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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.
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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.)
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Tsaballa A, Kelesidis G, Krigas N, Sarropoulou V, Bagatzounis P, Grigoriadou K. Taxonomic Identification and Molecular DNA Barcoding of Collected Wild-Growing Orchids Used Traditionally for Salep Production. PLANTS (BASEL, SWITZERLAND) 2023; 12:3038. [PMID: 37687285 PMCID: PMC10489719 DOI: 10.3390/plants12173038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023]
Abstract
Molecular DNA barcoding combined with botanical taxonomy can be used for the identification and conservation of collected Greek orchids used for salep production as well as in the regulation of fair salep trade. A modified CTAB protocol was used for DNA extraction, amplification of barcoding regions (ITS, matK, rbcL, trnH-psbA), and sequencing. Sequencing data were assembled using Bioedit software, and the BLAST algorithm was used on the NCBI database for species identification at the genus level. Molecular barcoding data based on genetic similarity identification was in full coherence with taxonomic classification based on morphological data. The combination of ITS and matK exhibited a greater capacity to identify a species among the Greek salep samples. Out of the 53 samples examined, 52.9% were classified as Dactylorhiza spp. and 33.3% as Anacamptis spp., whereas only 6 samples were identified as Orchis spp. (11.8%). Given that a superior-quality salep beverage comes from tubers of the latter, the number of samples classified as such in northwestern Greece is unexpectedly low. A database of 53 original reference sequences from wild-growing samples of Greek origin was generated, providing a valuable resource for the identification of other salep samples from different regions. The DNA barcoding results unveiled that salep samples from northwestern Greece are related to nine members of four different genera of Orchidaceae. All species are nationally protected and covered by the CITES convention, while many of these orchids are included in the EU Directive 92/43/EEC appendix as "Other Important Species". Thus, expedited coordinated management actions are needed to ensure their survival in the future.
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Affiliation(s)
- Aphrodite Tsaballa
- Hellenic Agricultural Organization Demeter (ELGO-DIMITRA), Institute of Plant Breeding and Genetic Resources, Thermi, 57001 Thessaloniki, Greece; (A.T.); (G.K.); (N.K.); (V.S.)
| | - George Kelesidis
- Hellenic Agricultural Organization Demeter (ELGO-DIMITRA), Institute of Plant Breeding and Genetic Resources, Thermi, 57001 Thessaloniki, Greece; (A.T.); (G.K.); (N.K.); (V.S.)
| | - Nikos Krigas
- Hellenic Agricultural Organization Demeter (ELGO-DIMITRA), Institute of Plant Breeding and Genetic Resources, Thermi, 57001 Thessaloniki, Greece; (A.T.); (G.K.); (N.K.); (V.S.)
| | - Virginia Sarropoulou
- Hellenic Agricultural Organization Demeter (ELGO-DIMITRA), Institute of Plant Breeding and Genetic Resources, Thermi, 57001 Thessaloniki, Greece; (A.T.); (G.K.); (N.K.); (V.S.)
| | - Panagiotis Bagatzounis
- ‘Spices Bagatzounis’ Company: El Greco, Natural Herbs & Teas, Vatero, 50100 Kozani, Greece;
| | - Katerina Grigoriadou
- Hellenic Agricultural Organization Demeter (ELGO-DIMITRA), Institute of Plant Breeding and Genetic Resources, Thermi, 57001 Thessaloniki, Greece; (A.T.); (G.K.); (N.K.); (V.S.)
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Erst A, Nikulin A, Nikulin V, Ebel A, Zibzeev E, Sharples M, Baasanmunkh S, Choi HJAE, Olonova M, Pyak A, Gureyeva I, Erst T, Kechaykin A, Luferov A, Maltseva SYU, Nobis M, Lian L, Wang W. Distribution analysis, updated checklist, and DNA barcodes of the endemic vascular flora of the Altai mountains, a Siberian biodiversity hotspot. SYST BIODIVERS 2022. [DOI: 10.1080/14772000.2022.2049391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- A.S. Erst
- Central Siberian Botanical Garden, Russian Academy of Sciences, Novosibirsk, Russia
- Laboratory of the Herbarium, Tomsk State University, Tomsk, Russia
| | - A.YU. Nikulin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - V.YU. Nikulin
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - A.L. Ebel
- Laboratory of the Herbarium, Tomsk State University, Tomsk, Russia
- Research Organization Department, Tuvan State University, 36 Lenin St., Kyzyl, 667000, Republic of Tuva, Russia
| | - E.V. Zibzeev
- Central Siberian Botanical Garden, Russian Academy of Sciences, Novosibirsk, Russia
| | - M.T. Sharples
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 80309, Colorado, USA
| | - S. Baasanmunkh
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
| | - Hyeok JAE Choi
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, South Korea
| | - M.V. Olonova
- Laboratory of the Herbarium, Tomsk State University, Tomsk, Russia
| | - A.I. Pyak
- Laboratory of the Herbarium, Tomsk State University, Tomsk, Russia
- Research Organization Department, Tuvan State University, 36 Lenin St., Kyzyl, 667000, Republic of Tuva, Russia
| | - I.I. Gureyeva
- Laboratory of the Herbarium, Tomsk State University, Tomsk, Russia
| | - T.V. Erst
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - A. Kechaykin
- South-Siberian Botanical Garden, Altai State University, pr. Lenina, 61, Barnaul, 656049, Russia
| | - A. Luferov
- Federal State Autonomous Educational Institution of Higher Education I.M. Sechenov First Moscow State, Medical University of the Ministry of Health of the Russian Federation, 8 Izmailovsky Ave, Moscow, 105043, Russia
| | - S. YU. Maltseva
- Laboratory of Molecular Systematics of Aquatic Plants, К.А. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, Russia
| | - M. Nobis
- Department of Taxonomy, Phytogeography and Palaeobotany, Institute of Botany, Jagiellonian University, Kraków, Poland
| | - L. Lian
- Institute of Botany, Chinese Academy of Sciences, State Key Laboratory of Systematic and Evolutionary Botany, Beijing, 100093, China
| | - W. Wang
- Institute of Botany, Chinese Academy of Sciences, State Key Laboratory of Systematic and Evolutionary Botany, Beijing, 100093, China
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DNA Barcoding Medicinal Plant Species from Indonesia. PLANTS 2022; 11:plants11101375. [PMID: 35631799 PMCID: PMC9147630 DOI: 10.3390/plants11101375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/17/2022]
Abstract
Over the past decade, plant DNA barcoding has emerged as a scientific breakthrough and is often used to help with species identification or as a taxonomical tool. DNA barcoding is very important in medicinal plant use, not only for identification purposes but also for the authentication of medicinal products. Here, a total of 61 Indonesian medicinal plant species from 30 families and a pair of ITS2, matK, rbcL, and trnL primers were used for a DNA barcoding study consisting of molecular and sequence analyses. This study aimed to analyze how the four identified DNA barcoding regions (ITS2, matK, rbcL, and trnL) aid identification and conservation and to investigate their effectiveness for DNA barcoding for the studied species. This study resulted in 212 DNA barcoding sequences and identified new ones for the studied medicinal plant species. Though there is no ideal or perfect region for DNA barcoding of the target species, we recommend matK as the main region for Indonesian medicinal plant identification, with ITS2 and rbcL as alternative or complementary regions. These findings will be useful for forensic studies that support the conservation of medicinal plants and their national and global use.
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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.
