| |
Collapse
|
22
|
Li J, Wang Y, Jin H, Li W, Yan C, Yan P, Zhang X, He S, Song Z. Identification of Triplophysa species from the Qinghai-Tibetan Plateau (QTP) and its adjacent regions through DNA barcodes. Gene 2016; 605:12-19. [PMID: 28104086 DOI: 10.1016/j.gene.2016.11.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 11/30/2016] [Indexed: 11/16/2022]
Abstract
The genus Triplophysa is the largest and most difficult to identity morphologically fish group of superfamily Cobitoidea with 140 currently valid species, and is mainly distributed in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. Most species within this genus possess highly similar morphological characteristics for adaption to the highland environment and are very difficult to be identified only based on morphology. The traditional species identification, mainly based on external morphological diagnostic characters, leads to inconsistent results in many cases. Herein, we provided a molecular method based on mitochondrial cytochrome c subunit I (COI) for the identification of Triplophysa fishes. Thirty-three Triplophysa species, 244 individuals, were used to determine whether barcoding was effective in discriminating species for this genus. The mean intraspecific and interspecific K2P distances ranged from 0 to 14.9% (mean, 2.9%) and 0 to 23.4% (mean, 9.7%), respectively. The tree-based analysis displayed most of species formed discrete clusters with strong bootstrap support values (>90%). The results showed that most of Triplophysa species could be identified by DNA barcode and indicated DNA barcode could be used as a molecular marker for these species.
Collapse
Affiliation(s)
- Jiuxuan Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Ying Wang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; School of Life Sciences, Jianghan University, Wuhan 430056, PR China
| | - Huifang Jin
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Wujiao Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Chaochao Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Pengfei Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Shunping He
- Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Zhaobin Song
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, PR China; Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China.
| |
Collapse
|
23
|
Poovitha S, Stalin N, Balaji R, Parani M. Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L. Genome 2016; 59:1150-1156. [DOI: 10.1139/gen-2015-0205] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%–9.6% with individual markers, which increased to 0%–12.5% and 0.8%–20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.
Collapse
Affiliation(s)
- Sundar Poovitha
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Nithaniyal Stalin
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Raju Balaji
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| | - Madasamy Parani
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
- Centre for DNA Barcoding, Department of Genetic Engineering, SRM University, Kattankulathur, Tamil Nadu, India
| |
Collapse
|
24
|
Georgescu L, Stefanakis MK, Kokkini S, Katerinopoulos HE, Pirintsos SA. Chemical and genetic characterization of Phlomis species and wild hybrids in Crete. PHYTOCHEMISTRY 2016; 122:91-102. [PMID: 26612318 DOI: 10.1016/j.phytochem.2015.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 11/10/2015] [Accepted: 11/14/2015] [Indexed: 06/05/2023]
Abstract
The genus Phlomis is represented in the island of Crete (Greece, Eastern Mediterranean) by three species Phlomis cretica C. Presl., Phlomis fruticosa L., the island endemic Phlomis lanata Willd. and three hybrids Phlomis x cytherea Rech.f. (P. cretica x P. fruticosa), Phlomis x commixta Rech.f. (P. cretica x P. lanata) and Phlomis x sieberi Vierh. (P. fruticosa x P. lanata). This work describes (a) the profile of hybrids and parental species concerning their volatile compounds, (b) the suitability of ribosomal nuclear (ITS region), chloroplast (trnH-psbA), and AFLP markers to identify hybrids and (c) their competence to characterize the different chemotypes of both hybrids and their parental species. The cluster analysis and PCA constructed from chemical data (volatile oils) suggest that there are three groups of taxa. Group IA includes P. cretica and P. fruticosa, group IB includes P. x cytherea, whereas group II consists of P. x commixta, P. x sieberi and P. lanata. Volatile compounds detected only in the hybrids P. x sieberi and P. x commixta correspond to the 3% of the total compounds, value that is much higher in P. x cytherea (21%). Neighbor-joining, statistical parsimony analysis and the observations drawn from ribotypes spectrum of ITS markers divided Phlomis species in two groups, P. lanata and the complex P. cretica/P. fruticosa. In contrast to the ITS region, the plastid DNA marker follows a geographically related pattern. Neighbor-Net, PCA and Bayesian assignment analysis performed for AFLP markers separated the genotypes into three groups corresponding to populations of P. cretica, P. fruticosa, and P. lanata, respectively, while populations of P. x commixta, P. x cytherea, and P. x sieberi presented admixed ancestry. Most of the P. x cytherea samples were identified as F1 hybrids by Bayesian assignment test, while those of P. x commixta and P. x sieberi were identified as F2 hybrids. Overall, high chemical differentiation is revealed in one of the three hybrids, which is likely related with niche variation. Moreover, molecular markers show potential to identify Phlomis taxa.
