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Veltman MA, Anthoons B, Schrøder-Nielsen A, Gravendeel B, de Boer HJ. Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids. Mol Ecol Resour 2024:e13986. [PMID: 38899721 DOI: 10.1111/1755-0998.13986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 05/16/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.
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Affiliation(s)
- Margaretha A Veltman
- Natural History Museum, Oslo, Norway
- Naturalis Biodiversity Center, Leiden, Netherlands
| | | | | | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden, Netherlands
- Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, Netherlands
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Large-Scale In Vitro Multiplication and Phytochemical Analysis of Himantoglossum affine (Boiss.) Schltr.: An Endangered Euro-Mediterranean Terrestrial Orchid. DIVERSITY 2022. [DOI: 10.3390/d14121137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Himantoglossum affine is a threatened terrestrial orchid. We aimed to optimize asymbiotic seed germination and direct embryogenesis and to analyze the phytochemical profile and physico-biochemical analysis of leaf and tuber. The individual use of organic nitrogen compounds resulted in higher germination efficiencies, while the shortest times to germination were observed using coconut water plus casein hydrolysate. Plantlets grown on media supplemented with pineapple juice and peptone had the highest plantlet length and weight. For embryogenesis, the highest regeneration rate (44%) and embryo number/explant (10.12 ± 2.08) were observed in young protocorm-like body (PLB) explants with 0.5 mg/L naphthalene acetic acid (NAA) and 1 mg/L thidiazuron (TDZ). During the acclimatization process, the scattered vascular tubes converted to fully developed vascular tissues, ensuring maximum sap flux. Gas chromatography–mass spectrometry analysis identified 1,2,3-propanetriol, monoacetate, 4H-pyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl, and 2-butenedioic acid, 2-methyl-, (E)- as the most prevalent compounds. We reported higher contents of total phenolics and flavonoids and antioxidant activity compared to other terrestrial orchids. The glucomannan content (36.96%) was also higher than starch content (31.31%), comparable to those reported in other tuberous orchids. Based on the fragmentation of H. affine populations in the Middle East and Euro-Mediterranean countries due to over-harvesting, climate change, and/or human impact, our procedure offers a tool for the re-introduction of in vitro-raised plants to threatened areas.
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Abstract
Growing popularity of herbal medicine has increased the demand of medicinal orchids in the global markets leading to their overharvesting from natural habitats for illegal trade. To stop such illegal trade, the correct identification of orchid species from their traded products is a foremost requirement. Different species of medicinal orchids are traded as their dried or fresh parts (tubers, pseudobulbs, stems), which look similar to each other making it almost impossible to identify them merely based on morphological observation. To overcome this problem, DNA barcoding could be an important method for accurate identification of medicinal orchids. Therefore, this research evaluated DNA barcoding of medicinal orchids in Asia where illegal trade of medicinal orchids has long existed. Based on genetic distance, similarity-based and tree-based methods with sampling nearly 7,000 sequences from five single barcodes (ITS, ITS2, matK, rbcL, trnH-psbA and their seven combinations), this study revealed that DNA barcoding is effective for identifying medicinal orchids. Among single locus, ITS performed the best barcode, whereas ITS + matK exhibited the most efficient barcode among multi-loci. A barcode library as a resource for identifying medicinal orchids has been established which contains about 7,000 sequences of 380 species (i.e. 90%) of medicinal orchids in Asia.
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Vasconcelos S, Nunes GL, Dias MC, Lorena J, Oliveira RRM, Lima TGL, Pires ES, Valadares RBS, Alves R, Watanabe MTC, Zappi DC, Hiura AL, Pastore M, Vasconcelos LV, Mota NFO, Viana PL, Gil ASB, Simões AO, Imperatriz‐Fonseca VL, Harley RM, Giulietti AM, Oliveira G. Unraveling the plant diversity of the Amazonian canga through DNA barcoding. Ecol Evol 2021; 11:13348-13362. [PMID: 34646474 PMCID: PMC8495817 DOI: 10.1002/ece3.8057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 01/04/2023] Open
Abstract
The canga of the Serra dos Carajás, in Eastern Amazon, is home to a unique open plant community, harboring several endemic and rare species. Although a complete flora survey has been recently published, scarce to no genetic information is available for most plant species of the ironstone outcrops of the Serra dos Carajás. In this scenario, DNA barcoding appears as a fast and effective approach to assess the genetic diversity of the Serra dos Carajás flora, considering the growing need for robust biodiversity conservation planning in such an area with industrial mining activities. Thus, after testing eight different DNA barcode markers (matK, rbcL, rpoB, rpoC1, atpF-atpH, psbK-psbI, trnH-psbA, and ITS2), we chose rbcL and ITS2 as the most suitable markers for a broad application in the regional flora. Here we describe DNA barcodes for 1,130 specimens of 538 species, 323 genera, and 115 families of vascular plants from a highly diverse flora in the Amazon basin, with a total of 344 species being barcoded for the first time. In addition, we assessed the potential of using DNA metabarcoding of bulk samples for surveying plant diversity in the canga. Upon achieving the first comprehensive DNA barcoding effort directed to a complete flora in the Brazilian Amazon, we discuss the relevance of our results to guide future conservation measures in the Serra dos Carajás.