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Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [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: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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Zhou T, Jiang W, Wang H, Cui Y. DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China. Biodivers Data J 2021; 9:e73556. [PMID: 34949956 PMCID: PMC8692306 DOI: 10.3897/bdj.9.e73556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 12/08/2021] [Indexed: 11/17/2022] Open
Abstract
Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifextubifex and Lumbriculusvariegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.
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Affiliation(s)
- Tingting Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences Beijing China
| | - Wei Jiang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan China.,University of Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences Beijing China
| | - Hongzhu Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan China
| | - Yongde Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences Wuhan China
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Bianchi FM, Gonçalves LT. Borrowing the Pentatomomorpha tome from the DNA barcode library: Scanning the overall performance of
cox1
as a tool. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12476] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Filipe Michels Bianchi
- Laboratório de Entomologia Sistemática Departamento de Zoologia Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
- Programa de Pós‐Graduação em Biologia Animal Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Leonardo Tresoldi Gonçalves
- Laboratório de Drosophila Departamento de Genética Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
- Programa de Pós‐Graduação em Genética e Biologia Molecular Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
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Wang N, Xing RR, Zhou MY, Sun RX, Han JX, Zhang JK, Zheng WJ, Chen Y. Application of DNA barcoding and metabarcoding for species identification in salmon products. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2021; 38:754-768. [PMID: 33783328 DOI: 10.1080/19440049.2020.1869324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mislabelling is a significant manifestation of food fraud. Traditional Sanger sequencing technology is the gold standard for seafood species identification. However, this method is not suitable for analysing processed samples that may contain more than one species. This study tested the feasibility of next-generation sequencing in identifying mixed salmon products. Salmon samples containing up to eight species were amplified using 16S rRNA mini-barcode primers, and sequenced on an Illumina HiSeq2500 platform. All species were accurately identified, and mixtures as low as 1% (w/w) could be detected. Furthermore, this study conducted a market survey of 32 products labelled as salmon. For pure and mixed fish products, Sanger and next-generation sequencing techniques were respectively used for species identification, and for NGS results, we also used real-time PCR method to cross-validate the mixed products to further verify the accuracy of the DNA metabarcoding technology established in this study. DNA barcoding and metabarcoding of commercial salmon food products revealed the presence of mislabelling in 16 of 32 (50%) samples. The developed DNA barcoding and metabarcoding methods are useful for the identification of salmon species in food and can be used for quality control of various types of salmon products.
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Affiliation(s)
- Nan Wang
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Ran-Ran Xing
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Meng-Yue Zhou
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Rui-Xue Sun
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China.,College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Jian-Xun Han
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Jiu-Kai Zhang
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Wen-Jie Zheng
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Normal University, Tianjin, China
| | - Ying Chen
- Agro-product Safety Research Center, Chinese Academy of Inspection and Quarantine, Beijing, China
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Baharmand I, Coatsworth H, Peach DAH, Belton P, Lowenberger C. Molecular relationships of introduced Aedes japonicus (Diptera: Culicidae) populations in British Columbia, Canada using mitochondrial DNA. JOURNAL OF VECTOR ECOLOGY : JOURNAL OF THE SOCIETY FOR VECTOR ECOLOGY 2020; 45:285-296. [PMID: 33207061 DOI: 10.1111/jvec.12399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Aedes japonicus japonicus (Theobald) is a relatively recent immigrant to the Pacific Northwest, having been collected in Washington State in 2001 and in British Columbia (BC) since 2014. We applied a molecular barcoding approach to determine the phylogenetic relationship of Ae. j. japonicus populations in BC with those from around the world. We sequenced a 617 base-pair segment of the cytochrome c oxidase 1 gene and a 330 base-pair region of the NADH dehydrogenase 4 gene to find genetic variation and characterize phylogenetic and haplotypic relationships based on nucleotide divergences. Our results revealed low genetic diversity in the BC samples, suggesting that these populations arose from the same introduction event. However, our approach lacked the granularity to identify the exact country of origin of the Ae. j. japonicus collected in BC. Future efforts should focus on detecting and preventing new Ae. j. japonicus introductions, recognizing that current molecular techniques are unable to pin-point the precise source of an introduction.
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Affiliation(s)
- Iman Baharmand
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Heather Coatsworth
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Daniel A H Peach
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Peter Belton
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Carl Lowenberger
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
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Raupach MJ, Hannig K, Morinière J, Hendrich L. A DNA barcode library for ground beetles of Germany: the genus Pterostichus Bonelli, 1810 and allied taxa (Insecta, Coleoptera, Carabidae). Zookeys 2020; 980:93-117. [PMID: 33192140 PMCID: PMC7642132 DOI: 10.3897/zookeys.980.55979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/04/2020] [Indexed: 11/12/2022] Open
Abstract
Species of the ground beetle genus Pterostichus Bonelli, 1810 are some of the most common carabids in Europe. This publication provides a first comprehensive DNA barcode library for this genus and allied taxa including Abax Bonelli, 1810, Molops Bonelli, 1810, Poecilus Bonelli, 1810, and Stomis Clairville, 1806 for Germany and Central Europe in general. DNA barcodes were analyzed from 609 individuals that represent 51 species, including sequences from previous studies as well as more than 198 newly generated sequences. The results showed a 1:1 correspondence between BIN and traditionally recognized species for 44 species (86%), whereas two (4%) species were characterized by two BINs. Three BINs were found for one species (2%), while one BIN for two species was revealed for two species pairs (8%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for four species pairs. Haplotype sharing was found for two closely related species pairs: Pterostichusadstrictus Eschscholtz, 1823/Pterostichusoblongopunctatus (Fabricius, 1787) and Pterostichusnigrita Paykull, 1790/Pterostichusrhaeticus Heer, 1837. In contrast to this, high intraspecific sequence divergences with values above 2.2% were shown for three species (Molopspiceus (Panzer, 1793), Pterostichuspanzeri (Panzer, 1805), Pterostichusstrenuus (Panzer, 1793)). Summarizing the results, the present DNA barcode library does not only allow the identification of most of the analyzed species, but also provides valuable information for alpha-taxonomy as well as for ecological and evolutionary research. This library represents another step in building a comprehensive DNA barcode library of ground beetles as part of modern biodiversity research.
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Affiliation(s)
- Michael J Raupach
- Sektion Hemiptera, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany
| | | | - Jérome Morinière
- AIM - Advanced Identification Methods GmbH, Spinnereistraße 11, 04179 Leipzig
| | - Lars Hendrich
- Sektion Insecta varia, Bavarian State Collection of Zoology (SNSB - ZSM), Münchhausenstraße 21, 81247 München, Germany
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13
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Martín MP, Daniëls PP, Erickson D, Spouge JL. Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera. PLoS One 2020; 15:e0237507. [PMID: 32813726 PMCID: PMC7437900 DOI: 10.1371/journal.pone.0237507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding can identify biological species and provides an important tool in diverse applications, such as conserving species and identifying pathogens, among many others. If combined with statistical tests, DNA barcoding can focus taxonomic scrutiny onto anomalous species identifications based on morphological features. Accordingly, we put nonparametric tests into a taxonomic context to answer questions about our sequence dataset of the formal fungal barcode, the nuclear ribosomal internal transcribed spacer (ITS). For example, does DNA barcoding concur with annotated species identifications significantly better if expert taxonomists produced the annotations? Does species assignment improve significantly if sequences are restricted to lengths greater than 500 bp? Both questions require a figure of merit to measure of the accuracy of species identification, typically provided by the probability of correct identification (PCI). Many articles on DNA barcoding use variants of PCI to measure the accuracy of species identification, but do not provide the variants with names, and the absence of explicit names hinders the recognition that the different variants are not comparable from study to study. We provide four variant PCIs with a name and show that for fixed data they follow systematic inequalities. Despite custom, therefore, their comparison is at a minimum problematic. Some popular PCI variants are particularly vulnerable to errors in species annotation, insensitive to improvements in a barcoding pipeline, and unable to predict identification accuracy as a database grows, making them unsuitable for many purposes. Generally, the Fractional PCI has the best properties as a figure of merit for species identification. The fungal genus Ramaria provides unusual taxonomic difficulties. As a case study, it shows that a good taxonomic background can be combined with the pertinent summary statistics of molecular results to improve the identification of doubtful samples, linking both disciplines synergistically.