Collapse
Affiliation(s)
- Luciana Georgescu
- Department of Biology, University of Crete, Heraklion 714 09, Crete, Greece
| | | | - Stella Kokkini
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki 541 24, Greece
| | - Haralambos E Katerinopoulos
- Department of Chemistry, University of Crete, Heraklion 710 03, Crete, Greece; Botanical Garden, University of Crete, Gallos Campus, 741 00 Rethymnon, Greece
| | - Stergios A Pirintsos
- Department of Biology, University of Crete, Heraklion 714 09, Crete, Greece; Botanical Garden, University of Crete, Gallos Campus, 741 00 Rethymnon, Greece.
| |
Collapse
|
25
|
Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R, Sundaresan V. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:8-21. [PMID: 26079154 DOI: 10.1111/pbi.12419] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/28/2015] [Accepted: 05/16/2015] [Indexed: 05/21/2023]
Abstract
The past couple of decades have witnessed global resurgence of herbal-based health care. As a result, the trade of raw drugs has surged globally. Accurate and fast scientific identification of the plant(s) is the key to success for the herbal drug industry. The conventional approach is to engage an expert taxonomist, who uses a mix of traditional and modern techniques for precise plant identification. However, for bulk identification at industrial scale, the process is protracted and time-consuming. DNA barcoding, on the other hand, offers an alternative and feasible taxonomic tool box for rapid and robust species identification. For the success of DNA barcode, the barcode loci must have sufficient information to differentiate unambiguously between closely related plant species and discover new cryptic species. For herbal plant identification, matK, rbcL, trnH-psbA, ITS, trnL-F, 5S-rRNA and 18S-rRNA have been used as successful DNA barcodes. Emerging advances in DNA barcoding coupled with next-generation sequencing and high-resolution melting curve analysis have paved the way for successful species-level resolution recovered from finished herbal products. Further, development of multilocus strategy and its application has provided new vistas to the DNA barcode-based plant identification for herbal drug industry. For successful and acceptable identification of herbal ingredients and a holistic quality control of the drug, DNA barcoding needs to work harmoniously with other components of the systems biology approach. We suggest that for effectively resolving authentication challenges associated with the herbal market, DNA barcoding must be used in conjunction with metabolomics along with need-based transcriptomics and proteomics.
Collapse
Affiliation(s)
- Priyanka Mishra
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Amit Kumar
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Akshitha Nagireddy
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| | - Daya N Mani
- Herbal Medicinal Products Department, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Ashutosh K Shukla
- Biotechnology Division, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Rakesh Tiwari
- Publication Division, CSIR - Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Velusamy Sundaresan
- Department of Biology & Systematics, CSIR - Central Institute of Medicinal and Aromatic Plants, Research Centre, Bangalore, Karnataka, India
| |
Collapse
|
26
|
Bolson M, Smidt EDC, Brotto ML, Silva-Pereira V. ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests. PLoS One 2015; 10:e0143049. [PMID: 26630282 PMCID: PMC4704546 DOI: 10.1371/journal.pone.0143049] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023] Open
Abstract
The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the 'best close match' test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.