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Affiliation(s)
| | | | - Mariana C. Dias
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Renato R. M. Oliveira
- Instituto Tecnológico ValeBelémBrazil
- Programa Interunidades de Pós‐Graduação em BioinformáticaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | | | | | - Daniela C. Zappi
- Instituto Tecnológico ValeBelémBrazil
- Instituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaBrazil
| | | | - Mayara Pastore
- Instituto Tecnológico ValeBelémBrazil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - Liziane V. Vasconcelos
- Instituto Tecnológico ValeBelémBrazil
- Programa de Pós‐Graduação em EcologiaUniversidade Federal do ParáBelémBrazil
| | - Nara F. O. Mota
- Instituto Tecnológico ValeBelémBrazil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - Pedro L. Viana
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - André S. B. Gil
- Coordenação de BotânicaMuseu Paraense Emílio GoeldiBelémBrazil
| | - André O. Simões
- Departamento de Biologia VegetalUniversidade Estadual de CampinasCampinasBrazil
| | | | | | - Ana M. Giulietti
- Instituto Tecnológico ValeBelémBrazil
- Programa de Pós‐Graduação em BotânicaUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
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Gholami S, Vafaee Y, Nazari F, Ghorbani A. Exploring genetic variations in threatened medicinal orchids using start codon targeted (SCoT) polymorphism and marker-association with seed morphometric traits. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:769-785. [PMID: 33967461 PMCID: PMC8055808 DOI: 10.1007/s12298-021-00978-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/03/2021] [Accepted: 03/12/2021] [Indexed: 05/05/2023]
Abstract
We aimed to study the genetic diversity and population structure of eight Iranian terrestrial orchid species, including Anacamptis coriophora (L.) R. M. Bateman, Pridgeon and M. W. Chase, Dactylorhiza umbrosa (Kar. & Kir.) Nevski, Himantoglossum affine (Boiss.) Schltr., Orchis collina Banks and Solander, Orchis mascula (L.) L., Orchis simia Lam., Ophrys schulzei Bornm. and Fleischm., and Ophrys straussii H. Fleischm. and Bornm. using start target codon markers (SCoT) and finding markers associated with seed morphometric traits. A total of 254 reproducible SCoT fragments were generated, of which 248 fragments were polymorphic (average polymorphism of 96.18%). The SCoT markers showed a narrow range of polymorphism information content (PIC) varied from 0.397 for S9 primer to 0.499 for S11 and S20 primers. Based on the population analysis results, the Orchis simia accessions collected from Paveh region (Os.P) represented the lowest observed number of alleles (Na) (1.13) and effective number of alleles (Ne) (1.09). At the same time, the highest Na (1.29) and Ne (1.18) values were obtained in O. schulzei collected from Javanrood (Oyst.JA). Shannon's information index (I) was ranged from 0.03 for D. umbrosa accessions collected from Marivan (Du.M population) to 0.263 for Ha.Ja population (H. affine accessions collected from Javanrood). The UPGMA dendrogram obtained with the Jaccard similarity coefficient (r = 0.97295) divided 97 studied terrestrial orchid accessions into eight groups mainly based on species type and geographical origin. Based on the Bayesian statistical index, the highest probability of the data was achieved when accessions were divided into eight groups (K = 8). Multiple association analysis (MRA) revealed significant associations between some of SCoT bands with seed morphometric traits. Our findings can be useful for germplasm characterization, conservation, and improvement of Iranian terrestrial orchid species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00978-4.