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Affiliation(s)
- María P. Martín
- Department of Mycology, Real Jardín Botánico-CSIC, Madrid, Spain
| | - Pablo P. Daniëls
- Department of Botany, Ecology and Plant Physiology, Campus Rabanales, University of Córdoba, Córdoba, Spain
| | - David Erickson
- Joint Institute of Food Safety and Applied Nutrition, University of Maryland, College Park, Maryland, United States of America
| | - John L. Spouge
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, United States of America
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Gaillard CM, Pion SD, Hamou H, Sirima C, Bizet C, Lemarcis T, Rodrigues J, Esteban A, Peeters M, Mpoudi Ngole E, Mombo I, Liégeois F, Martin C, Boussinesq M, Locatelli S. Detection of DNA of filariae closely related to Mansonella perstans in faecal samples from wild non-human primates from Cameroon and Gabon. Parasit Vectors 2020; 13:313. [PMID: 32546281 PMCID: PMC7298833 DOI: 10.1186/s13071-020-04184-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/12/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The Onchocercidae is a family of filarial nematodes with several species of medical or veterinary importance. Microfilariae are found in the blood and/or the dermis and are usually diagnosed in humans by microscopy examination of a blood sample or skin biopsy. The main objectives of this study were to evaluate whether filariae DNA can be detected in faecal samples of wild non-human primates (NHPs), whether the detected parasites were closely related to those infecting humans and whether filarial DNA detection in faeces is associated with co-infections with nematodes (Oesophagostumum sp. and Necator sp.) known to cause blood loss while feeding on the host intestinal mucosa. METHODS A total of 315 faecal samples from 6 species of NHPs from Cameroon and Gabon were analysed. PCRs targeted DNA fragments of cox1 and 12S rDNA genes, to detect the presence of filariae, and the internal transcribed spacer 2 (ITS2), to detect the presence of Oesophagostomum sp. and Necator sp. infections. RESULTS Among the 315 samples analysed, 121 produced sequences with > 90% homology with Onchocercidae reference sequences. However, 63% of the 12S rDNA and 78% of the cox1 gene sequences were exploitable for phylogenetic analyses and the amplification of the 12S rDNA gene showed less discriminating power than the amplification of the cox1 fragment. Phylogenetic analyses showed that the cox1 sequences obtained from five chimpanzee DNA faecal samples from Gabon and two from Cameroon cluster together with Mansonella perstans with high bootstrap support. Most of the remaining sequences clustered together within the genus Mansonella, but the species could not be resolved. Among the NHP species investigated, a significant association between filarial DNA detection and Oesophagostomum sp. and Necator sp. infection was observed only in gorillas. CONCLUSIONS To our knowledge, this is the first study reporting DNA from Mansonella spp. in faecal samples. Our results raise questions about the diversity and abundance of these parasites in wildlife, their role as sylvatic reservoirs and their potential for zoonotic transmission. Future studies should focus on detecting variants circulating in both human and NHPs, and improve the molecular information to resolve or support taxonomy classification based on morphological descriptions.
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Affiliation(s)
| | | | - Hadjira Hamou
- IRD UMI 233-INSERM U1175, University of Montpellier, Montpellier, France
| | - Constant Sirima
- IRD UMI 233-INSERM U1175, University of Montpellier, Montpellier, France
| | - Charlotte Bizet
- IRD UMI 233-INSERM U1175, University of Montpellier, Montpellier, France
| | - Thomas Lemarcis
- IRD UMI 233-INSERM U1175, University of Montpellier, Montpellier, France
| | - Jules Rodrigues
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM UMR7245), Muséum national d'Histoire naturelle, CNRS, Paris, France
| | - Amandine Esteban
- IRD UMI 233-INSERM U1175, University of Montpellier, Montpellier, France
| | - Martine Peeters
- IRD UMI 233-INSERM U1175, University of Montpellier, Montpellier, France
| | - Eitel Mpoudi Ngole
- Projet Prévention du Sida au Cameroun (PRESICA) and Virology Laboratory IMPM/IRD, Yaoundé, Cameroon
| | - Illich Mombo
- Centre International de Recherches Médicales, BP 769, Franceville, Gabon
| | - Florian Liégeois
- Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution, Contrôle, UMR 224 IRD/CNRS/UM1, 34394, Montpellier, France
| | - Coralie Martin
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM UMR7245), Muséum national d'Histoire naturelle, CNRS, Paris, France
| | - Michel Boussinesq
- IRD UMI 233-INSERM U1175, University of Montpellier, Montpellier, France
| | - Sabrina Locatelli
- IRD UMI 233-INSERM U1175, University of Montpellier, Montpellier, France.
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15
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A world review of reported myiases caused by flower flies (Diptera: Syrphidae), including the first case of human myiasis from Palpada scutellaris (Fabricius, 1805). Parasitol Res 2020; 119:815-840. [PMID: 32006229 DOI: 10.1007/s00436-020-06616-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/22/2020] [Indexed: 10/25/2022]
Abstract
Rat-tailed larvae of the syrphid species Palpada scutellaris (Fabricius, 1805) are documented causing an enteric human myiasis in Costa Rica. This is the first time that the genus Palpada is recorded as a human myiasis agent. We report a 68-year-old woman with intestinal pain and bloody diarrhea with several live Palpada larvae present in the stool. Using molecular techniques (DNA barcodes) and both electronic and optical microscopy to study the external morphology, the preimaginal stages of the fly were unambiguously identified. An identification key to all syrphid genera actually known as agents of human and animal myiases is provided for larvae, puparia, and adults. Moreover, a critical world review of more than 100 references of Syrphidae as myiasis agents is also given, with emphasis on the species with rat-tailed larvae.
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16
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Singh M, Singh N. DNA Barcoding for Species Identification in Genetically Engineered Fungi. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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17
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Naseem MT, Ashfaq M, Khan AM, Rasool A, Asif M, Hebert PDN. BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae). PLoS One 2019; 14:e0220426. [PMID: 31821347 PMCID: PMC6903727 DOI: 10.1371/journal.pone.0220426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 11/25/2022] Open
Abstract
DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.