Collapse
Affiliation(s)
- Mônica Bolson
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Eric de Camargo Smidt
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | - Viviane Silva-Pereira
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| |
Collapse
|
27
|
Species discrimination in the subfamily Ostertagiinae of Northern China: assessment of DNA barcode in a taxonomically challenging group. Parasitol Res 2015; 115:987-96. [PMID: 26584827 DOI: 10.1007/s00436-015-4826-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/10/2015] [Indexed: 10/22/2022]
Abstract
Gastrointestinal nematodes within the subfamily Ostertagiinae (Teladorsagia, Ostertagia, and Marshallagia et al.) are among the most common infections of domesticated livestock. These parasites are of particular interest, as many of the species within this group are of economic importance worldwide. Traditionally, nematode species designations have been based on morphological criteria. However, this group possesses poorly defined species. There is an urgent need to develop a reliable technique that can distinguish species of Ostertagiinae. DNA barcoding has been proved to be a powerful tool to identify species of birds, mammals, and arthropods, but this technique has not yet been examined for identifying species of Ostertagiinae. In this study, a total of 138 mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) sequences from individuals representing 11 species of Ostertagiinae were acquired by PCR for the first time. The specimens were collected from pastoral area of northern China. Genetic divergence analyses showed that mean interspecific Kimura two-parameter distances of COI (13.61 %) were about four times higher than the mean value of the intraspecific divergence (3.69 %). Then, the performance of the COI to identify species of Ostertagiinae was evaluated by identification success rates using nearest neighbor (NN) and BLASTn. The results indicated that the rates of correct sequence identification for COI were high (>80 %) when using the NN and BLASTn methods. Besides, the deep lineage divergences are detected in Teladorsagia circumcincta. Meanwhile, the analyses also detected no genetic differentiation between some species such as Ostertagia hahurica and Ostertagia buriatica. These results indicate that the traditional status of species within Ostertagiinae should be closely examined based on the molecular data.
Collapse
|
28
|
Zhang J, Chen M, Dong X, Lin R, Fan J, Chen Z. Evaluation of four commonly used DNA barcoding Loci for chinese medicinal plants of the family schisandraceae. PLoS One 2015; 10:e0125574. [PMID: 25938480 PMCID: PMC4418597 DOI: 10.1371/journal.pone.0125574] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/25/2015] [Indexed: 11/19/2022] Open
Abstract
Many species of Schisandraceae are used in traditional Chinese medicine and are faced with contamination and substitution risks due to inaccurate identification. Here, we investigated the discriminatory power of four commonly used DNA barcoding loci (ITS, trnH-psbA, matK, and rbcL) and corresponding multi-locus combinations for 135 individuals from 33 species of Schisandraceae, using distance-, tree-, similarity-, and character-based methods, at both the family level and the genus level. Our results showed that the two spacer regions (ITS and trnH-psbA) possess higher species-resolving power than the two coding regions (matK and rbcL). The degree of species resolution increased with most of the multi-locus combinations. Furthermore, our results implied that the best DNA barcode for the species discrimination at the family level might not always be the most suitable one at the genus level. Here we propose the combination of ITS+trnH-psbA+matK+rbcL as the most ideal DNA barcode for discriminating the medicinal plants of Schisandra and Kadsura, and the combination of ITS+trnH-psbA as the most suitable barcode for Illicium species. In addition, the closely related species Schisandra rubriflora Rehder & E. H. Wilson and Schisandra grandiflora Hook.f. & Thomson, were paraphyletic with each other on phylogenetic trees, suggesting that they should not be distinct species. Furthermore, the samples of these two species from the southern Hengduan Mountains region formed a distinct cluster that was separated from the samples of other regions, implying the presence of cryptic diversity. The feasibility of DNA barcodes for identification of geographical authenticity was also verified here. The database and paradigm that we provide in this study could be used as reference for the authentication of traditional Chinese medicinal plants utilizing DNA barcoding.
Collapse
Affiliation(s)
- Jian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Min Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
- Graduate University of the Chinese Academy of Sciences, Beijing, P.R. China
| | - Xiaoyu Dong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences/Nanjing Botanical Garden Memorial Sun Yat-Sen, Nanjing, Jiangsu, P.R. China
| | - Ruozhu Lin
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, P.R. China
| | - Jianhua Fan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| | - Zhiduan Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, P.R. China
| |
Collapse
|
29
|
Stefanaki A, Kokkini S. Phytogeographical affinities at the crossroads of two continents: Distribution patterns of Lamiaceae in Chios Island (East Aegean Islands, Greece) and Çeşme–Karaburun Peninsula (West Anatolia, Turkey). SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2015.1019949] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
30
|
Efficiency of ITS sequences for DNA barcoding in Passiflora (Passifloraceae). Int J Mol Sci 2015; 16:7289-303. [PMID: 25837628 PMCID: PMC4425017 DOI: 10.3390/ijms16047289] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 03/21/2015] [Accepted: 03/25/2015] [Indexed: 01/20/2023] Open
Abstract
DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species.
