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Wu Q, Kinoti WM, Habili N, Tyerman SD, Rinaldo A, Constable FE. Genetic Diversity of Grapevine Virus A in Three Australian Vineyards Using Amplicon High Throughput Sequencing (Amplicon-HTS). Viruses 2023; 16:42. [PMID: 38257742 PMCID: PMC10819895 DOI: 10.3390/v16010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Shiraz disease (SD) is one of the most destructive viral diseases of grapevines in Australia and is known to cause significant economic loss to local growers. Grapevine virus A (GVA) was reported to be the key pathogen associated with this disease. This study aimed to better understand the diversity of GVA variants both within and between individual SD and grapevine leafroll disease (LRD) affected grapevines located at vineyards in South Australia. Amplicon high throughput sequencing (Amplicon-HTS) combined with median-joining networks (MJNs) was used to analyze the variability in specific gene regions of GVA variants. Several GVAII variant groups contain samples from both vineyards studied, suggesting that these GVAII variants were from a common origin. Variant groups analyzed by MJNs using the overall data set denote that there may be a possible relationship between variant groups of GVA and the geographical location of the grapevines.
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Affiliation(s)
- Qi Wu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Wycliff M. Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
| | - Nuredin Habili
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Stephen D. Tyerman
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
| | - Amy Rinaldo
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Fiona E. Constable
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
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2
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Ben Mansour K, Komínek P, Komínková M, Brožová J. Characterization of Prunus Necrotic Ringspot Virus and Cherry Virus A Infecting Myrobalan Rootstock. Viruses 2023; 15:1723. [PMID: 37632065 PMCID: PMC10459944 DOI: 10.3390/v15081723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Prunus necrotic ringspot virus (PNRSV) and cherry virus A (CVA) are two viruses that mainly infect plants of the genus Prunus. Full-length sequences of these two viruses, collected in the Czech Republic from Prunus cerasifera plants, were obtained via HTS sequencing. Phylogenetic analyses based on the NJ method and Splitstree tools showed that the Czech PNRSV isolate (ON088600-ON088602) is a divergent isolate from other molecular groups, sharing less than 97% pairwise nucleotide identity with members of other groups. The Czech CVA isolate (ON088603) belonged to molecular subgroup III-2, clustered with isolates from non-cherry hosts, and shared the highest pairwise nucleotide identity (99.7%) with an isolate of Australian origin.
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Affiliation(s)
- Karima Ben Mansour
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (K.B.M.); (M.K.); (J.B.)
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Petr Komínek
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (K.B.M.); (M.K.); (J.B.)
| | - Marcela Komínková
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (K.B.M.); (M.K.); (J.B.)
| | - Jana Brožová
- Ecology, Diagnostics and Genetic Resources of Agriculturally Important Viruses, Fungi and Phytoplasmas, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic; (K.B.M.); (M.K.); (J.B.)
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3
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Howe-Kerr LI, Grupstra CGB, Rabbitt KM, Conetta D, Coy SR, Klinges JG, Maher RL, McConnell KM, Meiling SS, Messyasz A, Schmeltzer ER, Seabrook S, Sims JA, Veglia AJ, Thurber AR, Thurber RLV, Correa AMS. Viruses of a key coral symbiont exhibit temperature-driven productivity across a reefscape. ISME Commun 2023; 3:27. [PMID: 37009785 PMCID: PMC10068613 DOI: 10.1038/s43705-023-00227-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 02/17/2023] [Accepted: 03/01/2023] [Indexed: 05/31/2023]
Abstract
Viruses can affect coral health by infecting their symbiotic dinoflagellate partners (Symbiodiniaceae). Yet, viral dynamics in coral colonies exposed to environmental stress have not been studied at the reef scale, particularly within individual viral lineages. We sequenced the viral major capsid protein (mcp) gene of positive-sense single-stranded RNA viruses known to infect symbiotic dinoflagellates ('dinoRNAVs') to analyze their dynamics in the reef-building coral, Porites lobata. We repeatedly sampled 54 colonies harboring Cladocopium C15 dinoflagellates, across three environmentally distinct reef zones (fringing reef, back reef, and forereef) around the island of Moorea, French Polynesia over a 3-year period and spanning a reef-wide thermal stress event. By the end of the sampling period, 28% (5/18) of corals in the fringing reef experienced partial mortality versus 78% (14/18) of corals in the forereef. Over 90% (50/54) of colonies had detectable dinoRNAV infections. Reef zone influenced the composition and richness of viral mcp amino acid types ('aminotypes'), with the fringing reef containing the highest aminotype richness. The reef-wide thermal stress event significantly increased aminotype dispersion, and this pattern was strongest in the colonies that experienced partial mortality. These findings demonstrate that dinoRNAV infections respond to environmental fluctuations experienced in situ on reefs. Further, viral productivity will likely increase as ocean temperatures continue to rise, potentially impacting the foundational symbiosis underpinning coral reef ecosystems.