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Affiliation(s)
- Muhammad Tayyib Naseem
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | - Arif Muhammad Khan
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Zoology, University of Swat, Swat, Pakistan
| | - Muhammad Asif
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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18
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Rao MS, Chakraborty G, Murthy KS. Market Drivers and Discovering Technologies in Meat Species Identification. FOOD ANAL METHOD 2019. [DOI: 10.1007/s12161-019-01591-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Kreuzer M, Howard C, Adhikari B, Pendry CA, Hawkins JA. Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis. FRONTIERS IN PLANT SCIENCE 2019; 10:586. [PMID: 31139202 PMCID: PMC6527895 DOI: 10.3389/fpls.2019.00586] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/18/2019] [Indexed: 05/12/2023]
Abstract
DNA barcoding of herbal medicines has been mainly concerned with authentication of products in trade and has raised awareness of species substitution and adulteration. More recently DNA barcodes have been included in pharmacopoeias, providing tools for regulatory purposes. The commonly used DNA barcoding regions in plants often fail to resolve identification to species level. This can be especially challenging in evolutionarily complex groups where incipient or reticulate speciation is ongoing. In this study, we take a phylogenomic approach, analyzing whole plastid sequences from the evolutionarily complex genus Berberis in order to develop DNA barcodes for the medicinally important species Berberis aristata. The phylogeny reconstructed from an alignment of ∼160 kbp of chloroplast DNA for 57 species reveals that the pharmacopoeial species in question is polyphyletic, complicating development of a species-specific DNA barcode. Instead we propose a DNA barcode that is clade specific, using our phylogeny to define Operational Phylogenetic Units (OPUs). The plastid alignment is then reduced to small, informative DNA regions including nucleotides diagnostic for these OPUs. These DNA barcodes were tested on commercial samples, and shown to discriminate plants in trade and therefore to meet the requirement of a pharmacopoeial standard. The proposed method provides an innovative approach for inferring DNA barcodes for evolutionarily complex groups for regulatory purposes and quality control.
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Affiliation(s)
- Marco Kreuzer
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Caroline Howard
- BP-NIBSC Herbal Laboratory, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | | | - Julie A. Hawkins
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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20
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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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21
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Khilare V, Tiknaik A, Prakash B, Ughade B, Korhale G, Nalage D, Ahmed N, Khedkar C, Khedkar G. Multiple tests on saffron find new adulterant materials and reveal that Ist grade saffron is rare in the market. Food Chem 2019; 272:635-642. [DOI: 10.1016/j.foodchem.2018.08.089] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022]
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22
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Oliveira RRM, Nunes GL, de Lima TGL, Oliveira G, Alves R. PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly. BMC Bioinformatics 2018; 19:297. [PMID: 30089465 PMCID: PMC6083499 DOI: 10.1186/s12859-018-2307-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 07/30/2018] [Indexed: 11/19/2022] Open
Abstract
Background Taxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it’s often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discovery and identification and have been widely used for taxonomic identification by targeting known gene regions that permit to discriminate these species. DNA barcode sequence analysis is usually carried out with processes and tools that still demand a high interaction with the user or researcher. To reduce at most such interaction, we proposed PIPEBAR, a pipeline for DNA chromatograms analysis of Sanger platform sequencing, ensuring high quality consensus sequences along with efficient running time. We also proposed a paired-end reads assembly tool, OverlapPER, which is used in sequence or independently of PIPEBAR. Results PIPEBAR is a command line tool to automatize the processing of large number of trace files. It is accurate as the proprietary Geneious tool and faster than most popular software for barcoding analysis. It is 7 times faster than Geneious and 14 times faster than SeqTrace for processing hundreds of barcoding sequences. OverlapPER is a novel tool for overlapping paired-end reads accurately that accepts both substitution and indel errors and returns both overlapped and non-overlapped regions between a pair of reads. OverlapPER obtained the best results compared to currently used tools when merging 1,000,000 simulated paired-end reads. Conclusions PIPEBAR and OverlapPER run on most operating systems and are freely available, along with supporting code and documentation, at https://sourceforge.net/projects/PIPEBAR/ and https://sourceforge.net/projects/overlapper-reads/. Electronic supplementary material The online version of this article (10.1186/s12859-018-2307-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Renato Renison Moreira Oliveira
- Instituto Tecnológico Vale, Belém, Pará, Brazil. .,Computer Science Graduate Program (PPGCC), UFPA (Pará-PA), Belém, Pará, Brazil. .,Laboratory of Bioinformatics and High-performance Computing (LaBioCAD), UFPA (Pará-PA), Belém, Pará, Brazil.
| | | | | | - Guilherme Oliveira
- Instituto Tecnológico Vale, Belém, Pará, Brazil.,Genetics Graduate Program, UFPA (Pará-PA), Belém, Pará, Brazil
| | - Ronnie Alves
- Instituto Tecnológico Vale, Belém, Pará, Brazil. .,Computer Science Graduate Program (PPGCC), UFPA (Pará-PA), Belém, Pará, Brazil. .,Laboratory of Bioinformatics and High-performance Computing (LaBioCAD), UFPA (Pará-PA), Belém, Pará, Brazil.
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23
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Zhong W, Tan Z, Wang B, Yan H. Next-generation sequencing analysis of Pardosa pseudoannulata's diet composition in different habitats. Saudi J Biol Sci 2018; 26:165-172. [PMID: 30622422 PMCID: PMC6319085 DOI: 10.1016/j.sjbs.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/03/2018] [Accepted: 08/05/2018] [Indexed: 11/24/2022] Open
Abstract
Spiders are the most common and predominant predators in terrestrial ecosystems. The predatory behavior of spiders affects the energy flow across the food web within an ecosystem. Traditiaonal methods for analyzing spider diets such as field observation, anatomy and faeces analysis are not suitable for spider experiments due to spiders’ special dietary behavior. The molecular method based on the specific primers of prey DNA seems to be inefficient either in spite of its wide application in diet analysis. As the next-generation sequencing (NGS) technology becomes prevalent in many different areas, several cases of the NGS-based analysis of mammal diets have been published. This study analyzed the diet differences of Pardosa pseudoannulata (Araneae: Lycosidae) in four habitats (a wetland, a tea plantation, an alpine meadow and a paddy field) by using the NGS technology, combined with the DNA barcode method. The results suggested that the Pardosa pseudoannulata feed on a broad range of prey, and 7 orders and 24 families of insects were detected in the four investigated habitats. Moreover, it is found that the diet diversity of Pardosa pseudoannulata is greatly influenced by their living environments and seasons. In a nutshell, this study established an NGS-based methodology for spider diets analysis, and the results provided some basic materials to inform the protection and utilization of the Pardosa pseudoannulata as a potential eco-friendly predator against pests.
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Affiliation(s)
- Wentao Zhong
- College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
- Testing Institute of Product and Commodity Supervision, Changsha 410007, Hunan, China
| | - Zhaojun Tan
- College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
- Dongkou No.1 Middle School, Dongkou 422300, Hunan, China
| | - Bo Wang
- College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
- College of Engineering and Technology, Beijing Normal University, Zhuhai Campus, Zhuhai 519087, Guangdong, China
| | - Hengmei Yan
- College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China
- College of Engineering and Technology, Beijing Normal University, Zhuhai Campus, Zhuhai 519087, Guangdong, China
- Corresponding author at: College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, China.
