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Rivarez MPS, Faure C, Svanella-Dumas L, Pecman A, Tušek-Žnidaric M, Schönegger D, De Jonghe K, Blouin A, Rasmussen DA, Massart S, Ravnikar M, Kutnjak D, Marais A, Candresse T. Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data. PHYTOPATHOLOGY 2023; 113:1729-1744. [PMID: 37399026 DOI: 10.1094/phyto-12-22-0465-v] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a diverse set of source organisms is atypical for ilarviruses, thus warranting further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and a literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared with other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, whereas the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near-identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Koch's postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provides information to better understand the diversity, global presence, and pathobiology of SnIV1; however, its possible emergence as a destructive pathogen remains uncertain. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Chantal Faure
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Laurence Svanella-Dumas
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Magda Tušek-Žnidaric
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Deborah Schönegger
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Merelbeke, 9820, Belgium
| | - Arnaud Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, 27606, U.S.A
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Armelle Marais
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Thierry Candresse
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
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Puthanveed V, Singh K, Poimenopoulou E, Pettersson J, Siddique AB, Kvarnheden A. Milder Autumns May Increase Risk for Infection of Crops with Turnip Yellows Virus. PHYTOPATHOLOGY 2023; 113:1788-1798. [PMID: 36802872 DOI: 10.1094/phyto-11-22-0446-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Climate change has increased the risk for infection of crops with insect-transmitted viruses. Mild autumns provide prolonged active periods to insects, which may spread viruses to winter crops. In autumn 2018, green peach aphids (Myzus persicae) were found in suction traps in southern Sweden that presented infection risk for winter oilseed rape (OSR; Brassica napus) with turnip yellows virus (TuYV). A survey was carried out in spring 2019 with random leaf samples from 46 OSR fields in southern and central Sweden using DAS-ELISA, and TuYV was detected in all fields except one. In the counties of Skåne, Kalmar, and Östergötland, the average incidence of TuYV-infected plants was 75%, and the incidence reached 100% for nine fields. Sequence analyses of the coat protein gene revealed a close relationship between TuYV isolates from Sweden and other parts of the world. High-throughput sequencing for one of the OSR samples confirmed the presence of TuYV and revealed coinfection with TuYV-associated RNA. Molecular analyses of seven sugar beet (Beta vulgaris) plants with yellowing, collected in 2019, revealed that two of them were infected by TuYV, together with two other poleroviruses: beet mild yellowing virus and beet chlorosis virus. The presence of TuYV in sugar beet suggests a spillover from other hosts. Poleroviruses are prone to recombination, and mixed infection with three poleroviruses in the same plant poses a risk for the emergence of new polerovirus genotypes. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Vinitha Puthanveed
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Khushwant Singh
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Division of Crop Protection and Plant Health, Crop Research Institute, Prague 161 06, Czech Republic
| | - Efstratia Poimenopoulou
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Josefin Pettersson
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Abu Bakar Siddique
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Anders Kvarnheden
- Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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Dell’Olmo E, Tiberini A, Sigillo L. Leguminous Seedborne Pathogens: Seed Health and Sustainable Crop Management. PLANTS (BASEL, SWITZERLAND) 2023; 12:2040. [PMID: 37653957 PMCID: PMC10221191 DOI: 10.3390/plants12102040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 09/02/2023]
Abstract
Pulses have gained popularity over the past few decades due to their use as a source of protein in food and their favorable impact on soil fertility. Despite being essential to modern agriculture, these species face a number of challenges, such as agronomic crop management and threats from plant seed pathogens. This review's goal is to gather information on the distribution, symptomatology, biology, and host range of seedborne pathogens. Important diagnostic techniques are also discussed as a part of a successful process of seed health certification. Additionally, strategies for sustainable control are provided. Altogether, the data collected are suggested as basic criteria to set up a conscious laboratory approach.
