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Khemira H, Mahdhi M, Afzal M, Oteef MD, Tounekti T, AL-Faifi Z, Alsolami W. Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding. PeerJ 2023; 11:e16486. [PMID: 38025745 PMCID: PMC10680449 DOI: 10.7717/peerj.16486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.
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Affiliation(s)
- Habib Khemira
- Centre for Environmental Research and Studies, Jazan University, Jazan, Saudi Arabia
| | - Mosbah Mahdhi
- Centre for Environmental Research and Studies, Jazan University, Jazan, Saudi Arabia
- Laboratory of Biodiversity and Valorization of Bioresources in Arid Zones, Faculty of Sciences of Gabes, University of Gabes, Gabes, Tunisia
| | - Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed D.Y. Oteef
- Department of Chemistry, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Taieb Tounekti
- Laboratory of Process Engineering & Industrial Systems (LR11ES54), National Engineering School of Gabes, University of Gabes, Gabes, Tunisia
| | - Zarraq AL-Faifi
- Department of Biology, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Wail Alsolami
- Department of Biology, College of Science, Jazan University, Jazan, Saudi Arabia
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The young fruit of Citrus aurantium L. or Citrus sinensis Osbeck as a natural health food: A deep insight into the scientific evidence of its health benefits. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
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3
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Dawan J, Ahn J. Application of DNA barcoding for ensuring food safety and quality. Food Sci Biotechnol 2022; 31:1355-1364. [PMID: 36060568 PMCID: PMC9433498 DOI: 10.1007/s10068-022-01143-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
With increasing international food trade, food quality and safety are high priority worldwide. The consumption of contaminated and adulterated food can cause serious health problems such as infectious diseases and allergies. Therefore, the authentication and traceability systems are needed to improve food safety. The mitochondrial DNA can be used for species authentication of food and food products. Effective DNA barcode markers have been developed to correctly identify species. The US FDA approved to the use of DNA barcoding for various food products. The DNA barcoding technology can be used as a regulatory tool for identification and authenticity. The application of DNA barcoding can reduce the microbiological and toxicological risks associated with the consumption of food and food products. DNA barcoding can be a gold-standard method in food authenticity and fraud detection. This review describes the DNA barcoding method for preventing food fraud and adulteration in meat, fish, and medicinal plants.
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Xavier JKAM, Maia L, Figueiredo PLB, Folador A, Ramos AR, Andrade EH, Maia JGS, Setzer WN, da Silva JKR. Essential Oil Composition and DNA Barcode and Identification of Aniba species (Lauraceae) Growing in the Amazon Region. Molecules 2021; 26:1914. [PMID: 33805452 PMCID: PMC8036375 DOI: 10.3390/molecules26071914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 11/17/2022] Open
Abstract
Lauraceae species are widely represented in the Amazon, presenting a significant essential oil yield, large chemical variability, various biological applications, and high economic potential. Its taxonomic classification is difficult due to the accentuated morphological uniformity, even among taxa from a different genus. For this reason, the present work aimed to find chemical and molecular markers to discriminate Aniba species collected in the Pará State (Brazil). The chemical composition of the essential oils from Aniba canelilla, A. parviflora, A. rosaeodora, and A. terminalis were grouped by multivariate statistical analysis. The major compounds were rich in benzenoids and terpenoids such as 1-nitro-2-phenylethane (88.34-70.85%), linalool (15.2-75.3%), α-phellandrene (36.0-51.8%), and β-phellandrene (11.6-25.6%). DNA barcodes were developed using the internal transcribed spacer (ITS) nuclear region, and the matK, psbA-trnH, rbcL, and ycf1 plastid regions. The markers psbA-trnH and ITS showed the best discrimination for the species, and the phylogenic analysis in the three- (rbcL + matK + trnH - psbA and rbcL + matK + ITS) and four-locus (rbcL + matK + trnH - psbA + ITS) combination formed clades with groups strongly supported by the Bayesian inference (BI) (PP:1.00) and maximum likelihood (ML) (BS ≥ 97%). Therefore, based on statistical multivariate and phylogenetic analysis, the results showed a significant correlation between volatile chemical classes and genetic characteristics of Aniba species.