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24
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Ahmed N, Sangale D, Tiknaik A, Prakash B, Hange R, Sanil R, Khan S, Khedkar G. Authentication of origin of meat species processed under various Indian culinary procedures using DNA barcoding. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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25
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Keroack CD, Williams KM, Fessler M, DeAngelis KE, Tsekitsidou E, Tozloski JM, Williams SA. A novel quantitative real-time PCR diagnostic assay for seal heartworm ( Acanthocheilonema spirocauda) provides evidence for possible infection in the grey seal ( Halichoerus grypus). Int J Parasitol Parasites Wildl 2018; 7:147-154. [PMID: 29988808 PMCID: PMC6031957 DOI: 10.1016/j.ijppaw.2018.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/29/2018] [Accepted: 04/05/2018] [Indexed: 11/15/2022]
Abstract
The distinct evolutionary pressures faced by Pinnipeds have likely resulted in strong coevolutionary ties to their parasites (Leidenberger et al., 2007). This study focuses on the phocid seal filarial heartworm species Acanthocheilonema spirocauda. A. spirocauda is known to infect a variety of phocid seals, but does not appear to be restricted to a single host species (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). However, to date, seal heartworm has never been reported in grey seals (Halichoerus grypus) (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). The proposed vector for seal heartworm is Echinophthirius horridus, the seal louse. Seal lice are known to parasitize a wide array of phocid seal species, including the grey seal. With the advent of climate change, disease burden is expected to increase across terrestrial and marine mammals (Harvell et al., 2002). Accordingly, increased prevalence of seal heartworm has recently been reported in harbor seals (Phoca vitulina) (Lehnert et al., 2015). Thus, the need for improved, rapid, and cost-effective diagnostics is urgent. Here we present the first A. spirocauda-specific rapid diagnostic test (a quantitative real-time PCR assay), based on a highly repetitive genomic DNA repeat identified using whole genome sequencing and subsequent bioinformatic analysis. The presence of an insect vector provides the opportunity to develop a multifunctional diagnostic tool that can be used not only to detect the parasite directly from blood or tissue specimens, but also as a molecular xenomonitoring (XM) tool that can be used to assess the epidemiological profile of the parasite by screening the arthropod vector. Using this assay, we provide evidence for the first reported case of seal heartworm in a grey seal.
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Campanaro A, Tommasi N, Guzzetti L, Galimberti A, Bruni I, Labra M. DNA barcoding to promote social awareness and identity of neglected, underutilized plant species having valuable nutritional properties. Food Res Int 2018; 115:1-9. [PMID: 30599919 DOI: 10.1016/j.foodres.2018.07.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/18/2018] [Accepted: 07/26/2018] [Indexed: 12/21/2022]
Abstract
It is estimated that about 7000 plant species and a large number of cultivars and varieties have been cultivated for consumption in human history. However, <0.5% of these currently provide the majority of human food energy needs worldwide (e.g., rice, wheat, maize, and potato). Global issues such as climate change, diffusion of pests, and resistance to agrochemical treatments are posing great concern about the sustainable cultivation of these major staples, especially in equatorial and tropical countries, such as Sub Saharan Africa. In addition, most of these regions contain malnutrition and micronutrient deficiencies, and the sum of such problems create serious implications at social, political, and economic levels. A possible solution relies on the exploitation of plant biodiversity and particularly on the so-called NUS (Neglected and Underutilized Species). These plants are traditionally grown in their centres of origin and continue to be maintained by sociocultural preferences, however they remain inadequately documented and neglected by formal research and conservation programs. Although they are important in terms of micronutrients and the ability to grow in harsh conditions, these species are falling into disuse due to agronomic, genetic, economic, and cultural reasons. To promote and spread their cultivation at the global scale, along with knowledge on their suitability for human nutrition, reliable identification systems are necessary to guarantee adequate authenticity along the entire supply chain and distribution network. A precise identification of the different species and their varieties is fundamental both to retrieve information on their origin and authenticate the raw materials (i.e., seeds, leaves and fruit) and related processed products that can be distributed at the local or global scale. DNA-based techniques can help achieve this mission. In particular, the DNA barcoding approach has gained a role of primary importance due to its universality and versatility. Here, we discuss the advantages in using DNA barcoding for the identification of some of the most representative NUS species, as well as their traceability and conservation of cultural practices around them.
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Affiliation(s)
- Ausilia Campanaro
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Nicola Tommasi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Lorenzo Guzzetti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Andrea Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Ilaria Bruni
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za Della Scienza 2, I-20126 Milan, Italy.
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Paixão RV, Ribolli J, Zaniboni-Filho E. Genetic Variation of the Endangered Neotropical Catfish Steindachneridion scriptum (Siluriformes: Pimelodidae). Front Genet 2018. [PMID: 29520295 PMCID: PMC5827538 DOI: 10.3389/fgene.2018.00048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Steindachneridion scriptum is an important species as a resource for fisheries and aquaculture; it is currently threatened and has a reduced occurrence in South America. The damming of rivers, overfishing, and contamination of freshwater environments are the main impacts on the maintenance of this species. We accessed the genetic diversity and structure of S. scriptum using the DNA barcode and control region (D-loop) sequences of 43 individuals from the Upper Uruguay River Basin (UUR) and 10 sequences from the Upper Paraná River Basin (UPR), which were obtained from GenBank. S. scriptum from the UUR and the UPR were assigned in two distinct molecular operational taxonomic units (MOTUs) with higher inter-specific K2P distance than the optimum threshold (OT = 0.0079). The COI Intra-MOTU distances of S. scriptum specimens from the UUR ranged from 0.0000 to 0.0100. The control region indicated a high number of haplotypes and low nucleotide diversity, compatible with a new population in recent expansion process. Genetic structure was observed, with high differentiation between UUR and UPR basins, identified by BAPS, haplotype network, AMOVA (FST = 0.78, p < 0.05) and Mantel test. S. scriptum from the UUR showed a slight differentiation (FST = 0.068, p < 0.05), but not isolation-by-distance. Negative values of Tajima’s D and Fu’s Fs suggest recent demographic oscillations. The Bayesian skyline plot analysis indicated possible population expansion from beginning 2,500 years ago and a recent reduction in the population size. Low nucleotide diversity, spatial population structure, and the reduction of effective population size should be considered for the planning of strategies aimed at the conservation and rehabilitation of this important fisheries resource.
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Affiliation(s)
- Rômulo V Paixão
- Laboratório de Biologia e Cultivo de Peixes de Água Doce, Departamento de Aquicultura, Universidade Federal de Santa Catarina, Florianópolis, Brazil.,Programa de Pós-Graduação em Aquicultura, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Josiane Ribolli
- Laboratório de Biologia e Cultivo de Peixes de Água Doce, Departamento de Aquicultura, Universidade Federal de Santa Catarina, Florianópolis, Brazil.,Programa de Pós-Graduação em Aquicultura, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Evoy Zaniboni-Filho
- Laboratório de Biologia e Cultivo de Peixes de Água Doce, Departamento de Aquicultura, Universidade Federal de Santa Catarina, Florianópolis, Brazil.,Programa de Pós-Graduação em Aquicultura, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Florianópolis, Brazil
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Phylogeography of the Red Algal Laurencia Complex in the Macaronesia Region and Nearby Coastal Areas: Recent Advances and Future Perspectives. DIVERSITY 2018. [DOI: 10.3390/d10010010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yu M, Jiao L, Guo J, Wiedenhoeft AC, He T, Jiang X, Yin Y. DNA barcoding of vouchered xylarium wood specimens of nine endangered Dalbergia species. PLANTA 2017; 246:1165-1176. [PMID: 28825134 DOI: 10.1007/s00425-017-2758-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/08/2017] [Indexed: 06/07/2023]
Abstract
ITS2+ trnH - psbA was the best combination of DNA barcode to resolve the Dalbergia wood species studied. We demonstrate the feasibility of building a DNA barcode reference database using xylarium wood specimens. The increase in illegal logging and timber trade of CITES-listed tropical species necessitates the development of unambiguous identification methods at the species level. For these methods to be fully functional and deployable for law enforcement, they must work using wood or wood products. DNA barcoding of wood has been promoted as a promising tool for species identification; however, the main barrier to extensive application of DNA barcoding to wood is the lack of a comprehensive and reliable DNA reference library of barcodes from wood. In this study, xylarium wood specimens of nine Dalbergia species were selected from the Wood Collection of the Chinese Academy of Forestry and DNA was then extracted from them for further PCR amplification of eight potential DNA barcode sequences (ITS2, matK, trnL, trnH-psbA, trnV-trnM1, trnV-trnM2, trnC-petN, and trnS-trnG). The barcodes were tested singly and in combination for species-level discrimination ability by tree-based [neighbor-joining (NJ)] and distance-based (TaxonDNA) methods. We found that the discrimination ability of DNA barcodes in combination was higher than any single DNA marker among the Dalbergia species studied, with the best two-marker combination of ITS2+trnH-psbA analyzed with NJ trees performing the best (100% accuracy). These barcodes are relatively short regions (<350 bp) and amplification reactions were performed with high success (≥90%) using wood as the source material, a necessary factor to apply DNA barcoding to timber trade. The present results demonstrate the feasibility of using vouchered xylarium specimens to build DNA barcoding reference databases.