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Affiliation(s)
- Eliana Dell’Olmo
- Council for Agricultural Research and Economics, Research Center for Vegetable and Ornamental Crops (CREA-OF), Via Cavalleggeri 25, 84098 Pontecagnano Faiano, Italy
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification (CREA-DC), Via C. G. Bertero, 22, 00156 Rome, Italy
| | - Loredana Sigillo
- Council for Agricultural Research and Economics, Research Center for Vegetable and Ornamental Crops (CREA-OF), Via Cavalleggeri 25, 84098 Pontecagnano Faiano, Italy
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Rivarez MPS, Pecman A, Bačnik K, Maksimović O, Vučurović A, Seljak G, Mehle N, Gutiérrez-Aguirre I, Ravnikar M, Kutnjak D. In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem. MICROBIOME 2023; 11:60. [PMID: 36973750 PMCID: PMC10042675 DOI: 10.1186/s40168-023-01500-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/20/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data. RESULTS Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments. CONCLUSIONS We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.
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Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
- Jožef Stefan International Postgraduate School, Jamova cesta 39, Ljubljana, 1000 Slovenia
- Present Address: College of Agriculture and Agri-Industries, Caraga State University, Ampayon, Butuan City, 8600 Philippines
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
- Jožef Stefan International Postgraduate School, Jamova cesta 39, Ljubljana, 1000 Slovenia
| | - Katarina Bačnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Olivera Maksimović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
- Jožef Stefan International Postgraduate School, Jamova cesta 39, Ljubljana, 1000 Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Gabrijel Seljak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Dvorec Lanthieri Glavni trg 8, Vipava, 5271 Slovenia
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, Ljubljana, 1000 Slovenia
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Olmedo-Velarde A, Ochoa-Corona FM, Larrea-Sarmiento AE, Elbeaino T, Flores F. In-silico prediction of RT-qPCR-high resolution melting for broad detection of emaraviruses. PLoS One 2023; 18:e0272980. [PMID: 37155676 PMCID: PMC10166557 DOI: 10.1371/journal.pone.0272980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/30/2022] [Indexed: 05/10/2023] Open
Abstract
Twenty-four species of RNA viruses contain members infecting economically important crops that are classified within the genus Emaravirus, family Fimoviridae. There are at least two other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. This research aimed to explore the ability to predict HRM outputs coupled to reverse transcription-quantitative polymerase chain reaction (RT-qPCR). To approach this goal a pair of degenerate genus-specific primers were designed for endpoint RT-PCR and RT-qPCR-HRM and the species in the genus Emaravirus were selected to framework the development of the assays. Both nucleic acid amplification methods were able to detect in-vitro several members of seven Emaravirus species with sensitivity up to one fg of cDNA. Specific parameters for in-silico prediction of the melting temperatures of each expected emaravirus amplicon are compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The high-resolution DNA melting curves of the RT-PCR products predicted in-silico using uMeltSM allowed saving time while designing and developing the RT-qPCR-HRM assay since the approach avoided extensive searching for optimal HRM assay regions and rounds of HRM tests in-vitro for optimization. The resultant assay provides sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolqui, Ecuador
| | - Francisco M Ochoa-Corona
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
| | - Adriana E Larrea-Sarmiento
- Institute for Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK, United States of America
| | - Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Valenzano, BA, Italy
| | - Francisco Flores
- Departamento de Ciencias de la Vida y de la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolqui, Ecuador
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador
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Rashid S, Wani F, Ali G, Sofi TA, Dar ZA, Hamid A. Viral metatranscriptomic approach to study the diversity of virus(es) associated with Common Bean (Phaseolus vulgaris L.) in the North-Western Himalayan region of India. Front Microbiol 2022; 13:943382. [PMID: 36212886 PMCID: PMC9532741 DOI: 10.3389/fmicb.2022.943382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate that HTS followed by multiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses.