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Affiliation(s)
- Soheila Gholami
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Yavar Vafaee
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
- Medicinal Plants Breeding and Development Research Institute, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Farzad Nazari
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Abdolbaset Ghorbani
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236 Uppsala, Sweden
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Gholami S, Vafaee Y, Nazari F, Ghorbani A. Molecular characterization of endangered Iranian terrestrial orchids using ISSR markers and association with floral and tuber-related phenotypic traits. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:53-68. [PMID: 33627962 PMCID: PMC7873147 DOI: 10.1007/s12298-020-00920-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/20/2020] [Accepted: 12/28/2020] [Indexed: 05/13/2023]
Abstract
We aimed to study the genetic diversity, population structure, and phylogeny of Iranian orchids using inter-simple sequence repeat (ISSR) markers to find markers associated with phenotypic traits. Based on the phenotypic analysis, the inflorescence length and the flower number of studied accessions ranged from 3.92 to 27.13 cm and 5 to 50, respectively. On the other hand, the tuber length ranged from 1.80 to 9.35 cm. A total of 310 reproducible ISSR fragments with a size range of 150 to 3000 bp were amplified. ISSR primers provided an average polymorphism information content of 0.391, varied from 0.488 for UBC-876 to 0.351 for UBC-842. Os.J population showed the lowest genetic diversity (H = 0.057 and I = 0.075), while Oyst.JA population showed the highest genetic diversity (H = 0.114 and I = 0.158). At species level, the average coefficient of genetic differentiation (G ST) ranged from 0.265 for Orchis simia to 0.587 for Himantoglossum affine. Gene flow (Nm) varied from 1.38 (O. simia) to 0.756 (Anacamptis collina). The UPGMA genetic similarity dendrogram using Jaccard coefficients (r = 0.973) revealed six main clusters. Based on the Bayesian clustering method, the highest probability of the data was achieved when accessions were divided into eight groups. Floral and tuber-related phenotypic traits represented high correlations together, and they were associated with some ISSR bands based on the multiple association analysis. Altogether, ISSR markers proved to be useful for discrimination and clarification of the relationships among species and populations collected from geographically different locations. Furthermore, it could identify the polymorphism among accessions within each population and species. SUPPLEMENTARY INFORMATION The online version of this article (10.1007/s12298-020-00920-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Soheila Gholami
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Yavar Vafaee
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
- Medicinal Plants Breeding and Development Research Institute, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Farzad Nazari
- Department of Horticultural Science and Engineering, Faculty of Agriculture, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Abdolbaset Ghorbani
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, 75236 Uppsala, Sweden
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Sherif NA, Senthil Kumar T, Rao MV. DNA barcoding and genetic fidelity assessment of micropropagated Aenhenrya rotundifolia (Blatt.) C.S. Kumar and F.N. Rasm.: a critically endangered jewel orchid. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2391-2405. [PMID: 33424154 PMCID: PMC7772124 DOI: 10.1007/s12298-020-00917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/26/2020] [Accepted: 12/06/2020] [Indexed: 05/03/2023]
Abstract
Aenhenrya rotundifolia is a critically endangered terrestrial jewel orchid. It is monotypic and endemic to evergreen forests of southern western ghats of India. In the present study, identification of this plant species is validated with DNA barcoding using matK and rbcL chloroplast markers. Further, germ-free juvenile axillary bud explants were cultured on Mitra medium supplemented with different kinds of cytokinins like 6-benzyladenine, 6-furfurylaminopurine, N6-(Δ2-isopentyl) adenine, thidiazuron, zeatin and meta-topolin as well as auxins such as α-naphthaleneacetic acid, indole-3-acetic acid and indole-3-butyric acid at different concentrations and combinations for successful proliferation and establishment in vitro. After 12 weeks of culture, axillary bud explants produced an average of 30.12 ± 0.71 shoots per explant, 3.87 ± 0.06 cm shoot length, 1671 ± 2.82 mg fresh mass of proliferated shoots with a proliferation frequency of 100% on Mitra medium supplemented with 6.20 µM meta-topolin and 2.25 µM thidiazuron. No root formation was observed in in vitro proliferated microshoots. However, tiny hair like projections were observed in some elongated shoots on Mitra medium pertaining to 5.37 µM NAA. The tiny hair like structure bearing plantlets were hardened and acclimatized with 100% survival rate in the polytunnel chamber. After 8-10 months of establishment ex vitro, flowering was observed. Additionally, the genetic fidelity of in vitro derived plants was tested with ISSR and SCoT marker profiling. The test results revealed that the plants derived from the protocol has 99% genetic similarity to that of the donor mother plant. This study can be applied in forensic interventions of this species, describes the maintenance of germplasm in vitro and establishment of new viable population in its original habitats by restoring existing sites of this critically endangered jewel orchid.