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Affiliation(s)
| | - Carsten G B Grupstra
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Biology, Boston University, Boston, MA, USA
| | - Kristen M Rabbitt
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA, USA
| | - Dennis Conetta
- Department of BioSciences, Rice University, Houston, TX, USA
| | - Samantha R Coy
- Department of BioSciences, Rice University, Houston, TX, USA
- Department of Oceanography, Texas A & M University, College Station, TX, USA
| | - J Grace Klinges
- Mote Marine Laboratory, Elizabeth Moore International Center for Coral Reef Research & Restoration, Summerland Key, FL, USA
| | - Rebecca L Maher
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | | | - Sonora S Meiling
- University of the Virgin Islands, St. Thomas, US Virgin Islands, USA
| | - Adriana Messyasz
- Rutgers School of Environmental and Biological Sciences, New Brunswick, NJ, USA
| | | | - Sarah Seabrook
- Oregon State University, Corvallis, OR, USA
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Jordan A Sims
- Department of BioSciences, Rice University, Houston, TX, USA
- Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Alex J Veglia
- Department of BioSciences, Rice University, Houston, TX, USA
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4
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Costa LC, Atha B, Hu X, Lamour K, Yang Y, O’Connell M, McFarland C, Foster JA, Hurtado-Gonzales OP. High-throughput detection of a large set of viruses and viroids of pome and stone fruit trees by multiplex PCR-based amplicon sequencing. Front Plant Sci 2022; 13:1072768. [PMID: 36578329 PMCID: PMC9791224 DOI: 10.3389/fpls.2022.1072768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
A comprehensive diagnostic method of known plant viruses and viroids is necessary to provide an accurate phytosanitary status of fruit trees. However, most widely used detection methods have a small limit on either the number of targeted viruses/viroids or the number of samples to be evaluated at a time, hampering the ability to rapidly scale up the test capacity. Here we report that by combining the power of high multiplexing PCR (499 primer pairs) of small amplicons (120-135bp), targeting 27 viruses and 7 viroids of fruit trees, followed by a single high-throughput sequencing (HTS) run, we accurately diagnosed the viruses and viroids on as many as 123 pome and stone fruit tree samples. We compared the accuracy, sensitivity, and reproducibility of this approach and contrast it with other detection methods including HTS of total RNA (RNA-Seq) and individual RT-qPCR for every fruit tree virus or viroid under the study. We argue that this robust and high-throughput cost-effective diagnostic tool will enhance the viral/viroid knowledge of fruit trees while increasing the capacity for large scale diagnostics. This approach can also be adopted for the detection of multiple viruses and viroids in other crops.