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Affiliation(s)
- Shahjahan Rashid
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Farhana Wani
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Gowhar Ali
- Department of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Tariq A. Sofi
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Zahoor Ahmed Dar
- Department of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
| | - Aflaq Hamid
- Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Srinagar, India
- *Correspondence: Aflaq Hamid
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Fox A, Gibbs AJ, Fowkes AR, Pufal H, McGreig S, Jones RAC, Boonham N, Adams IP. Enhanced Apiaceous Potyvirus Phylogeny, Novel Viruses, and New Country and Host Records from Sequencing Apiaceae Samples. PLANTS 2022; 11:plants11151951. [PMID: 35956429 PMCID: PMC9370115 DOI: 10.3390/plants11151951] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022]
Abstract
The family Apiaceae comprises approximately 3700 species of herbaceous plants, including important crops, aromatic herbs and field weeds. Here we report a study of 10 preserved historical or recent virus samples of apiaceous plants collected in the United Kingdom (UK) import interceptions from the Mediterranean region (Egypt, Israel and Cyprus) or during surveys of Australian apiaceous crops. Seven complete new genomic sequences and one partial sequence, of the apiaceous potyviruses apium virus Y (ApVY), carrot thin leaf virus (CaTLV), carrot virus Y (CarVY) and celery mosaic virus (CeMV) were obtained. When these 7 and 16 earlier complete non-recombinant apiaceous potyvirus sequences were subjected to phylogenetic analyses, they split into 2 separate lineages: 1 containing ApVY, CeMV, CarVY and panax virus Y and the other CaTLV, ashitabi mosaic virus and konjac virus Y. Preliminary dating analysis suggested the CarVY population first diverged from CeMV and ApVY in the 17th century and CeMV from ApVY in the 18th century. They also showed the “time to most recent common ancestor” of the sampled populations to be more recent: 1997 CE, 1983 CE and 1958 CE for CarVY, CeMV and ApVY, respectively. In addition, we found a new family record for beet western yellows virus in coriander from Cyprus; a new country record for carrot torradovirus-1 and a tentative novel member of genus Ophiovirus as a co-infection in a carrot sample from Australia; and a novel member of the genus Umbravirus recovered from a sample of herb parsley from Israel.
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Affiliation(s)
- Adrian Fox
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
- Correspondence:
| | - Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia;
| | - Aimee R. Fowkes
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
| | - Hollie Pufal
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, King’s Road, Newcastle upon Tyne NE1 7RU, UK; (H.P.); (N.B.)
| | - Sam McGreig
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
| | - Roger A. C. Jones
- UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia;
| | - Neil Boonham
- School of Natural and Environmental Sciences, Newcastle University, Agriculture Building, King’s Road, Newcastle upon Tyne NE1 7RU, UK; (H.P.); (N.B.)
| | - Ian P. Adams
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (A.R.F.); (S.M.); (I.P.A.)
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Luan Y, Zhang L, Sun T, Jiang X, Wu X, Cheng X. First Report of a Secovirus Associated with Mountain Celery Chlorotic Spot Disease in Heilongjiang, China. PLANT DISEASE 2022; 106:1311. [PMID: 34668404 DOI: 10.1094/pdis-07-21-1418-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Affiliation(s)
- Yameng Luan
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Lili Zhang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Ting Sun
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xue Jiang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaoyun Wu
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaofei Cheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150030, China
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Fowkes AR, McGreig S, Pufal H, Duffy S, Howard B, Adams IP, Macarthur R, Weekes R, Fox A. Integrating High throughput Sequencing into Survey Design Reveals Turnip Yellows Virus and Soybean Dwarf Virus in Pea ( Pisum Sativum) in the United Kingdom. Viruses 2021; 13:2530. [PMID: 34960799 PMCID: PMC8707713 DOI: 10.3390/v13122530] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/03/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
