1
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Silva JMF, Melo FL, Elena SF, Candresse T, Sabanadzovic S, Tzanetakis IE, Blouin AG, Villamor DEV, Mollov D, Constable F, Cao M, Saldarelli P, Cho WK, Nagata T. Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Currently, many viruses are classified based on their genome organization and nucleotide/amino acid sequence identities of their capsid and replication-associated proteins. Although biological traits such as vector specificities and host range are also considered, this later information is scarce for the majority of recently identified viruses, characterized only from genomic sequences. Accordingly, genomic sequences and derived information are being frequently used as the major, if not only, criteria for virus classification and this calls for a full review of the process. Herein, we critically addressed current issues concerning classification of viruses in the family Betaflexiviridae in the era of high-throughput sequencing and propose an updated set of demarcation criteria based on a process involving pairwise identity analyses and phylogenetics. The proposed framework has been designed to solve the majority of current conundrums in taxonomy and to facilitate future virus classification. Finally, the analyses performed herein, alongside the proposed approaches, could be used as a blueprint for virus classification at-large.
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Affiliation(s)
- João Marcos Fagundes Silva
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
| | - Fernando Lucas Melo
- Departamento de Fitopatologia, Instituto de Biología Integrativa de Sistemas, University of Brasília, Brasília 70910-900, Brazil
| | - Santiago F. Elena
- The Santa Fe Institute, Santa Fe, NM 87501, USA
- Instituto de Biología Integrativa de Sistemas (I2 13 SysBio), CSIC-Universitat de València, Paterna 14 46980 València, Spain
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 BFP, 33140 Villenave d’Ornon, France
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | | | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland
| | | | - Dimitre Mollov
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, 97330, USA
| | - Fiona Constable
- Department of Jobs Precincts and Regions, Agriculture Victoria Research, Agribio, Bundoora, VIC 3083, Australia
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, PR China
| | - Pasquale Saldarelli
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection (IPSP), Via Amendola 122/D, 70126 Bari, Italy
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Gyeonggi, Republic of Korea
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
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2
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Tahzima R, Foucart Y, Peusens G, Reynard JS, Massart S, Beliën T, De Jonghe K. An Advanced One-Step RT-LAMP for Rapid Detection of Little cherry virus 2 Combined with High-Throughput Sequence-Based Phylogenomics Reveal Divergent Flowering Cherry Isolates. PLANT DISEASE 2022; 106:835-845. [PMID: 34546772 DOI: 10.1094/pdis-03-21-0677-re] [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: 06/13/2023]
Abstract
Little cherry virus 2 (LChV-2, genus Ampelovirus) is considered to be the main causal agent of the economically damaging little cherry disease, which can only be controlled by removal of infected trees. The widespread viral disease of sweet cherry (Prunus avium L.) is affecting the survival of long-standing orchards in North America and Europe, hence the dire need for an early and accurate diagnosis to establish a sound disease control strategy. The endemic presence of LChV-2 is mainly confirmed using laborious time-consuming reverse-transcription (RT-PCR). A rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay targeting a conserved region of the coat protein was developed and compared with conventional RT-PCR for the specific detection of LChV-2. This affordable assay, combined with a simple RNA extraction, deploys desirable characteristics such as higher ability for faster (<15 min), more analytically sensitive (100-fold), and robust broad-range diagnosis of LChV-2 isolates from sweet cherry, ornamental flowering cherry displaying heterogenous viral etiology and, for the first time, newly identified potential insect vectors. Moreover, use of Sanger and total RNA high-throughput sequencing as complementary metaviromics approaches confirmed the LChV-2 RT-LAMP detection of divergent LChV-2 isolates in new hosts and the relationship of their whole-genome was exhaustively inferred using maximum-likelihood phylogenomics. This entails unprecedented critical understanding of a novel evolutionary clade further expanding LChV-2 viral diversity. In conclusion, this highly effective diagnostic platform facilitates strategical support for early in-field testing to reliably prevent dissemination of new LChV-2 outbreaks from propagative plant stocks or newly postulated insect vectors. Validated results and major advantages are herein thoroughly discussed, in light of the knowledge required to increase the potential accuracy of future diagnostics and the essential epidemiological considerations to proactively safeguard cherries and Prunus horticultural crop systems from little cherry disease.