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Affiliation(s)
- Min Yu
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Lichao Jiao
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Juan Guo
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Alex C Wiedenhoeft
- Center for Wood Anatomy Research, USDA Forest Service, Forest Products Laboratory, Madison, WI, 53726, USA
- Department of Botany, University of Wisconsin, Madison, WI, 53706, USA
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, 47907, USA
- Ciências Biológicas (Botânica), Univesidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Tuo He
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaomei Jiang
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China
| | - Yafang Yin
- Department of Wood Anatomy and Utilization, Chinese Research Institute of Wood Industry, Chinese Academy of Forestry, Beijing, 100091, China.
- Wood Collections (WOODPEDIA), Chinese Academy of Forestry, Beijing, 100091, China.
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El Sheikha AF, Mokhtar NFK, Amie C, Lamasudin DU, Isa NM, Mustafa S. Authentication technologies using DNA-based approaches for meats and halal meats determination. FOOD BIOTECHNOL 2017. [DOI: 10.1080/08905436.2017.1369886] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Aly Farag El Sheikha
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Department of Food Science and Technology, Faculty of Agriculture, Minufiya University, Shibin El Kom, Egypt
| | - Nur Fadhilah Khairil Mokhtar
- Laboratory of Halal Products Research Institute, Halal Products Research Institute, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Ceesay Amie
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Dhilia Udie Lamasudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Nurulfiza Mat Isa
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor, Malaysia
| | - Shuhaimi Mustafa
- Laboratory of Halal Products Research Institute, Halal Products Research Institute, Universiti Putra Malaysia (UPM), Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Selangor, Malaysia
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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.
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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
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Arenas M, Pereira F, Oliveira M, Pinto N, Lopes AM, Gomes V, Carracedo A, Amorim A. Forensic genetics and genomics: Much more than just a human affair. PLoS Genet 2017; 13:e1006960. [PMID: 28934201 PMCID: PMC5608170 DOI: 10.1371/journal.pgen.1006960] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
While traditional forensic genetics has been oriented towards using human DNA in criminal investigation and civil court cases, it currently presents a much wider application range, including not only legal situations sensu stricto but also and, increasingly often, to preemptively avoid judicial processes. Despite some difficulties, current forensic genetics is progressively incorporating the analysis of nonhuman genetic material to a greater extent. The analysis of this material-including other animal species, plants, or microorganisms-is now broadly used, providing ancillary evidence in criminalistics in cases such as animal attacks, trafficking of species, bioterrorism and biocrimes, and identification of fraudulent food composition, among many others. Here, we explore how nonhuman forensic genetics is being revolutionized by the increasing variety of genetic markers, the establishment of faster, less error-burdened and cheaper sequencing technologies, and the emergence and improvement of models, methods, and bioinformatics facilities.
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Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Filipe Pereira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Porto, Portugal
| | - Manuela Oliveira
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Centre of Mathematics of the University of Porto, Porto, Portugal
| | - Alexandra M. Lopes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Veronica Gomes
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - Angel Carracedo
- Institute of Forensic Sciences Luis Concheiro, University of Santiago de Compostela, Santiago de Compostela, Spain
- Genomics Medicine Group, CIBERER, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Amorim
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
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Mishra P, Kumar A, Nagireddy A, Shukla AK, Sundaresan V. Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia. PLoS One 2017; 12:e0182836. [PMID: 28829803 PMCID: PMC5567895 DOI: 10.1371/journal.pone.0182836] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 07/25/2017] [Indexed: 11/19/2022] Open
Abstract
DNA barcoding is used as a universal tool for delimiting species boundaries in taxonomically challenging groups, with different plastid and nuclear regions (rbcL, matK, ITS and psbA-trnH) being recommended as primary DNA barcodes for plants. We evaluated the feasibility of using these regions in the species-rich genus Terminalia, which exhibits various overlapping morphotypes with pantropical distribution, owing to its complex taxonomy. Terminalia bellerica and T. chebula are ingredients of the famous Ayurvedic Rasayana formulation Triphala, used for detoxification and rejuvenation. High demand for extracted phytochemicals as well as the high trade value of several species renders mandatory the need for the correct identification of traded plant material. Three different analytical methods with single and multilocus barcoding regions were tested to develop a DNA barcode reference library from 222 individuals representing 41 Terminalia species. All the single barcodes tested had a lower discriminatory power than the multilocus regions, and the combination of matK+ITS had the highest resolution rate (94.44%). The average intra-specific variations (0.0188±0.0019) were less than the distance to the nearest neighbour (0.106±0.009) with matK and ITS. Distance-based Neighbour Joining analysis outperformed the character-based Maximum Parsimony method in the identification of traded species such as T. arjuna, T. chebula and T. tomentosa, which are prone to adulteration. rbcL was shown to be a highly conservative region with only 3.45% variability between all of the sequences. The recommended barcode combination, rbcL+matK, failed to perform in the genus Terminalia. Considering the complexity of resolution observed with single regions, the present study proposes the combination of matK+ITS as the most successful barcode in Terminalia.
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Affiliation(s)
- Priyanka Mishra
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Amit Kumar
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Akshitha Nagireddy
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
| | - Ashutosh K. Shukla
- Biotechnology Division, CSIR—Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Velusamy Sundaresan
- Plant Biology and Systematics, CSIR—Central Institute of Medicinal and Aromatic Plants, Research Center, Bengaluru, Karnataka, India
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Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics 2017; 33:1630-1638. [PMID: 28108445 PMCID: PMC5447239 DOI: 10.1093/bioinformatics/btx025] [Citation(s) in RCA: 239] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/27/2016] [Accepted: 01/17/2017] [Indexed: 11/15/2022] Open
Abstract
MOTIVATION In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets; it does not account for divergent intraspecific variation and is slow for a large number of sequences. RESULTS We introduce the multi-rate PTP (mPTP), an improved method that alleviates the theoretical and technical shortcomings of PTP. It incorporates different levels of intraspecific genetic diversity deriving from differences in either the evolutionary history or sampling of each species. Results on empirical data suggest that mPTP is superior to PTP and popular distance-based methods as it, consistently yields more accurate delimitations with respect to the taxonomy (i.e., identifies more taxonomic species, infers species numbers closer to the taxonomy). Moreover, mPTP does not require any similarity threshold as input. The novel dynamic programming algorithm attains a speedup of at least five orders of magnitude compared to PTP, allowing it to delimit species in large (meta-) barcoding data. In addition, Markov Chain Monte Carlo sampling provides a comprehensive evaluation of the inferred delimitation in just a few seconds for millions of steps, independently of tree size. AVAILABILITY AND IMPLEMENTATION mPTP is implemented in C and is available for download at http://github.com/Pas-Kapli/mptp under the GNU Affero 3 license. A web-service is available at http://mptp.h-its.org . CONTACT : paschalia.kapli@h-its.org or alexandros.stamatakis@h-its.org or tomas.flouri@h-its.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- P Kapli
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - S Lutteropp
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - J Zhang
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - K Kobert
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - P Pavlidis
- Foundation for Research and Technology, Hellas Institute of Computer Science GR, Heraklion, Crete, Greece
| | - A Stamatakis
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - T Flouri
- The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Opportunities and challenges in metabarcoding approaches for helminth community identification in wild mammals. Parasitology 2017; 145:608-621. [PMID: 28534454 DOI: 10.1017/s0031182017000610] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite metabarcoding being widely used to analyse bacterial community composition, its application in parasitological research remains limited. What interest there has been has focused on previously intractable research settings where traditional methods are inappropriate, for example, in longitudinal studies and studies involving endangered species. In settings such as these, non-invasive sampling combined with metabarcoding can provide a fast and accurate assessment of component communities. In this paper we review the use of metabarcoding in the study of helminth communities in wild mammals, outlining the necessary procedures from sample collection to statistical analysis. We highlight the limitations of the metabarcoding approach and speculate on what type of parasitological study would benefit from such methods in the future.