Collapse
|
31
|
|
32
|
Sarwat M, Yamdagni MM. DNA barcoding, microarrays and next generation sequencing: recent tools for genetic diversity estimation and authentication of medicinal plants. Crit Rev Biotechnol 2014; 36:191-203. [PMID: 25264574 DOI: 10.3109/07388551.2014.947563] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA barcoding, microarray technology and next generation sequencing have emerged as promising tools for the elucidation of plant genetic diversity and its conservation. They are proving to be immensely helpful in authenticating the useful medicinal plants for herbal drug preparations. These newer versions of molecular markers utilize short genetic markers in the genome to characterize the organism to a particular species. This has the potential not only to classify the known and yet unknown species but also has a promising future to link the medicinally important plants according to their properties. The newer trends being followed in DNA chips and barcoding pave the way for a future with many different possibilities. Several of these possibilities might be: characterization of unknown species in a considerably less time than usual, identification of newer medicinal properties possessed by the species and also updating the data of the already existing but unnoticed properties. This can assist us to cure many different diseases and will also generate novel opportunities in medicinal drug delivery and targeting.
Collapse
Affiliation(s)
- Maryam Sarwat
- a Pharmaceutical Biotechnology, Amity Institute of Pharmacy, Amity University , NOIDA , Uttar Pradesh , India
| | - Manu Mayank Yamdagni
- a Pharmaceutical Biotechnology, Amity Institute of Pharmacy, Amity University , NOIDA , Uttar Pradesh , India
| |
Collapse
|
33
|
Chen J, Zhao J, Erickson DL, Xia N, Kress WJ. Testing DNA barcodes in closely related species ofCurcuma(Zingiberaceae) from Myanmar and China. Mol Ecol Resour 2014; 15:337-48. [DOI: 10.1111/1755-0998.12319] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/13/2014] [Accepted: 08/15/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; the Chinese Academy of Sciences; No 723 Xingke Road Tianhe District Guangzhou 510650 China
| | - Jietang Zhao
- College of Horticulture; South China Agricultural University; Guangzhou 510642 China
| | - David L. Erickson
- Department of Botany; MRC-166; National Museum of Natural History; Smithsonian Institution; P.O. Box 37012 Washington DC 20013-7012 USA
| | - Nianhe Xia
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; the Chinese Academy of Sciences; No 723 Xingke Road Tianhe District Guangzhou 510650 China
| | - W. John Kress
- Department of Botany; MRC-166; National Museum of Natural History; Smithsonian Institution; P.O. Box 37012 Washington DC 20013-7012 USA
| |
Collapse
|
34
|
Vinitha MR, Kumar US, Aishwarya K, Sabu M, Thomas G. Prospects for discriminating Zingiberaceae species in India using DNA barcodes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:760-773. [PMID: 24612741 DOI: 10.1111/jipb.12189] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/20/2014] [Indexed: 06/03/2023]
Abstract
We evaluated nine plastid (matK, rbcL, rpoC1, rpoB, rpl36-rps8, ndhJ, trnL-F, trnH-psbA, accD) and two nuclear (ITS and ITS2) barcode loci in family Zingiberaceae by analyzing 60 accessions of 20 species belonging to seven genera from India. Bidirectional sequences were recovered for every plastid locus by direct sequencing of polymerase chain reaction (PCR) amplicons in all the accessions tested. However, only 35 (58%) and 40 accessions (66%) yielded ITS and ITS2 sequences, respectively, by direct sequencing. In different bioinformatics analyses, matK and rbcL consistently resolved 15 species (75%) into monophyletic groups and five species into two paraphyletic groups. The 173 ITS sequences, including 138 cloned sequences from 23 accessions, discriminated only 12 species (60%), and the remaining species were entered into three paraphyletic groups. Phylogenetic and genealogic analyses of plastid and ITS sequences imply the possible occurrence of natural hybridizations in the evolutionary past in giving rise to species paraphyly and intragenomic ITS heterogeneity in the species tested. The results support using matK and rbcL loci for barcoding Zingiberaceae members and highlight the poor utility of ITS and the highly regarded ITS2 in barcoding this family, and also caution against proposing ITS loci for barcoding taxa based on limited sampling.