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Affiliation(s)
- Rachid Tahzima
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
- Department of Integrated and Urban Phytopathology, Gembloux Agro-BioTech, University of Liège, 5030 Gembloux, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Gertie Peusens
- Department of Zoology, Proefcentrum Fruitteelt vzw, 3800 Sint-Truiden, Belgium
| | | | - Sébastien Massart
- Department of Integrated and Urban Phytopathology, Gembloux Agro-BioTech, University of Liège, 5030 Gembloux, Belgium
| | - Tim Beliën
- Department of Zoology, Proefcentrum Fruitteelt vzw, 3800 Sint-Truiden, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
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3
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Reynard JS, Brodard J, Remoliff E, Lefebvre M, Schumpp O, Candresse T. A novel foveavirus identified in wild grapevine (Vitis vinifera subsp. sylvestris). Arch Virol 2020; 165:2999-3002. [PMID: 32990843 PMCID: PMC7588375 DOI: 10.1007/s00705-020-04817-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 08/18/2020] [Indexed: 12/01/2022]
Abstract
We report the genome sequence of a putative new foveavirus infecting non-cultivated Vitis vinifera, tentatively named "grapevine foveavirus A" (GFVA). This virus was identified by high-throughput sequencing analysis of a European wild Vitis collected in Switzerland. Phylogenetic analysis revealed that this virus clustered with known grapevine virus T (GVT) isolates but was clearly distinct from any of them. If considering the International Committee of Taxonomy of Viruses (ICTV)-suggested foveavirus species demarcation criterion based on sequence similarity in the replicase gene/protein, this virus should be considered a member of a new species closely related to GVT. On the other hand, comparison of capsid gene/protein sequences using the same criteria indicates that GFVA is at the border of species demarcation. Whether this virus represents a highly divergent GVT isolate or a member of a distinct but closely related species is discussed.
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Affiliation(s)
| | | | - Eric Remoliff
- Agroscope, route de Duiller 50, 1260, Nyon, Switzerland
| | - Marie Lefebvre
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon cedex, France
| | | | - Thierry Candresse
- UMR 1332 BFP, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon cedex, France
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4
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Jo Y, Choi H, Lian S, Cho JK, Chu H, Cho WK. Identification of viruses infecting six plum cultivars in Korea by RNA-sequencing. PeerJ 2020; 8:e9588. [PMID: 32821540 PMCID: PMC7395596 DOI: 10.7717/peerj.9588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 07/01/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Plums are a kind of stone fruit, a category that includes peaches, cherries, apricots, and almonds. In Korea, Japanese plum trees are usually cultivated as they best suit the climate. To date, there have been few studies in Korea on viruses infecting plum trees compared to those infecting peach trees. METHODS To identify viruses and viroids infecting plum trees, we collected leaf samples from six different plum cultivars and subjected them to RNA-sequencing (RNA-seq). Six different plum transcriptomes were de novo assembled using the Trinity assembler followed by BLAST searching against a viral reference database. RESULTS We identified hop stunt viroid (HSVd) and six viruses, including apple chlorotic leaf spot virus (ACLSV), little cherry virus-1 (LChV-1), peach virus D (PeVD), peach leaf pitting-associated virus (PLPaV), plum bark necrosis stem pitting-associated virus (PBNSPaV), and prunus necrotic ringspot virus (PNRSV), from six plum cultivars by RNA-seq. RT-PCR confirmed the infection of HSVd and three viruses-ACLSV, PBNSPaV, and PNRSV-in plum trees. However, RT-PCR demonstrated that plum trees in this study were not infected by LChV-1, PeVD, or PLPaV. It is likely that the three viruses LChV-1, PeVD, and PLPaV as identified by RNA-seq were contaminants from other peach libraries caused by index misassignment, which suggests that careful confirmation by other methods should be carried out in next-generation sequencing (NGS)-based virus identification. Taken together, we identified a viroid and three viruses infecting plum trees in Korea.