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Affiliation(s)
- N. Ahamed Sherif
- PG and Research Department of Botany, Jamal Mohamed College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, 620020 Tamil Nadu India
- Department of Botany, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024 Tamil Nadu India
| | - T. Senthil Kumar
- Department of Botany, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024 Tamil Nadu India
| | - M. V. Rao
- Department of Botany, School of Life Sciences, Bharathidasan University, Tiruchirappalli, 620024 Tamil Nadu India
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Zhang D, Jiang B. Species identification in complex groups of medicinal plants based on DNA barcoding: a case study on Astragalus spp. (Fabaceae) from southwest China. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01119-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Kabacaoğlu E, Budak BK. Detection and quantification of salep with real time PCR utilizing the nr-ITS2 region. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:2447-2454. [PMID: 30362130 DOI: 10.1002/jsfa.9453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/14/2018] [Accepted: 10/17/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Salep is a highly valued food product, susceptible to adulteration with less costly additives such as starch. The aim of this study is to develop a real-time polymerase chain reaction (PCR) method for the detection and quantification of authentic salep using primers designed from the nr-ITS2 region. RESULTS The designed primers were shown to amplify selectively with salep DNA and cloning/sequencing of end-point PCR products obtained with authentic salep (Orchideceae) confirmed amplimers to be copies of the intended target region. Detection of salep DNA using the designed primer set was possible at levels as low as 20 pg. After initial evaluation of the real-time PCR method with binary DNA mixtures of salep and cornflour, quantification of salep was conducted in binary mixtures of potato starch (a more likely adulterant) and salep, showing that quantification within the range 25%-100% could be achieved. The real-time assay was performed using the 18S rDNA region co-amplified as an internal standard and evaluated using the ΔΔCt method. The calibration curves obtained as a result of real-time PCR runs showed linearity, with R2 values above 99%. CONCLUSION A real-time PCR method using SybreGreen intercalating dye was established for salep detection and quantification based on the specific amplification of salep DNA. Method validation was performed utilizing blind and commercial samples. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Eda Kabacaoğlu
- Faculty of Engineering, Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Barçın Karakaş Budak
- Faculty of Engineering, Department of Food Engineering, Akdeniz University, Antalya, Turkey
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Veldman S, Kim SJ, van Andel TR, Bello Font M, Bone RE, Bytebier B, Chuba D, Gravendeel B, Martos F, Mpatwa G, Ngugi G, Vinya R, Wightman N, Yokoya K, de Boer HJ. Trade in Zambian Edible Orchids-DNA Barcoding Reveals the Use of Unexpected Orchid Taxa for Chikanda. Genes (Basel) 2018; 9:E595. [PMID: 30513666 PMCID: PMC6315803 DOI: 10.3390/genes9120595] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/17/2018] [Accepted: 11/22/2018] [Indexed: 02/01/2023] Open
Abstract
In Zambia, wild edible terrestrial orchids are used to produce a local delicacy called chikanda, which has become increasingly popular throughout the country. Commercialization puts orchid populations in Zambia and neighbouring countries at risk of overharvesting. Hitherto, no study has documented which orchid species are traded on local markets, as orchid tubers are difficult to identify morphologically. In this study, the core land-plant DNA barcoding markers rbcL and matK were used in combination with nrITS to determine which species were sold in Zambian markets. Eighty-two interviews were conducted to determine harvesting areas, as well as possible sustainability concerns. By using nrITS DNA barcoding, a total of 16 orchid species in six different genera could be identified. Both rbcL and matK proved suitable to identify the tubers up to the genus or family level. Disa robusta, Platycoryne crocea and Satyrium buchananii were identified most frequently and three previously undocumented species were encountered on the market. Few orchid species are currently listed on the global International Union for the Conservation of Nature (IUCN) Red List. Local orchid populations and endemic species could be at risk of overharvesting due to the intensive and indiscriminate harvesting of chikanda orchids, and we therefore encourage increased conservation assessment of terrestrial African orchids.