There is only limited knowledge of the presence and incidence of viruses in peas within the United Kingdom, therefore high-throughput sequencing (HTS) in combination with a bulk sampling strategy and targeted testing was used to determine the virome in cultivated pea crops. Bulks of 120 leaves collected from twenty fields from around the UK were initially tested by HTS, and presence and incidence of virus was then determined using specific real-time reverse-transcription PCR assays by testing smaller mixed-bulk size samples. This study presents the first finding of turnip yellows virus (TuYV) in peas in the UK and the first finding of soybean dwarf virus (SbDV) in the UK. While TuYV was not previously known to be present in UK peas, it was found in 13 of the 20 sites tested and was present at incidences up to 100%. Pea enation mosaic virus-1, pea enation mosaic virus-2, pea seed-borne mosaic virus, bean yellow mosaic virus, pea enation mosaic virus satellite RNA and turnip yellows virus associated RNA were also identified by HTS. Additionally, a subset of bulked samples were re-sequenced at greater depth to ascertain whether the relatively low depth of sequencing had missed any infections. In each case the same viruses were identified as had been identified using the lower sequencing depth. Sequencing of an isolate of pea seed-borne mosaic virus from 2007 also revealed the presence of TuYV and SbDV, showing that both viruses have been present in the UK for at least a decade, and represents the earliest whole genome of SbDV from Europe. This study demonstrates the potential of HTS to be used as a surveillance tool, or for crop-specific field survey, using a bulk sampling strategy combined with HTS and targeted diagnostics to indicate both presence and incidence of viruses in a crop.
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Affiliation(s)
- Aimee R. Fowkes
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Sam McGreig
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Hollie Pufal
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle NE1 7RU, UK;
| | - Shona Duffy
- Processors & Growers Research Organisation (PGRO), Peterborough PE8 6HJ, UK; (S.D.); (B.H.)
| | - Becky Howard
- Processors & Growers Research Organisation (PGRO), Peterborough PE8 6HJ, UK; (S.D.); (B.H.)
| | - Ian P. Adams
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Roy Macarthur
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Rebecca Weekes
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
| | - Adrian Fox
- Fera Science Ltd., Sand Hutton, York YO41 1LZ, UK; (S.M.); (I.P.A.); (R.M.); (R.W.); (A.F.)
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Olmedo-Velarde A, Ochoa-Corona FM, Larrea-Sarmiento AE, Elbeaino T, Flores F. Exploring in-silico prediction for the development of a RT-qPCR-high resolution melting assay for the broad detection of emaraviruses. J Virol Methods 2021:114425. [PMID: 34902460 DOI: 10.1016/j.jviromet.2021.114425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 03/09/2021] [Accepted: 12/09/2021] [Indexed: 01/13/2023]
Abstract
High-resolution melting (HRM) has shown to be reliable for the detection, discrimination, and diagnosis of several diseases of plants, animals, and humans. The aim of this research was to explore the ability to predict HRM outputs when coupled to reverse transcription quantitative polymerase chain reaction (RT-qPCR). This research used the species in the Emaravirus genus as model to framework the development of genus-specific RT-qPCR-HRM assays. A pair of degenerate genus-specific primers were designed for use in endpoint RT-PCR and RT-qPCR-HRM detection of emaraviruses. Eleven species of RNA viruses infecting economically important crops are classified within the genus Emaravirus, family Fimoviridae. There are at least fifteen other non-classified species that may be added. Some of these viruses are spreading rapidly and cause economically important diseases on several crops, raising a need for a sensitive diagnostic technique for taxonomic and quarantine purposes. RT-PCR and RT-qPCR-HRM were able to detect seven emaravirus species in-vitro with sensitivity up to one fg of cDNA. Specific parameters for prediction in-silico of the melting temperatures of each expected emaravirus amplicon are provided and compared to the data obtained in-vitro. A very distinct isolate of the High Plains wheat mosaic virus was also detected. The prediction in-silico of fluorescence of high-resolution DNA melting curves of predicted RT-PCR products using uMeltSM speeded the design and development of RT-qPCR-HRM assay. This approach avoided rounds of HRM tests in-vitro when searching for the optimal regions that provides accurate diagnosis. The resultant assay provided sensitive detection and reliable diagnosis for potentially any emaravirus, including new species or strains.