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Affiliation(s)
- Yeonhwa Jo
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sen Lian
- College of Crop Protection and Agronomy, Qingdao Agricultural University, Qingdao, China
| | | | - Hyosub Chu
- Core Protein Resources Center, Daegu Gyeongbuk Institute of Science and Technology, Daegu, Republic of Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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5
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Zheng L, Chen M, Li R. Camellia ringspot-associated virus 4, a proposed new foveavirus from Camellia japonica. Arch Virol 2020; 165:1707-1710. [PMID: 32409876 DOI: 10.1007/s00705-020-04655-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 04/11/2020] [Indexed: 01/23/2023]
Abstract
One large contig with high sequence similarity to Asian prunus virus 2 was identified by high-throughput sequencing from a camellia (Camellia japonica) tree with ringspot symptoms. The complete genome of this new virus was determined to be 8829 nucleotides long, excluding the 3' poly(A) tail. Its genome organization resembles that of known foveaviruses but contains an additional open reading frame in the 3'-terminal region. Phylogenetic analysis also places this virus with members of the genus Foveavirus in the family Betaflexiviridae in the same subgroup. The virus, which is provisionally named "camellia ringspot-associated virus 4″, shares 50-56% nucleotide sequence identity with other foveaviruses and should represent a new species in the genus.
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Affiliation(s)
- Luping Zheng
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Madeleine Chen
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA.
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6
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Kinoti WM, Nancarrow N, Dann A, Rodoni BC, Constable FE. Updating the Quarantine Status of Prunus Infecting Viruses in Australia. Viruses 2020; 12:v12020246. [PMID: 32102210 PMCID: PMC7077234 DOI: 10.3390/v12020246] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/30/2022] Open
Abstract
One hundred Prunus trees, including almond (P. dulcis), apricot (P. armeniaca), nectarine (P. persica var. nucipersica), peach (P. persica), plum (P. domestica), purple leaf plum (P. cerasifera) and sweet cherry (P. avium), were selected from growing regions Australia-wide and tested for the presence of 34 viruses and three viroids using species-specific reverse transcription-polymerase chain reaction (RT-PCR) or polymerase chain reaction (PCR) tests. In addition, the samples were tested using some virus family or genus-based RT-PCR tests. The following viruses were detected: Apple chlorotic leaf spot virus (ACLSV) (13/100), Apple mosaic virus (ApMV) (1/100), Cherry green ring mottle virus (CGRMV) (4/100), Cherry necrotic rusty mottle virus (CNRMV) (2/100), Cherry virus A (CVA) (14/100), Little cherry virus 2 (LChV2) (3/100), Plum bark necrosis stem pitting associated virus (PBNSPaV) (4/100), Prune dwarf virus (PDV) (3/100), Prunus necrotic ringspot virus (PNRSV) (52/100), Hop stunt viroid (HSVd) (9/100) and Peach latent mosaic viroid (PLMVd) (6/100). The results showed that PNRSV is widespread in Prunus trees in Australia. Metagenomic high-throughput sequencing (HTS) and bioinformatics analysis were used to characterise the genomes of some viruses that were detected by RT-PCR tests and Apricot latent virus (ApLV), Apricot vein clearing associated virus (AVCaV), Asian Prunus Virus 2 (APV2) and Nectarine stem pitting-associated virus (NSPaV) were also detected. This is the first report of ApLV, APV2, CGRMV, CNRNV, LChV1, LChV2, NSPaV and PBNSPaV occurring in Australia. It is also the first report of ASGV infecting Prunus species in Australia, although it is known to infect other plant species including pome fruit and citrus.
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Affiliation(s)
- Wycliff M. Kinoti
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
- Correspondence:
| | | | - Alison Dann
- Plant Biosecurity and Diagnostic Branch, Bioisecurity Tasmania, Hobart, TAS 7001, Australia
| | - Brendan C. Rodoni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia
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7
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Maree HJ, Blouin AG, Diaz-Lara A, Mostert I, Al Rwahnih M, Candresse T. Status of the current vitivirus taxonomy. Arch Virol 2019; 165:451-458. [PMID: 31845154 DOI: 10.1007/s00705-019-04500-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
Since the establishment of the genus Vitivirus, several additional viruses have been sequenced and proposed to represent new species of this genus. Currently, the International Committee on Taxonomy of Viruses recognizes 15 vitivirus species. The report of new vitiviruses that fail to completely adhere to the species demarcation criteria, the incorporation of non-vitivirus grapevine viruses in the unofficial "naming system", and the existence of non-grapevine vitiviruses lead to inconsistencies in classification. In this report, we give a brief overview of vitiviruses and use currently available information to clarify the present status of the vitivirus taxonomy.