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Affiliation(s)
- Larissa Carvalho Costa
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Benjamin Atha
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Xiaojun Hu
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Yu Yang
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Mary O’Connell
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Clint McFarland
- Plant Protection and Quarantine - Field Operations, Animal and Plant Health Inspection Service, United States Department of Agriculture, Raleigh, NC, United States
| | - Joseph A. Foster
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
| | - Oscar P. Hurtado-Gonzales
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Beltsville, MD, United States
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5
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Thompson JR. Analysis of the genome of grapevine red blotch virus and related grabloviruses indicates diversification prior to the arrival of Vitis vinifera in North America. J Gen Virol 2022; 103. [PMID: 36205485 DOI: 10.1099/jgv.0.001789] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study 163 complete whole-genome sequences of the emerging pathogen grapevine red blotch virus (GRBV; genus Grablovirus, family Geminiviridae) were used to reconstruct phylogenies using Bayesian analyses on time-tipped (heterochronous) data. Using different combinations of priors, Bayes factors identified heterochronous datasets (3×200 million chains) generated from strict clock and exponential tree priors as being the most robust. Substitution rates of 3.2×10-5 subsitutions per site per year (95% HPD 4.3-2.1×10-5) across the whole of the GRBV genome were estimated, suggesting ancestral GRBV diverged from ancestral wild Vitis latent virus 1 around 9 000 years ago, well before the first documented arrival of Vitis vinifera in North America. Whole-genome analysis of GRBV isolates in a single infected field-grown grapevine across 12 years identified 12 single nucleotide polymorphisms none of which were fixed substitutions: an observation not discordant with the in silico estimate. The substitution rate estimated here is lower than those estimated for other geminiviruses and is the first for a woody-host-infecting geminivirus.
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Affiliation(s)
- Jeremy R Thompson
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.,Present address: Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand
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6
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Villamor DEV, Keller KE, Martin RR, Tzanetakis IE. Comparison of High Throughput Sequencing to Standard Protocols for Virus Detection in Berry Crops. Plant Dis 2022; 106:518-525. [PMID: 34282931 DOI: 10.1094/pdis-05-21-0949-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We completed a comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium, and eight Rubus) with known virus profiles. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, reverse transcription (RT) PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared with RT-PCR on a wide spectrum of variants and discovery of novel viruses. More importantly, in most cases in which the two protocols showed parallel virus detection, 11 viruses in 16 selections were not consistently detected by both methods at all sampling points. Based on these data, we propose a testing requirement of four sampling times over two growing seasons for berry and potentially other crops, to ensure that no virus remains undetected independent of titer, distribution, or other virus-virus or virus-host interactions.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - K E Keller
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - R R Martin
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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7
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Leigh DM, Peranić K, Prospero S, Cornejo C, Ćurković-Perica M, Kupper Q, Nuskern L, Rigling D, Ježić M. Long-read sequencing reveals the evolutionary drivers of intra-host diversity across natural RNA mycovirus infections. Virus Evol 2021; 7:veab101. [PMID: 35299787 PMCID: PMC8923234 DOI: 10.1093/ve/veab101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 01/05/2023] Open
Abstract
Intra-host dynamics are a core component of virus evolution but most intra-host data come from a narrow range of hosts or experimental infections. Gaining broader information on the intra-host diversity and dynamics of naturally occurring virus infections is essential to our understanding of evolution across the virosphere. Here we used PacBio long-read HiFi sequencing to characterize the intra-host populations of natural infections of the RNA mycovirus Cryphonectria hypovirus 1 (CHV1). CHV1 is a biocontrol agent for the chestnut blight fungus (Cryphonectria parasitica), which co-invaded Europe alongside the fungus. We characterized the mutational and haplotypic intra-host virus diversity of thirty-eight natural CHV1 infections spread across four locations in Croatia and Switzerland. Intra-host CHV1 diversity values were shaped by purifying selection and accumulation of mutations over time as well as epistatic interactions within the host genome at defense loci. Geographical landscape features impacted CHV1 inter-host relationships through restricting dispersal and causing founder effects. Interestingly, a small number of intra-host viral haplotypes showed high sequence similarity across large geographical distances unlikely to be linked by dispersal.