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Affiliation(s)
- Júlia Karla A. M. Xavier
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-900, Brazil; (J.K.A.M.X.); (L.M.)
| | - Leonardo Maia
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-900, Brazil; (J.K.A.M.X.); (L.M.)
| | - Pablo Luis B. Figueiredo
- Departamento de Ciências Naturais, Centro de Ciências Sociais e Educação, Universidade do Estado do Pará, Belém, PA 66050-540, Brazil;
| | - Adriana Folador
- Laboratório de Genômica e Bioinformática, Centro De Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém, PA 66075-900, Brazil;
| | - Alessandra R. Ramos
- Instituto de Estudos em Saúde e Biológicas, Universidade Federal do Sul e Sudeste do Pará, Marabá, PA 68507-590, Brazil;
| | - Eloísa H. Andrade
- Coordenação de Botânica, Museu Paraense Emílio Goeldi, Belém, PA 66040-170, Brazil;
| | - José Guilherme S. Maia
- Programa de Pós-Graduação em Química, Universidade Federal do Maranhão, São Luís, MA 64080-040, Brazil;
| | - William N. Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA;
- Aromatic Plant Research Center, 230 N 1200 E, Suite 102, Lehi, UT 84043, USA
| | - Joyce Kelly R. da Silva
- Programa de Pós-Graduação em Química, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, PA 66075-900, Brazil; (J.K.A.M.X.); (L.M.)
- Aromatic Plant Research Center, 230 N 1200 E, Suite 102, Lehi, UT 84043, USA
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Feng T, Qiu S, Tan G, Tian D, Wu D, Zhou L, Yang M, Zhu S. Identification of Suitable Barcodes for Specifically Detecting Adulterants of Turnip (Brassica rapa) and Radish (Raphanus sativus) in Maca (Lepidium meyenii). FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01857-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Mahima K, Sudhakar JV, Sathishkumar R. Molecular phylogeny of the Ficus virens complex (Moraceae). Genome 2020; 63:597-606. [PMID: 32822559 DOI: 10.1139/gen-2019-0210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The closely related species present in the subgenera of Urostigma are challenging to classify due to the existence of overlapping morphological characteristics, which makes identification habitually problematic. It is still unresolved whether the species of the Ficus virens complex, which includes F. virens, F. middletonii, F. caulocarpa, F. concinna, and F. superba, are the same or distinct species due to the complexities in classification. To clarify the circumscription between the species and re-evaluate the taxonomical status, morphological characteristics were extensively examined; further, a phylogenetic reconstruction based on two DNA markers (ITS2 and trnH-psbA) in combination with morphological traits was carried out. The phylogenetic tree constructed using the combined morphology and DNA markers revealed that the five species should be demarcated as independent species. This study supports the importance of using both molecular and morphological data for efficient discrimination of species having high similarities. Further investigation into the species present in the subgenera Urostigma may provide additional information regarding the ancestral traits and its evolutionary history.
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Affiliation(s)
- Karthikeyan Mahima
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Jana Venkata Sudhakar
- Department of Botany, S.R.K. Govt. Arts College, Affiliated to Pondicherry University, Yanam 533 464, UT of Puducherry, India
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
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Uncu AO. A trnH-psbA barcode genotyping assay for the detection of common apricot (Prunus armeniaca L.) adulteration in almond (Prunus dulcis Mill.). CYTA - JOURNAL OF FOOD 2020. [DOI: 10.1080/19476337.2020.1727961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Ayse Ozgur Uncu
- Department of Biotechnology, Necmettin Erbakan University, Konya, Turkey
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Morello L, Braglia L, Gavazzi F, Gianì S, Breviario D. Tubulin-Based DNA Barcode: Principle and Applications to Complex Food Matrices. Genes (Basel) 2019; 10:genes10030229. [PMID: 30889932 PMCID: PMC6471244 DOI: 10.3390/genes10030229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/13/2022] Open
Abstract
The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.