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Affiliation(s)
- H J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
- Citrus Research International, P.O. Box 2201, Matieland, 7602, South Africa.
| | - A G Blouin
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - A Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - I Mostert
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - M Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - T Candresse
- INRAE, Univ. Bordeaux, UMR BFP, 33882, Villenave d'Ornon Cedex, France
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8
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Candresse T, Chatzivassiliou E, Finelli F, Winter S, Bosco D, Chiumenti M, Di Serio F, Kaluski T, Minafra A, Rubino L. Pest categorisation of non-EU viruses and viroids of Prunus L. EFSA J 2019; 17:e05735. [PMID: 32626421 PMCID: PMC7009144 DOI: 10.2903/j.efsa.2019.5735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Prunus L. determined as being either non-EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of Ilarvirus S1 and Ilarvirus S2, for which very limited information exists, the pest categorisation was completed for 26 viruses and 1 viroid having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative plant propagation techniques, with plants for planting representing the major pathway for long-distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Prunus seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Apple scar skin viroid, American plum line pattern virus, cherry mottle leaf virus, cherry rasp leaf virus, cherry rosette virus, cherry rusty mottle-associated virus, cherry twisted leaf-associated virus, peach enation virus, peach mosaic virus, peach rosette mosaic virus, tobacco ringspot virus and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact in the EU territory, on which the Panel was unable to conclude, apricot vein clearing virus, Asian prunus virus 1, Asian prunus virus 2, Asian prunus virus 3, Caucasus prunus virus, cherry virus B, Mume virus A, nectarine stem pitting-associated virus, nectarine virus M, peach chlorotic mottle virus, peach leaf pitting-associated virus, peach virus D, prunus virus F and prunus virus T satisfy all the other criteria to be considered as potential Union QPs. Prunus geminivirus A does not meet the criterion of having negative impact in the EU. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non-EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests.
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9
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Analyses of virus/viroid communities in nectarine trees by next-generation sequencing and insight into viral synergisms implication in host disease symptoms. Sci Rep 2019; 9:12261. [PMID: 31439919 PMCID: PMC6706421 DOI: 10.1038/s41598-019-48714-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/09/2019] [Indexed: 01/02/2023] Open
Abstract
We analyzed virus and viroid communities in five individual trees of two nectarine cultivars with different disease phenotypes using next-generation sequencing technology. Different viral communities were found in different cultivars and individual trees. A total of eight viruses and one viroid in five families were identified in a single tree. To our knowledge, this is the first report showing that the most-frequently identified viral and viroid species co-infect a single individual peach tree, and is also the first report of peach virus D infecting Prunus in China. Combining analyses of genetic variation and sRNA data for co-infecting viruses/viroid in individual trees revealed for the first time that viral synergisms involving a few virus genera in the Betaflexiviridae, Closteroviridae, and Luteoviridae families play a role in determining disease symptoms. Evolutionary analysis of one of the most dominant peach pathogens, peach latent mosaic viroid (PLMVd), shows that the PLMVd sequences recovered from symptomatic and asymptomatic nectarine leaves did not all cluster together, and intra-isolate divergent sequence variants co-infected individual trees. Our study provides insight into the role that mixed viral/viroid communities infecting nectarine play in host symptom development, and will be important in further studies of epidemiological features of host-pathogen interactions.
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10
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Knierim D, Menzel W, Winter S. Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences. PLoS One 2019; 14:e0216713. [PMID: 31071169 PMCID: PMC6542260 DOI: 10.1371/journal.pone.0216713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/26/2019] [Indexed: 12/21/2022] Open
Abstract
Virus discovery based on high-throughput sequencing relies on enrichment for virus sequences prior to library preparation to achieve a sufficient number of viral reads. In general, preparations of double-stranded RNA or total RNA preparations treated to remove rRNA are used for sequence enrichment. We used virus-specific antibodies to immunocapture virions from plant sap to conduct cDNA synthesis, followed by library preparation and HTS. For the four potato viruses PLRV, PVY, PVA and PYV, template preparation by virion immunocapture provided a simpler and less expensive method than the enrichment of total RNA by ribosomal depletion. Specific enrichment of viral sequences without an intermediate amplification step was achieved, and this high coverage of sequences across the viral genomes was important to identify rare sequence variations. Using this approach, the first complete genome sequence of a potato yellowing virus isolate (PYV, DSMZ PV-0706) was determined in this study. PYV can be confidently assigned as a distinct species in the genus Ilarvirus.