Collapse
|
35
|
Techen N, Parveen I, Pan Z, Khan IA. DNA barcoding of medicinal plant material for identification. Curr Opin Biotechnol 2013; 25:103-10. [PMID: 24484887 DOI: 10.1016/j.copbio.2013.09.010] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/27/2013] [Indexed: 01/13/2023]
Abstract
Because of the increasing demand for herbal remedies and for authentication of the source material, it is vital to provide a single database containing information about authentic plant materials and their potential adulterants. The database should provide DNA barcodes for data retrieval and similarity search. In order to obtain such barcodes, several molecular methods have been applied to develop markers that aid with the authentication and identification of medicinal plant materials. In this review, we discuss the genomic regions and molecular methods selected to provide barcodes, available databases and the potential future of barcoding using next generation sequencing.
Collapse
Affiliation(s)
- Natascha Techen
- National Center for Natural Products Research and Research Institute of Pharmaceutical Sciences, Department of Pharmacognosy, School of Pharmacy, University of Mississippi, P.O. Box 1848, MS 38677, USA
| | - Iffat Parveen
- National Center for Natural Products Research and Research Institute of Pharmaceutical Sciences, Department of Pharmacognosy, School of Pharmacy, University of Mississippi, P.O. Box 1848, MS 38677, USA
| | - Zhiqiang Pan
- USDA-ARS-NPURU, P.O. Box 8048, University, MS 38677, USA
| | - Ikhlas A Khan
- National Center for Natural Products Research and Research Institute of Pharmaceutical Sciences, Department of Pharmacognosy, School of Pharmacy, University of Mississippi, P.O. Box 1848, MS 38677, USA; School of Pharmacy, King Saud University, Saudi Arabia.
| |
Collapse
|
36
|
S Alves TL, Chauveau O, Eggers L, de Souza-Chies TT. Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus. Mol Ecol Resour 2013; 14:324-35. [PMID: 24119215 DOI: 10.1111/1755-0998.12182] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 09/19/2013] [Accepted: 09/29/2013] [Indexed: 11/28/2022]
Abstract
DNA barcoding aims to develop an efficient tool for species identification based on short and standardized DNA sequences. In this study, the DNA barcode paradigm was tested among the genera of the tribe Sisyrinchieae (Iridoideae). Sisyrinchium, with more than 77% of the species richness in the tribe, is a taxonomically complex genus. A total of 185 samples belonging to 98 species of Sisyrinchium, Olsynium, Orthrosanthus and Solenomelus were tested using matK, trnH-psbA and internal transcribed spacer (ITS). Candidate DNA barcodes were analysed either as single markers or in combination. Detection of a barcoding gap, similarity-based methods and tree-based analyses were used to assess the discrimination efficiency of DNA barcodes. The levels of species identification obtained from plastid barcodes were low and ranged from 17.35% to 20.41% for matK and 5.11% to 7.14% for trnH-psbA. The ITS provided better results with 30.61-38.78% of species identified. The analyses of the combined data sets did not result in a significant improvement in the discrimination rate. Among the tree-based methods, the best taxonomic resolution was obtained with Bayesian inference, particularly when the three data sets were combined. The study illustrates the difficulties for DNA barcoding to identify species in evolutionary complex lineages. Plastid markers are not recommended for barcoding Sisyrinchium due to the low discrimination power observed. ITS gave better results and may be used as a starting point for species identification.
Collapse
Affiliation(s)
- Tiago L S Alves
- Programa de Pós-Graduação em Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves, 9500 - Prédio 43433, 91501-970, Porto Alegre, Brazil
| | | | | | | |
Collapse
|
37
|
Krawczyk K, Szczecińska M, Sawicki J. Evaluation of 11 single-locus and seven multilocus DNA barcodes inLamiumL. (Lamiaceae). Mol Ecol Resour 2013; 14:272-85. [DOI: 10.1111/1755-0998.12175] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 09/06/2013] [Accepted: 09/13/2013] [Indexed: 11/28/2022]
Affiliation(s)
- K. Krawczyk
- Department of Botany and Nature Protection; University of Warmia and Mazury in Olsztyn; Plac Lodzki 1 10-727 Olsztyn Poland
| | - M. Szczecińska
- Department of Botany and Nature Protection; University of Warmia and Mazury in Olsztyn; Plac Lodzki 1 10-727 Olsztyn Poland
| | - J. Sawicki
- Department of Botany and Nature Protection; University of Warmia and Mazury in Olsztyn; Plac Lodzki 1 10-727 Olsztyn Poland
| |
Collapse
|