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Palasio RGS, Guimarães MCDA, Ohlweiler FP, Tuan R. Molecular and morphological identification of Biomphalaria species from the state of São Paulo, Brazil. Zookeys 2017; 668:11-32. [PMID: 28769640 PMCID: PMC5534528 DOI: 10.3897/zookeys.668.10562] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/21/2017] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding and morphological characters were used to identify adult snails belonging to the genus Biomphalaria from 17 municipalities in the state of São Paulo, Brazil. The DNA barcode analysis also included twenty-nine sequences retrieved from GenBank. The final data set of 104 sequences of the mitochondrial cytochrome oxidase I (COI) gene was analyzed for K2P intraspecific and interspecific divergences, through tree-reconstruction methods (Neighbor-Joining, Maximum Likelihood and Bayesian inference), and by applying different models (ABGD, bPTP, GMYC) to partition the sequences according to the pattern of genetic variation. Twenty-seven morphological parameters of internal organs were used to identify specimens. The molecular taxonomy of Biomphalaria agreed with the morphological identification of specimens from the same collection locality. DNA barcoding may therefore be a useful supporting tool for identifying Biomphalaria snails in areas at risk for schistosomiasis.
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Affiliation(s)
- Raquel Gardini Sanches Palasio
- Department of Epidemiology, Faculty of Public Health, University of São Paulo, Pinheiros, SP, Brazil
- Biochemistry and Molecular Biology Laboratory, Superintendency for the Control of Endemic Diseases, Rua Paula Sousa, 166, Luz, São Paulo, SP, Brazil
| | - Marisa Cristina de Almeida Guimarães
- Malacology Laboratory, Regional Service SR-02, Superintendency for the Control of Endemic Diseases, São Vicente, Rua João Ramalho, 587, Centro, SP, Brazil
| | - Fernanda Pires Ohlweiler
- Malacology Laboratory, Special Programs Division SR-01, Superintendency for the Control of Endemic Diseases, Rua Cardeal Arcoverde, 2878 - Pinheiros, SP, Brazil
| | - Roseli Tuan
- Biochemistry and Molecular Biology Laboratory, Superintendency for the Control of Endemic Diseases, Rua Paula Sousa, 166, Luz, São Paulo, SP, Brazil
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Raja H, Miller AN, Pearce CJ, Oberlies NH. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community. JOURNAL OF NATURAL PRODUCTS 2017; 80:756-770. [PMID: 28199101 PMCID: PMC5368684 DOI: 10.1021/acs.jnatprod.6b01085] [Citation(s) in RCA: 373] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 05/17/2023]
Abstract
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community.
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Affiliation(s)
- Huzefa
A. Raja
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
| | - Andrew N. Miller
- Illinois
Natural History Survey, University of Illinois, Champaign, Illinois 61820, United States
| | - Cedric J. Pearce
- Mycosynthetix,
Inc., 505 Meadowland
Drive, Suite 103, Hillsborough, North Carolina 27278, United States
| | - Nicholas H. Oberlies
- Department
of Chemistry and Biochemistry, University
of North Carolina at Greensboro, Greensboro, North Carolina 27402, United States
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Mezzasalma V, Bruni I, Fontana D, Galimberti A, Magoni C, Labra M. A DNA barcoding approach for identifying species in Amazonian traditional medicine: The case of Piri-Piri. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Revised classification and phylogeny of an Afrotropical species group based on molecular and morphological data, with the description of a new genus (Coleoptera: Scarabaeidae: Onthophagini). ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0297-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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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.
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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
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de Sousa TP, Marques DKS, Vitorino CDA, Faria KDC, Braga GDSF, Ferreira DC, Venere PC. Cytogenetic and Molecular Data Support the Occurrence of Three Gymnotus Species (Gymnotiformes: Gymnotidae) Used as Live Bait in Corumbá, Brazil: Implications for Conservation and Management of Professional Fishing. Zebrafish 2017; 14:177-186. [PMID: 28151699 DOI: 10.1089/zeb.2016.1356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
In the Pantanal of Mato Grosso do Sul, electric fish (Gymnotus spp.) are the primary source of live bait, accounting for more than three-quarters of total sales. Based on chromosomal and molecular markers, the present study attempted to identify the Gymnotus species used as bait in the region of Corumbá, Mato Grosso do Sul, Brazil. Three species were detected, based on their distinct karyotypes: G. paraguensis (2n = 54), G. sylvius (2n = 40), and G. pantanal (2n = 39-40, X1X2Y/X1X1X2X2), with no evidence being found of interspecific hybrids. All three species presented a single nucleolar organizer regions (NOR) (heterochromatin CMA3+/DAPI-) and pericentromeric heterochromatin in almost all chromosomes, with a few distal and/or interstitial blocks. G. sylvius and G. pantanal had one and two pairs of chromosomes with 5S rDNA sites, respectively, while G. paraguensis had 17 chromosome pairs with these markers. The three species formed well-defined clusters in the DNA barcoding analysis. The integrated analysis of the cytogenetic and DNA barcoding data confirmed that the diversity of Gymnotus species exploited as live bait in the study region has been underestimated. These findings indicate that the markers analyzed represent valuable tools for the conservation and fishery management of the Gymnotus stocks exploited.
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Affiliation(s)
- Tatiane Pires de Sousa
- 1 Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil
| | | | - Carla de Andrade Vitorino
- 3 Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Karina de Cassia Faria
- 1 Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil
| | - Gisele da Silva Ferreira Braga
- 3 Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Daniela Cristina Ferreira
- 4 Programa de Pós-graduação em Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
| | - Paulo Cesar Venere
- 1 Programa de Pós-graduação em Ecologia e Conservação, Universidade do Estado de Mato Grosso, Nova Xavantina, MT, Brazil .,3 Programa de Pós-graduação em Ecologia e Conservação da Biodiversidade, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil .,4 Programa de Pós-graduação em Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, Brazil
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Machado CDB, Ishizuka TK, Freitas PDD, Valiati VH, Galetti PM. DNA barcoding reveals taxonomic uncertainty in Salminus (Characiformes). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1254390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Carolina De Barros Machado
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235 - SP-310, São Carlos, SP, 13565-905, Brazil
| | - Tamylin Kaori Ishizuka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235 - SP-310, São Carlos, SP, 13565-905, Brazil
| | - PatrÍcia Domingues De Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235 - SP-310, São Carlos, SP, 13565-905, Brazil
| | - Victor Hugo Valiati
- Laboratório de Biologia Molecular, Universidade do Vale do Rio dos Sinos, Avenida Unisinos, 950, São Leopoldo, RS, 93022-000, Brazil
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rodovia Washington Luís, Km 235 - SP-310, São Carlos, SP, 13565-905, Brazil
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Poisonous or non-poisonous plants? DNA-based tools and applications for accurate identification. Int J Legal Med 2016; 131:1-19. [PMID: 27796590 DOI: 10.1007/s00414-016-1460-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022]
Abstract
Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.