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Affiliation(s)
- Alejandro Olmedo-Velarde
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA; Universidad de las Fuerzas Armadas ESPE, Departamento de Ciencias de la Vida y de la Agricultura, Sangolqui, Ecuador
| | - Francisco M Ochoa-Corona
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA.
| | - Adriana E Larrea-Sarmiento
- Oklahoma State University, Institute for Biosecurity and Microbial Forensics, Stillwater, OK, USA; Oklahoma State University, Department of Entomology and Plant Pathology, Stillwater, OK, USA
| | - Toufic Elbeaino
- Istituto Agronomico Mediterraneo di Bari, Valenzano, BA, Italy
| | - Francisco Flores
- Universidad de las Fuerzas Armadas ESPE, Departamento de Ciencias de la Vida y de la Agricultura, Sangolqui, Ecuador; Universidad UTE, Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Quito, Ecuador
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11
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Gaafar YZA, Westenberg M, Botermans M, László K, De Jonghe K, Foucart Y, Ferretti L, Kutnjak D, Pecman A, Mehle N, Kreuze J, Muller G, Vakirlis N, Beris D, Varveri C, Ziebell H. Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence. Pathogens 2021; 10:pathogens10091174. [PMID: 34578206 PMCID: PMC8469820 DOI: 10.3390/pathogens10091174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequencing (HTS) technologies and bioinformatic analyses are of growing interest to be used as a routine diagnostic tool in the field of plant viruses. The reliability of HTS workflows from sample preparation to data analysis and results interpretation for plant virus detection and identification must be evaluated (verified and validated) to approve this tool for diagnostics. Many different extraction methods, library preparation protocols, and sequence and bioinformatic pipelines are available for virus sequence detection. To assess the performance of plant virology diagnostic laboratories in using the HTS of ribosomal RNA depleted total RNA (ribodepleted totRNA) as a diagnostic tool, we carried out an interlaboratory comparison study in which eight participants were required to use the same samples, (RNA) extraction kit, ribosomal RNA depletion kit, and commercial sequencing provider, but also their own bioinformatics pipeline, for analysis. The accuracy of virus detection ranged from 65% to 100%. The false-positive detection rate was very low and was related to the misinterpretation of results as well as to possible cross-contaminations in the lab or sequencing provider. The bioinformatic pipeline used by each laboratory influenced the correct detection of the viruses of this study. The main difficulty was the detection of a novel virus as its sequence was not available in a publicly accessible database at the time. The raw data were reanalysed using Virtool to assess its ability for virus detection. All virus sequences were detected using Virtool in the different pools. This study revealed that the ribodepletion target enrichment for sample preparation is a reliable approach for the detection of plant viruses with different genomes. A significant level of virology expertise is needed to correctly interpret the results. It is also important to improve and complete the reference data.
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Affiliation(s)
- Yahya Z. A. Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104 Braunschweig, Germany;
| | - Marcel Westenberg
- National Reference Centre of Plant Health, Dutch National Plant Protection Organization, Geertjesweg 15, 6706 EA Wageningen, The Netherlands; (M.W.); (M.B.)
| | - Marleen Botermans
- National Reference Centre of Plant Health, Dutch National Plant Protection Organization, Geertjesweg 15, 6706 EA Wageningen, The Netherlands; (M.W.); (M.B.)
| | - Krizbai László
- Plant Health Diagnostics National Reference Laboratory, Directorate of Food Chain Safety Laboratory, National Food Chain Safety Office, Budaörsi út 141–145, H-1118 Budapest, Hungary;
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (Y.F.)
| | - Yoika Foucart
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (Y.F.)
| | - Luca Ferretti
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, Via C.G. Bertero 22, 00156 Rome, Italy;
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia; (D.K.); (A.P.); (N.M.)
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia; (D.K.); (A.P.); (N.M.)