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Affiliation(s)
- Sarina Veldman
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
| | - Seol-Jong Kim
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
| | - Tinde R van Andel
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
| | - Maria Bello Font
- Natural History Museum, University of Oslo, Postboks 1172, Blindern, 0318 Oslo, Norway.
| | - Ruth E Bone
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
| | - Benny Bytebier
- Bews Herbarium, School of Life Sciences, University of KwaZulu-Natal, Pr. Bag X01, Scottsville 3209, South Africa.
| | - David Chuba
- Department of Biological Sciences, University of Zambia, Box 32379 Lusaka, Zambia.
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
- Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands.
- University of Applied Sciences Leiden, Zernikedreef 11, 2333 CK Leiden, The Netherlands.
| | - Florent Martos
- Bews Herbarium, School of Life Sciences, University of KwaZulu-Natal, Pr. Bag X01, Scottsville 3209, South Africa.
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'histoire naturelle, CNRS, Sorbonne Université, EPHE, CP50, 45 rue Buffon 75005 Paris, France.
| | - Geophat Mpatwa
- School of Natural Resources, The Copperbelt University, PO Box 21692 Kitwe, Zambia.
| | - Grace Ngugi
- Bews Herbarium, School of Life Sciences, University of KwaZulu-Natal, Pr. Bag X01, Scottsville 3209, South Africa.
- East African Herbarium, National Museums of Kenya, P.O. Box 40658-00100 Nairobi, Kenya.
| | - Royd Vinya
- School of Natural Resources, The Copperbelt University, PO Box 21692 Kitwe, Zambia.
| | - Nicholas Wightman
- Homegarden Landscape Consultants Ltd., P/Bag 30C, Chilanga, Lusaka, Zambia.
| | | | - Hugo J de Boer
- Department of Organismal Biology, Systematic Biology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
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de Boer HJ, Ghorbani A, Manzanilla V, Raclariu AC, Kreziou A, Ounjai S, Osathanunkul M, Gravendeel B. DNA metabarcoding of orchid-derived products reveals widespread illegal orchid trade. Proc Biol Sci 2018; 284:rspb.2017.1182. [PMID: 28931735 DOI: 10.1098/rspb.2017.1182] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/10/2017] [Indexed: 11/12/2022] Open
Abstract
In eastern Mediterranean countries orchids continue to be collected from the wild for the production of salep, a beverage made of dried orchid tubers. In this study we used nrITS1 and nrITS2 DNA metabarcoding to identify orchid and other plant species present in 55 commercial salep products purchased in Iran, Turkey, Greece and Germany. Thirty samples yielded a total of 161 plant taxa, and 13 products (43%) contained orchid species and these belonged to 10 terrestrial species with tuberous roots. Another 70% contained the substitute ingredient Cyamopsis tetraganoloba (Guar). DNA metabarcoding using the barcoding markers nrITS1 and nrITS2 shows the potential of these markers and approach for identification of species used in salep products. The analysis of interspecific genetic distances between sequences of these markers for the most common salep orchid genera shows that species level identifications can be made with a high level of confidence. Understanding the species diversity and provenance of salep orchid tubers will enable the chain of commercialization of endangered species to be traced back to the harvesters and their natural habitats, and thus allow for targeted efforts to protect or sustainably use wild populations of these orchids.
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Affiliation(s)
- Hugo J de Boer
- Natural History Museum, University of Oslo, Oslo, Norway .,Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | - Ancuta-Cristina Raclariu
- Natural History Museum, University of Oslo, Oslo, Norway.,Stejarul Research Centre for Biological Sciences, NIRDBIS, Piatra Neamt, Romania
| | | | - Sarawut Ounjai
- Department of Biology, Chiang Mai University, Chiang Mai, Thailand
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Molnár V A, Nagy T, Löki V, Süveges K, Takács A, Bódis J, Tökölyi J. Turkish graveyards as refuges for orchids against tuber harvest. Ecol Evol 2017; 7:11257-11264. [PMID: 29299298 PMCID: PMC5743569 DOI: 10.1002/ece3.3562] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Revised: 09/21/2017] [Accepted: 10/08/2017] [Indexed: 11/11/2022] Open
Abstract
Harvest of orchid tubers for salep production is widespread in southwestern Asia and the Balkans and constitutes a major conservation risk for wild orchid populations. Synanthropic habitats, such as graveyards, are important refuges for orchids and other organisms and could offer protection from salep harvesting because of their special cultural role. However, little is known about the occurrence and factors influencing harvesting of salep in graveyards. During field surveys of 474 graveyards throughout Turkey, we observed 333 graveyards with orchids, 311 graveyards with tuberous orchids, and salep harvest in 14 graveyards. Altogether, 530 individuals of 17 orchid species were collected, representing 9% of the individuals recorded. Harvesting intensity was relatively low, and populations were usually not wholly destroyed. However, some species were clearly more affected than others. Salep harvesting risk of orchid species was significantly associated with flowering time, with early‐flowering species being more affected. A marginally significant positive relationship between harvesting risk and species‐specific tuber size was also detected. Our data suggest that graveyards might offer some protection against salep harvesting in Turkey, but they also show that some orchid taxa are much more affected than others. Overall, our observations add more weight to the conservation value of these special habitats.