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Affiliation(s)
- Dennis Knierim
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
| | - Wulf Menzel
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
- * E-mail:
| | - Stephan Winter
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
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11
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Maliogka VI, Minafra A, Saldarelli P, Ruiz-García AB, Glasa M, Katis N, Olmos A. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses 2018; 10:E436. [PMID: 30126105 PMCID: PMC6116224 DOI: 10.3390/v10080436] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.
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Affiliation(s)
- Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Pasquale Saldarelli
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
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12
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Baráth D, Jaksa-Czotter N, Molnár J, Varga T, Balássy J, Szabó LK, Kirilla Z, Tusnády GE, Preininger É, Várallyay É. Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary. Viruses 2018; 10:E318. [PMID: 29891760 PMCID: PMC6024520 DOI: 10.3390/v10060318] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 12/14/2022] Open
Abstract
Fruit trees, such as apricot trees, are constantly exposed to the attack of viruses. As they are propagated in a vegetative way, this risk is present not only in the field, where they remain for decades, but also during their propagation. Metagenomic diagnostic methods, based on next generation sequencing (NGS), offer unique possibilities to reveal all the present pathogens in the investigated sample. Using NGS of small RNAs, a special field of these techniques, we tested leaf samples of different varieties of apricot originating from an isolator house or open field stock nursery. As a result, we identified Cherry virus A (CVA) and little cherry virus 1 (LChV-1) for the first time in Hungary. The NGS results were validated by RT-PCR and also by Northern blot in the case of CVA. Cloned and Sanger sequenced viral-specific PCR products enabled us to investigate their phylogenetic relationships. However, since these pathogens have not been described in our country before, their role in symptom development and modification during co-infection with other viruses requires further investigation.
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Affiliation(s)
- Dániel Baráth
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | | | - János Molnár
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, 7632 Pécs, Hungary.
| | - Tünde Varga
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | - Júlia Balássy
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
| | | | - Zoltán Kirilla
- Fruitculture Research Institute, NARIC, 1223 Budapest, Hungary.
| | - Gábor E Tusnády
- Institute of Enzymology, Research Center of Natural Sciences, HAS, 1117 Budapest, Hungary.
| | - Éva Preininger
- Fruitculture Research Institute, NARIC, 1223 Budapest, Hungary.
| | - Éva Várallyay
- Agricultural Biotechnology Institute, NARIC, 2100 Gödöllő, Hungary.
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Abstract
Many recent studies have demonstrated that several known and unknown viruses infect many horticultural plants. However, the elucidation of a viral population and the understanding of the genetic complexity of viral genomes in a single plant are rarely reported. Here, we conducted metatranscriptome analyses using six different peach trees representing six individual peach cultivars. We identified six viruses including five viruses in the family Betaflexiviridae and a novel virus belonging to the family Tymoviridae as well as two viroids. The number of identified viruses and viroids in each transcriptome ranged from one to six. We obtained 18 complete or nearly complete genomes for six viruses and two viroids using transcriptome data. Furthermore, we analyzed single nucleotide variations for individual viral genomes. In addition, we analyzed the amount of viral RNA and copy number for identified viruses and viroids. Some viruses or viroids were commonly present in different cultivars; however, the list of infected viruses and viroids in each cultivar was different. Taken together, our study reveals the viral population in a single peach tree and a comprehensive overview for the diversities of viral communities in different peach cultivars.
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14
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Complete nucleotide sequence of a highly divergent cherry-associated luteovirus (ChALV) isolate from peach in South Korea. Arch Virol 2017; 162:2893-2896. [PMID: 28547383 DOI: 10.1007/s00705-017-3418-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 04/12/2017] [Indexed: 10/19/2022]
Abstract
We determined the complete genome sequence of a highly divergent South Korean (SK) isolate of a cherry-associated luteovirus (ChALV) from peach. The ChALV-SK genome consists of 5,815 nucleotides, and contains five open reading frames (ORFs). A comparative analysis of the full genome showed only 73.1% nucleotide sequence identity with a recently described ChALV from the Czech Republic (CZ). Amino acid similarities of the individual ORFs between ChALV-SK and other luteoviruses range from 17.3 to 92%, which places the new isolate close to the species demarcation value for luteoviruses. Results show our ChALV-SK isolate to be highly diverged from the ChALV-CZ isolate.