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Affiliation(s)
- Deborah M Leigh
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Karla Peranić
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
| | - Simone Prospero
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Carolina Cornejo
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | | | | | - Lucija Nuskern
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
| | - Daniel Rigling
- Phytopathology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf CH-8903, Switzerland
| | - Marin Ježić
- Faculty of Science, University of Zagreb, Zagreb, Grad Zagreb 10000, Croatia
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8
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Kamenova I, Borisova A. Biological and molecular characterization of Prunus necrotic ringspot virus isolates from sweet and sour cherry. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1901608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Ivanka Kamenova
- Biotic Stress Group, Agricultural Academy, AgroBioinstitute, Sofia, Bulgaria
| | - Aneliya Borisova
- Department of Agrotechnology, Plant Protection and Economics on Crops, Agricultural Academy, Institute of Agriculture, Kyustendil, Bulgaria
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9
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Maina S, Zheng L, Rodoni BC. Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses. Viruses 2021; 13:583. [PMID: 33808381 PMCID: PMC8066983 DOI: 10.3390/v13040583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/18/2022] Open
Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10-8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
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Affiliation(s)
- Solomon Maina
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
| | - Linda Zheng
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
| | - Brendan C. Rodoni
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Victoria 3083, Australia
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Mehetre GT, Leo VV, Singh G, Sorokan A, Maksimov I, Yadav MK, Upadhyaya K, Hashem A, Alsaleh AN, Dawoud TM, Almaary KS, Singh BP. Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review. Viruses 2021; 13:412. [PMID: 33807625 DOI: 10.3390/v13030412] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.
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11
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Pirrello C, Zeilmaker T, Bianco L, Giacomelli L, Moser C, Vezzulli S. Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing. Biomolecules 2021; 11:181. [PMID: 33525704 PMCID: PMC7912118 DOI: 10.3390/biom11020181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Several pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and the mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity, and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted in Arabidopsis, putative genes associated with downy mildew susceptibility have been discovered also in the grapevine genome. In this work, we deep-sequenced four putative susceptibility genes-namely VvDMR6.1, VvDMR6.2, VvDLO1, VvDLO2-in 190 genetically diverse grapevine genotypes to discover new sources of broad-spectrum and recessively inherited resistance. Identified Single Nucleotide Polymorphisms were screened in a bottleneck analysis from the genetic sequence to their impact on protein structure. Fifty-five genotypes showed at least one impacting mutation in one or more of the scouted genes. Haplotypes were inferred for each gene and two of them at the VvDMR6.2 gene were found significantly more represented in downy mildew resistant genotypes. The current results provide a resource for grapevine and plant genetics and could corroborate genomic-assisted breeding programs as well as tailored gene editing approaches for resistance to biotic stresses.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Tieme Zeilmaker
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Luca Bianco
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Lisa Giacomelli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Claudio Moser
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Silvia Vezzulli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
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12
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Mackie J, Higgins E, Chambers GA, Tesoriero L, Aldaoud R, Kelly G, Kinoti WM, Rodoni BC, Constable FE. Genome Analysis of Melon Necrotic Spot Virus Incursions and Seed Interceptions in Australia. Plant Dis 2020; 104:1969-1978. [PMID: 32484421 DOI: 10.1094/pdis-04-19-0846-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Melon necrotic spot virus (MNSV) was detected in field-grown Cucumis melo (rockmelon) and Citrullus lanatus (watermelon) plants in the Sunraysia district of New South Wales and Victoria, Australia, in 2012, 2013, and 2016, and in two watermelon seed lots tested at the Australian border in 2016. High-throughput sequencing was used to generate near full-length genomes of six isolates detected during the incursions and seed testing. Phylogenetic analysis of the genomes suggests that there have been at least two incursions of MNSV into Australia and none of the field isolates were the same as the isolates detected in seeds. The analysis indicated that one watermelon field sample (L10), the Victorian rockmelon field sample, and two seed interception samples may have European origins. The results showed that two isolates (L8 and L9) from watermelon were divergent from the type MNSV strain (MNSV-GA, D12536.2) and had 99% nucleotide identity to two MNSV isolates from human stool collected in the United States (KY124135.1, KY124136.1). These isolates also had high nucleotide pairwise identity (96%) to a partial sequence from a Spanish MNSV isolate (KT962848.1). The analysis supported the identification of three previously described MNSV genotype groups: EU-LA, Japan melon, and Japan watermelon. To account for the greater diversity of hosts and geographic regions of the MNSV isolates used in this study, it is suggested that the genotype groups EU-LA, Japan melon, and Japan watermelon be renamed to groups I, II, and III, respectively. The divergent isolates L8 and L9 from this study and the stool isolates from the United States formed a fourth genotype group, group IV. Soil collected from the site of the Victorian rockmelon MNSV outbreak was found to contain viable MNSV and the virus vector, a chytrid fungus, Olpidium bornovanus (Sahtiyanci) Karling, 18 months after the initial MNSV detection. This is a first report of O. bornovanus from soil sampled from an MNSV-contaminated site in Australia.