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Affiliation(s)
- Attila Molnár V
- Department of Botany University of Debrecen Debrecen Hungary
| | - Timea Nagy
- Department of Plant Sciences and Biotechnology Georgikon Faculty University of Pannonia Keszthely Hungary
| | - Viktor Löki
- Department of Botany University of Debrecen Debrecen Hungary
| | - Kristóf Süveges
- Department of Botany University of Debrecen Debrecen Hungary
| | - Attila Takács
- Department of Botany University of Debrecen Debrecen Hungary.,MTA-DE "Lendület" Evolutionary Phylogenomic Research Group University of Debrecen Debrecen Hungary
| | - Judit Bódis
- Department of Plant Sciences and Biotechnology Georgikon Faculty University of Pannonia Keszthely Hungary
| | - Jácint Tökölyi
- MTA-DE Behavioural Ecology Research Group University of Debrecen Debrecen Hungary
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Raclariu AC, Mocan A, Popa MO, Vlase L, Ichim MC, Crisan G, Brysting AK, de Boer H. Veronica officinalis Product Authentication Using DNA Metabarcoding and HPLC-MS Reveals Widespread Adulteration with Veronica chamaedrys. Front Pharmacol 2017; 8:378. [PMID: 28674497 PMCID: PMC5474480 DOI: 10.3389/fphar.2017.00378] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 05/31/2017] [Indexed: 11/13/2022] Open
Abstract
Studying herbal products derived from local and traditional knowledge and their value chains is one of the main challenges in ethnopharmacology. The majority of these products have a long history of use, but non-harmonized trade and differences in regulatory policies between countries impact their value chains and lead to concerns over product efficacy, safety and quality. Veronica officinalis L. (common speedwell), a member of Plantaginaceae family, has a long history of use in European traditional medicine, mainly in central eastern Europe and the Balkans. However, no specified control tests are available either to establish the quality of derived herbal products or for the discrimination of its most common substitute, V. chamaedrys L. (germander speedwell). In this study, we use DNA metabarcoding and high performance liquid chromatography coupled with mass spectrometry (HPLC-MS) to authenticate sixteen V. officinalis herbal products and compare the potential of the two approaches to detect substitution, adulteration and the use of unreported constituents. HPLC-MS showed high resolution in detecting phytochemical target compounds, but did not enable detection of specific plant species in the products. DNA metabarcoding detected V. officinalis in only 15% of the products, whereas it detected V. chamaedrys in 62% of the products. The results confirm that DNA metabarcoding can be used to test for the presence of Veronica species, and detect substitution and/or admixture of other Veronica species, as well as simultaneously detect all other species present. Our results confirm that none of the herbal products contained exactly the species listed on the label, and all included substitutes, contaminants or fillers. This study highlights the need for authentication of raw herbals along the value chain of these products. An integrative methodology can assess both the quality of herbal products in terms of target compound concentrations and species composition, as well as admixture and substitution with other chemical compounds and plants.
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Affiliation(s)
- Ancuta C Raclariu
- Plant Evolution and Metabarcoding Group, Natural History Museum, University of OsloOslo, Norway.,Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Andrei Mocan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca, Romania.,ICHAT and Institute for Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaCluj-Napoca, Romania
| | - Madalina O Popa
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Laurian Vlase
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of OsloOslo, Norway
| | - Mihael C Ichim
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences (NIRDBS)Piatra Neamţ, Romania
| | - Gianina Crisan
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Iuliu Hatieganu University of Medicine and PharmacyCluj-Napoca, Romania
| | - Anne K Brysting
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES)Oslo, Norway
| | - Hugo de Boer
- Plant Evolution and Metabarcoding Group, Natural History Museum, University of OsloOslo, Norway.,Department of Organismal Biology, Evolutionary Biology Centre, Uppsala UniversityUppsala, Sweden
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