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15
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Massart S, Candresse T, Gil J, Lacomme C, Predajna L, Ravnikar M, Reynard JS, Rumbou A, Saldarelli P, Škorić D, Vainio EJ, Valkonen JPT, Vanderschuren H, Varveri C, Wetzel T. A Framework for the Evaluation of Biosecurity, Commercial, Regulatory, and Scientific Impacts of Plant Viruses and Viroids Identified by NGS Technologies. Front Microbiol 2017; 8:45. [PMID: 28174561 PMCID: PMC5258733 DOI: 10.3389/fmicb.2017.00045] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/06/2017] [Indexed: 01/14/2023] Open
Abstract
Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.
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Affiliation(s)
- Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Thierry Candresse
- Institut National de la Recherche Agronomique (INRA), University of Bordeaux, CS20032 UMR 1332 BFP Villenave d'Ornon, France
| | - José Gil
- Plant Biology, Linnean Centre for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences Uppsala, Sweden
| | - Christophe Lacomme
- Virology and Zoology, Science and Advice for Scottish Agriculture Edinbourgh, UK
| | - Lukas Predajna
- Department of Plant Virology, Institute of Virology, Biomedical Research Center, Slovak Academy of Science (SAS) Bratislava, Slovakia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology Ljubljana, Slovenia
| | | | - Artemis Rumbou
- Division Phytomedicine Lentzeallee, Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-University of Berlin Berlin, Germany
| | - Pasquale Saldarelli
- National Research Council Institute for Sustainable Plant Protection Bari, Italy
| | - Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb Zagreb, Croatia
| | - Eeva J Vainio
- Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke) Helsinki, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki Helsinki, Finland
| | - Hervé Vanderschuren
- Plant Genetics, Gembloux Agro-Bio Tech, University of Liège Gembloux, Belgium
| | - Christina Varveri
- Department of Phytopathology, Benaki Phytopathological Institute Athens, Greece
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse Germany
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16
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Morelli M, Giampetruzzi A, Laghezza L, Catalano L, Savino VN, Saldarelli P. Identification and characterization of an isolate of apple green crinkle associated virus involved in a severe disease of quince (Cydonia oblonga, Mill.). Arch Virol 2016; 162:299-306. [PMID: 27709400 DOI: 10.1007/s00705-016-3074-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/17/2016] [Indexed: 12/01/2022]
Abstract
A quince tree showing severe symptoms of a previously undescribed viral disease occurring in northern Apulia (Italy) was analysed using high-throughput sequencing of small RNA libraries, leading to the identification of a new strain of apple green crinkle associated virus (isolate AGCaV-CYD) showing peculiar traits. RT-PCR with specific primers detected AGCaV-CYD in consistent association with symptoms in the surveyed orchards. Molecular characterization of the reconstructed genome, together with phylogenetic analysis, showed it to be closely related to an AGCaV strain causing green crinkle disease in apple (AGCaV-AUR) and divergent from the type strain of apple stem pitting virus (ASPV-PA66).
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Affiliation(s)
- Massimiliano Morelli
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), Via Amendola 122/D, 70126, Bari, Italy.
| | - Annalisa Giampetruzzi
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), Via Amendola 122/D, 70126, Bari, Italy
| | - Lorenzo Laghezza
- Agrimeca Grape and Fruit Consulting S.r.l., Via Elefante 17, 70010, Turi, Bari, Italy
| | - Luigi Catalano
- Agrimeca Grape and Fruit Consulting S.r.l., Via Elefante 17, 70010, Turi, Bari, Italy
| | - Vito Nicola Savino
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi Aldo Moro, Bari, Italy
| | - Pasquale Saldarelli
- CNR-Istituto per la Protezione Sostenibile delle Piante (IPSP), Via Amendola 122/D, 70126, Bari, Italy
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17
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Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus. BMC Genomics 2016; 17:579. [PMID: 27507588 PMCID: PMC4977635 DOI: 10.1186/s12864-016-2994-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/03/2016] [Indexed: 02/08/2023] Open
Abstract
Background Next-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study. Results We de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes. Conclusions Taken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2994-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Sun-Lim Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. .,The Taejin Genome Institute, Gadam-gil 61, Hoeongseong, 25239, Republic of Korea.
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