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Key Words
- The DNA polymorphism diffusely present in the introns of the members of the Eukaryotic beta-tubulin gene families, can be conveniently used to establish a DNA barcoding method, named tubulin-based polymorphism (TBP), that can reliably assign specific genomic fingerprintings to any plant or/and animal species. Similarly, many plant varieties can also be barcoded by TBP. The method is based on a simple cell biology concept that finds a conveniently exploitable molecular basis. It does not depend on DNA sequencing as the most classically established DNA barcode strategies. Successful applications, diversified for the different target sequences or experimental purposes, have been reported in many different plant species and, of late, a new a version applicable to animal species, including fishes, has been developed. Also, the TBP method is currently used for the genetic authentication of plant material and derived food products. Due to the use of a couple of universal primer pairs, specific for plant and animal organisms, respectively, it is effective in metabarcoding a complex matrix allowing an easy and rapid recognition of the different species present in a mixture. A simple, dedicated database made up by the genomic profile of reference materials is also part of the analytical procedure. Here we will provide some example of the TBP application and will discuss its features and uses in comparison with the DNA sequencing-based methods.
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Affiliation(s)
- Laura Morello
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Luca Braglia
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Floriana Gavazzi
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Silvia Gianì
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
| | - Diego Breviario
- Istituto Biologia e Biotecnologia Agraria, Via Adolfo Corti 12, 20131 Milano, Italy.
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Uncu AT, Uncu AO. Plastid trnH-psbA intergenic spacer serves as a PCR-based marker to detect common grain adulterants of coffee ( Coffea arabica L.). Food Control 2018. [DOI: 10.1016/j.foodcont.2018.03.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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10
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Uncu AO, Torlak E, Uncu AT. A Cost-Efficient and Simple Plant Oil DNA Extraction Protocol Optimized for DNA-Based Assessment of Product Authenticity. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1070-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Bishoyi AK, Kavane A, Sharma A, Geetha KA. A report on identification of sequence polymorphism in barcode region of six commercially important Cymbopogon species. Mol Biol Rep 2017; 44:19-24. [PMID: 28110431 DOI: 10.1007/s11033-017-4097-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 01/02/2017] [Indexed: 11/26/2022]
Abstract
CYMBOPOGON: is an important member of grass family Poaceae, cultivated for essential oils which have greater medicinal and industrial value. Taxonomic identification of Cymbopogon species is determined mainly by morphological markers, odour of essential oils and concentration of bioactive compounds present in the oil matrices which are highly influenced by environment. Authenticated molecular marker based taxonomical identification is also lacking in the genus; hence effort was made to evaluate potential DNA barcode loci in six commercially important Cymbopogon species for their individual discrimination and authentication at the species level. Four widely used DNA barcoding regions viz., ITS 1 & ITS 2 spacers, matK, psbA-trnH and rbcL were taken for the study. Gene sequences of the same or related genera of the concerned loci were mined from NCBI domain and primers were designed and validated for barcode loci amplification. Out of the four loci studied, sequences from matK and ITS spacer loci revealed 0.46% and 5.64% nucleotide sequence diversity, respectively whereas the other two loci i.e., psbA-trnH and rbcL showed 100% sequence homology. The newly developed primers can be used for barcode loci amplification in the genus Cymbopogon. The identified Single Nucleotide Polymorphisms from the studied sequences may be used as barcodes for the six Cymbopogon species. The information generated can also be utilized for barcode development of the genus by including more number of Cymbopgon species in future.
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Affiliation(s)
- Ashok Kumar Bishoyi
- PDPIAS, Charotar University of Science and Technology, Changa, Anand, Gujarat, India
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Boriavi, Anand, Gujarat, India
| | - Aarti Kavane
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Boriavi, Anand, Gujarat, India
| | - Anjali Sharma
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Boriavi, Anand, Gujarat, India
| | - K A Geetha
- ICAR-Directorate of Medicinal and Aromatic Plant Research, Boriavi, Anand, Gujarat, India.
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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.
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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
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