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Affiliation(s)
- Joanne Mackie
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria 3083, Australia
| | - Ellena Higgins
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Grant A Chambers
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Len Tesoriero
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, New South Wales 2568, Australia
| | - Ramez Aldaoud
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria 3083, Australia
| | - Geoff Kelly
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria 3083, Australia
| | - Wycliff M Kinoti
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria 3083, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria 3083, Australia
| | - Fiona E Constable
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, AgriBio, Bundoora, Victoria 3083, Australia
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Abstract
Rose rosette virus (RRV) (genus Emaravirus) is the causal agent of the homonymous disease, the most destructive malady of roses in the USA. Although the importance of the disease is recognized, little sequence information and no full genomes are available for RRV, a multi-segmented RNA virus. To better understand the population structure of the virus we implemented a Hi-Plex PCR amplicon high-throughput sequencing approach to sequence all 7 segments and to quantify polymorphisms in 91 RRV isolates collected from 16 states in the USA. Analysis revealed insertion/deletion (indel) polymorphisms primarily in the 5' and 3' non-coding, but also within coding regions, including some resulting in changes of protein length. Phylogenetic analysis showed little geographical structuring, suggesting that topography does not have a strong influence on virus evolution. Overall, the virus populations were homogeneous, possibly because of regular movement of plants, the recent emergence of RRV and/or because the virus is under strong purification selection to preserve its integrity and biological functions.
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Affiliation(s)
- Asimina Katsiani
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
| | - Daisy Stainton
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
| | - Kurt Lamour
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville AR 72701, USA
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14
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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15
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Abstract
Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists' utility in their research.
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Affiliation(s)
- D E V Villamor
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - T Ho
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - M Al Rwahnih
- 2 Department of Plant Pathology, University of California, Davis 95616; and
| | - R R Martin
- 3 Horticulture Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Katsiani A, Maliogka VI, Katis N, Svanella-Dumas L, Olmos A, Ruiz-García AB, Marais A, Faure C, Theil S, Lotos L, Candresse T. High-Throughput Sequencing Reveals Further Diversity of Little Cherry Virus 1 with Implications for Diagnostics. Viruses 2018; 10:E385. [PMID: 30037079 PMCID: PMC6070981 DOI: 10.3390/v10070385] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/11/2018] [Accepted: 07/19/2018] [Indexed: 12/21/2022] Open
Abstract
Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour cherry and other Prunus species, which exhibits high genetic diversity and lacks a putative efficient transmission vector. Thus far, four distinct phylogenetic clusters of LChV1 have been described, including isolates from different Prunus species. The recent application of high throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition of new viral genomes and the study of virus diversity. In the present work, several new LChV1 isolates from different countries were fully sequenced using different HTS approaches. Our results reveal the presence of further genetic diversity within the LChV1 species. Interestingly, mixed infections of the same sweet cherry tree with different LChV1 variants were identified for the first time. Taken together, the high intra-host and intra-species diversities of LChV1 might affect its pathogenicity and have clear implications for its accurate diagnostics.
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Affiliation(s)
- Asimina Katsiani
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Laurence Svanella-Dumas
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Naquera km 4.5, Moncada, 46113 Valencia, Spain.
| | - Armelle Marais
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Chantal Faure
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Sébastien Theil
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
| | - Leonidas Lotos
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, CS20032, Villenave d'Ornon CEDEX, F-33882 Bordeaux, France.