- Jožef Stefan International Postgraduate School, SI-1000 Ljubljana, Slovenia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia; (D.K.); (A.P.); (N.M.)
| | - Jan Kreuze
- Health and Quarantine Unit, International Potato Center (CIP), Av. La Molina 1895 La Molina, Lima 15023, Peru; (J.K.); (G.M.)
| | - Giovanna Muller
- Health and Quarantine Unit, International Potato Center (CIP), Av. La Molina 1895 La Molina, Lima 15023, Peru; (J.K.); (G.M.)
| | - Nikolaos Vakirlis
- Benaki Phytopathological Institute, Stefanou Delta 8, Kifissia, Attica, 14561 Athens, Greece; (N.V.); (D.B.); (C.V.)
| | - Despoina Beris
- Benaki Phytopathological Institute, Stefanou Delta 8, Kifissia, Attica, 14561 Athens, Greece; (N.V.); (D.B.); (C.V.)
| | - Christina Varveri
- Benaki Phytopathological Institute, Stefanou Delta 8, Kifissia, Attica, 14561 Athens, Greece; (N.V.); (D.B.); (C.V.)
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104 Braunschweig, Germany;
- Correspondence:
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12
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Chatzivassiliou EK. An Annotated List of Legume-Infecting Viruses in the Light of Metagenomics. PLANTS 2021; 10:plants10071413. [PMID: 34371616 PMCID: PMC8309371 DOI: 10.3390/plants10071413] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 11/16/2022]
Abstract
Legumes, one of the most important sources of human food and animal feed, are known to be susceptible to a plethora of plant viruses. Many of these viruses cause diseases which severely impact legume production worldwide. The causal agents of some important virus-like diseases remain unknown. In recent years, high-throughput sequencing technologies have enabled us to identify many new viruses in various crops, including legumes. This review aims to present an updated list of legume-infecting viruses. Until 2020, a total of 168 plant viruses belonging to 39 genera and 16 families, officially recognized by the International Committee on Taxonomy of Viruses (ICTV), were reported to naturally infect common bean, cowpea, chickpea, faba-bean, groundnut, lentil, peas, alfalfa, clovers, and/or annual medics. Several novel legume viruses are still pending approval by ICTV. The epidemiology of many of the legume viruses are of specific interest due to their seed-transmission and their dynamic spread by insect-vectors. In this review, major aspects of legume virus epidemiology and integrated control approaches are also summarized.
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Affiliation(s)
- Elisavet K Chatzivassiliou
- Plant Pathology Laboratory, Department of Crop Science, School of Plant Sciences, Agricultural University of Athens, 11855 Athens, Greece
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Mahony J, van Sinderen D. Virome studies of food production systems: time for 'farm to fork' analyses. Curr Opin Biotechnol 2021; 73:22-27. [PMID: 34252795 DOI: 10.1016/j.copbio.2021.06.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022]
Abstract
The food industry is under increasing pressure to produce high quality, traceable and minimally processed foods that are produced using sustainable approaches and ingredients. In line with the latter, there is an increased pressure for plant-based products to replace animal-derived products. Until recently, research efforts have mainly focused on dairy and meat products owing to their economic importance. The shift towards plant-based diets and food production requires a corresponding shift in research efforts to define the microbial requirements for and composition of (novel) plant-based foods, the (micro)organisms that are beneficial to such production systems, and the abundance and role of (bacterio)phages in shaping the microbial landscape of these foods. In this review, we explore current efforts in the area of virome analysis of foods and food production environments and highlight the need for more unified approaches to understand the contribution of phages in food safety and quality, and to develop novel tools to enhance the traceability of foods.
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Affiliation(s)
- Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland.
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland.