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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.
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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
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DNA Barcoding as a Molecular Tool to Track Down Mislabeling and Food Piracy. DIVERSITY-BASEL 2015. [DOI: 10.3390/d8010002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Ferri E, Galimberti A, Casiraghi M, Airoldi C, Ciaramelli C, Palmioli A, Mezzasalma V, Bruni I, Labra M. Towards a Universal Approach Based on Omics Technologies for the Quality Control of Food. BIOMED RESEARCH INTERNATIONAL 2015; 2015:365794. [PMID: 26783518 PMCID: PMC4691458 DOI: 10.1155/2015/365794] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/19/2015] [Indexed: 12/03/2022]
Abstract
In the last decades, food science has greatly developed, turning from the consideration of food as mere source of energy to a growing awareness on its importance for health and particularly in reducing the risk of diseases. Such vision led to an increasing attention towards the origin and quality of raw materials as well as their derived food products. The continuous advance in molecular biology allowed setting up efficient and universal omics tools to unequivocally identify the origin of food items and their traceability. In this review, we considered the application of a genomics approach known as DNA barcoding in characterizing the composition of foodstuffs and its traceability along the food supply chain. Moreover, metabolomics analytical strategies based on Nuclear Magnetic Resonance (NMR) and Mass Spectroscopy (MS) were discussed as they also work well in evaluating food quality. The combination of both approaches allows us to define a sort of molecular labelling of food that is easily understandable by the operators involved in the food sector: producers, distributors, and consumers. Current technologies based on digital information systems such as web platforms and smartphone apps can facilitate the adoption of such molecular labelling.
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Affiliation(s)
- Emanuele Ferri
- FEM2 Ambiente s.r.l., P.za della Scienza 2, 20126 Milan, Italy
| | - Andrea Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Cristina Airoldi
- BioNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Carlotta Ciaramelli
- BioNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Alessandro Palmioli
- FEM2 Ambiente s.r.l., P.za della Scienza 2, 20126 Milan, Italy
- BioNMR Lab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Valerio Mezzasalma
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Ilaria Bruni
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
| | - Massimo Labra
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
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Armani A, Giusti A, Guardone L, Castigliego L, Gianfaldoni D, Guidi A. Universal Primers Used for Species Identification of Foodstuff of Animal Origin: Effects of Oligonucleotide Tails on PCR Amplification and Sequencing Performance. FOOD ANAL METHOD 2015. [DOI: 10.1007/s12161-015-0301-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lawton SP, Lim RM, Dukes JP, Kett SM, Cook RT, Walker AJ, Kirk RS. Unravelling the riddle of Radix: DNA barcoding for species identification of freshwater snail intermediate hosts of zoonotic digeneans and estimating their inter-population evolutionary relationships. INFECTION GENETICS AND EVOLUTION 2015. [PMID: 26196736 DOI: 10.1016/j.meegid.2015.07.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Radix spp. are intermediate host snails for digenean parasites of medical and veterinary importance. Within this genus, species differentiation using shell and internal organ morphology can result in erroneous species identification, causing problems when trying to understand the population biology of Radix. In the present study, DNA barcoding, using cox1 and ITS2 sequences, identified populations of Radix auricularia and Radix balthica from specimens originally morphologically identified as Radix peregra from the UK. Assessment of cox1 and ITS2 as species identification markers showed that, although both markers differentiated species, cox1 possessed greater molecular diversity and higher phylogenetic resolution. Cox1 also proved useful for gaining insights into the evolutionary relationships of Radix species populations. Phylogenetic analysis and haplotype networks of cox1 indicated that R. auricularia appeared to have invaded the UK several times; some haplotypes forming a distinct UK specific clade, whilst others are more akin to those found on mainland Europe. This was in contrast to relationships between R. balthica populations, which had low molecular diversity and no distinct UK specific haplotypes, suggesting recent and multiple invasions from mainland Europe. Molecular techniques therefore appear to be crucial for distinguishing Radix spp., particularly using cox1. This barcoding marker also enables the population biology of Radix spp. to be explored, and is invaluable for monitoring the epidemiology of fluke diseases especially in the light of emerging diseases and food security.
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Affiliation(s)
- Scott P Lawton
- Molecular Parasitology Laboratory, School of Life Sciences, Kingston University, Kingston upon Thames, Surrey KT1 2EE, UK.
| | - Rivka M Lim
- Molecular Parasitology Laboratory, School of Life Sciences, Kingston University, Kingston upon Thames, Surrey KT1 2EE, UK
| | - Juliet P Dukes
- Molecular Parasitology Laboratory, School of Life Sciences, Kingston University, Kingston upon Thames, Surrey KT1 2EE, UK
| | - Stephen M Kett
- School of Life Sciences, Middlesex University, The Burroughs, London NW4 4BT, UK.
| | - Richard T Cook
- Molecular Parasitology Laboratory, School of Life Sciences, Kingston University, Kingston upon Thames, Surrey KT1 2EE, UK.
| | - Anthony J Walker
- Molecular Parasitology Laboratory, School of Life Sciences, Kingston University, Kingston upon Thames, Surrey KT1 2EE, UK.
| | - Ruth S Kirk
- Molecular Parasitology Laboratory, School of Life Sciences, Kingston University, Kingston upon Thames, Surrey KT1 2EE, UK.
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Rozo-Lopez P, Mengual X. Mosquito species (Diptera, Culicidae) in three ecosystems from the Colombian Andes: identification through DNA barcoding and adult morphology. Zookeys 2015; 513:39-64. [PMID: 26257568 PMCID: PMC4524277 DOI: 10.3897/zookeys.513.9561] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/01/2015] [Indexed: 01/09/2023] Open
Abstract
Colombia, one of the world's megadiverse countries, has a highly diverse mosquito fauna and a high prevalence of mosquito-borne diseases. In order to provide relevant information about the diversity and taxonomy of mosquito species in Colombia and to test the usefulness of DNA barcodes, mosquito species collected at different elevations in the departments of Antioquia and Caldas were identified combining adult morphology and barcode sequences. A total of 22 mosquito species from eight genera were identified using these combined techniques. We generated 77 barcode sequences with 16 species submitted as new country records for public databases. We examined the usefulness of DNA barcodes to discriminate mosquito species from the Neotropics by compiling 1,292 sequences from a total of 133 species and using the tree-based methods of neighbor-joining and maximum likelihood. Both methodologies provided similar results by resolving 105 species of mosquitoes separated into distinct clusters. This study shows the importance of combining classic morphological methodologies with molecular tools to accurately identify mosquitoes from Colombia.
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Affiliation(s)
- Paula Rozo-Lopez
- Rheinische Friedrich-Wilhelms-Universität Bonn. An der Immenburg 1, 53121 Bonn, Germany
| | - Ximo Mengual
- Zoologisches Forschungsmuseum Alexander Koenig. Adenauerallee 160, 53113 Bonn, Germany
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