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18
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Kinoti WM, Constable FE, Nancarrow N, Plummer KM, Rodoni B. The Incidence and Genetic Diversity of Apple Mosaic Virus (ApMV) and Prune Dwarf Virus (PDV) in Prunus Species in Australia. Viruses 2018; 10:E136. [PMID: 29562672 DOI: 10.3390/v10030136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/14/2018] [Accepted: 03/17/2018] [Indexed: 01/17/2023] Open
Abstract
Apple mosaic virus (ApMV) and prune dwarf virus (PDV) are amongst the most common viruses infecting Prunus species worldwide but their incidence and genetic diversity in Australia is not known. In a survey of 127 Prunus tree samples collected from five states in Australia, ApMV and PDV occurred in 4 (3%) and 13 (10%) of the trees respectively. High-throughput sequencing (HTS) of amplicons from partial conserved regions of RNA1, RNA2, and RNA3, encoding the methyltransferase (MT), RNA-dependent RNA polymerase (RdRp), and the coat protein (CP) genes respectively, of ApMV and PDV was used to determine the genetic diversity of the Australian isolates of each virus. Phylogenetic comparison of Australian ApMV and PDV amplicon HTS variants and full length genomes of both viruses with isolates occurring in other countries identified genetic strains of each virus occurring in Australia. A single Australian Prunus infecting ApMV genetic strain was identified as all ApMV isolates sequence variants formed a single phylogenetic group in each of RNA1, RNA2, and RNA3. Two Australian PDV genetic strains were identified based on the combination of observed phylogenetic groups in each of RNA1, RNA2, and RNA3 and one Prunus tree had both strains. The accuracy of amplicon sequence variants phylogenetic analysis based on segments of each virus RNA were confirmed by phylogenetic analysis of full length genome sequences of Australian ApMV and PDV isolates and all published ApMV and PDV genomes from other countries.
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Kinoti WM, Constable FE, Nancarrow N, Plummer KM, Rodoni B. Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus. Front Microbiol 2017; 8:1219. [PMID: 28713347 PMCID: PMC5491605 DOI: 10.3389/fmicb.2017.01219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/16/2017] [Indexed: 01/01/2023] Open
Abstract
The distribution of Ilarvirus species populations amongst 61 Australian Prunus trees was determined by next generation sequencing (NGS) of amplicons generated using a genus-based generic RT-PCR targeting a conserved region of the Ilarvirus RNA2 component that encodes the RNA dependent RNA polymerase (RdRp) gene. Presence of Ilarvirus sequences in each positive sample was further validated by Sanger sequencing of cloned amplicons of regions of each of RNA1, RNA2 and/or RNA3 that were generated by species specific PCRs and by metagenomic NGS. Prunus necrotic ringspot virus (PNRSV) was the most frequently detected Ilarvirus, occurring in 48 of the 61 Ilarvirus-positive trees and Prune dwarf virus (PDV) and Apple mosaic virus (ApMV) were detected in three trees and one tree, respectively. American plum line pattern virus (APLPV) was detected in three trees and represents the first report of APLPV detection in Australia. Two novel and distinct groups of Ilarvirus-like RNA2 amplicon sequences were also identified in several trees by the generic amplicon NGS approach. The high read depth from the amplicon NGS of the generic PCR products allowed the detection of distinct RNA2 RdRp sequence variant populations of PNRSV, PDV, ApMV, APLPV and the two novel Ilarvirus-like sequences. Mixed infections of ilarviruses were also detected in seven Prunus trees. Sanger sequencing of specific RNA1, RNA2, and/or RNA3 genome segments of each virus and total nucleic acid metagenomics NGS confirmed the presence of PNRSV, PDV, ApMV and APLPV detected by RNA2 generic amplicon NGS. However, the two novel groups of Ilarvirus-like RNA2 amplicon sequences detected by the generic amplicon NGS could not be associated to the presence of sequence from RNA1 or RNA3 genome segments or full Ilarvirus genomes, and their origin is unclear. This work highlights the sensitivity of genus-specific amplicon NGS in detection of virus sequences and their distinct populations in multiple samples, and the need for a standardized approach to accurately determine what constitutes an active, viable virus infection after detection by molecular based methods.
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Affiliation(s)
- Wycliff M. Kinoti
- Biosciences Research Division, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
- AgriBio, School of Applied Systems Biology, La Trobe UniversityMelbourne, VIC, Australia
| | - Fiona E. Constable
- Biosciences Research Division, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
| | - Narelle Nancarrow
- Biosciences Research Division, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
| | - Kim M. Plummer
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
| | - Brendan Rodoni
- Biosciences Research Division, AgriBio, La Trobe UniversityMelbourne, VIC, Australia
- AgriBio, School of Applied Systems Biology, La Trobe UniversityMelbourne, VIC, Australia
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