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Luoto A, Lehtonen M, Valkonen J, Santala J. First report of Soybean dwarf virus infecting white clover ( Trifolium repens) in Finland. PLANT DISEASE 2021; 105. [PMID: 34129350 DOI: 10.1094/pdis-04-21-0822-pdn] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Soybean dwarf virus (SbDV, genus Luteovirus) is a single-stranded positive-sense RNA virus able to infect several legume species. SbDV was first reported in Japan where it was associated with significant yield losses in soybean (Tamada, 1969). Since then the virus has been detected worldwide. In Europe, the virus has only been reported from Germany (Abraham et al. 2007; Gaafar et al. 2020). In July 2018, several white clover plants (Trifolium repens L.) with leaf discoloration were observed in different locations in Oulu region in northern Finland. Individual plants were collected and analysed for the presence of viruses using small-RNA (sRNA) sequencing (Kreuze et. al. 2009) and reverse transcription-PCR (RT-PCR). Total RNA was extracted using EZNA micro RNA kit (Omega Bio-Tek, GA, USA). For sRNA analysis, sequencing libraries were constructed using the TruSeq small RNA library prep kit (Illumina, CA, USA) and sequenced on Illumina MiSeq platform. On average, 1.3 million single-end reads were obtained per sample, of which 27% were 18-25 nt long and used for the subsequent analysis. Contig assembly and virus identification with VirusDetect software (Zheng et al. 2017) detected SbDV in five out of six white clover samples analysed. Depending on the sample, 26-39 contigs (with lengths up to 301-469 nt) aligned to complete genome of a SbDV isolate previously described from white clover in USA (accession no. JN674402). The cumulative alignment coverage ranged from 35.5 % to 65.3 % with nucleotide identities between 94.4 % and 97.3 %. Additionally, two samples seemed to contain an unidentified closterovirus and one contained White clover cryptic virus 2. No additional viruses were detected from two of the samples.To confirm the presence of SbDV, the samples were tested by RT-PCR using primers MDF, MYF and MUR in multiplex (Schneider et al. 2011) together with SuperScript III One-Step RT-PCR System with the Platinum Taq DNA polymerase kit (Thermo Fisher Scientific, USA), essentially as instructed by the manufacturer. RT-PCR product of approximately 400 bp was produced from each of the five samples previously tested SbDV positive by sRNA analysis. No products were produced from the sample that was SbDV negative in sRNA analysis. Direct sequencing of two of the PCR products produced 347 and 361 bp sequences (GenBank: MZ355392 and MW929169) that were 95.7 % and 95.2 % identical, respectively, to a SbDV isolate (accession no. AB038148) that causes yellowing on soybean and is transmitted by Acyrthosiphon pisum (Terauchi et al. 2003). To our knowledge this is the first report of SbDV in Finland. SbDV is transmitted only by aphids (neither mechanical nor seed transmission occurs). In siRNA analysis all the isolates from Finland formed contigs that aligned almost perfectly (100 % coverage with ≥ 99 % nucleotide identity) to the coat protein (accession no. EF466131) of an SbDV isolate transmittable from white clover to faba bean by A. pisum (Abraham et al. 2007), an aphid common in Finland. Although significant yield losses by SbDV have only been reported on soybean (Tamada, 1969), the virus also causes symptoms in other legume crops, such as growth reduction on pea (Tian et al. 2017) and faba bean (Abraham et al. 2007), both of which are cultivated in Finland. References: Abraham et al. 2007. Plant Dis. 91: 1059. Gaafar et al. 2020. Front microbiol. 11: 583242. Kreuze et al. 2009. Virology 388:1. Schneider et al. 2011. Virology 412: 46. Tamada. 1969. Ann Phytopathol Soc Jpn. 35: 282. Terauchi et al. 2003. Phytopathology 93: 1560. Tian et al. 2017. Viruses 9: 155. Zheng et al. 2017. Virology 500: 130.
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Affiliation(s)
- Annika Luoto
- University of Helsinki, Department of Agricultural Sciences, Helsinki, Finland;
| | - Mikko Lehtonen
- Finnish Food Authority, Laboratory and Research, Helsinki, Finland;
| | - Jari Valkonen
- University of Helsinki, Department of Agricultural Sciences, Helsinki, Finland;
| | - Johanna Santala
- Finnish Food Authority, Laboratory and Research, Mustialankatu 3, Helsinki, Finland, 00790;
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