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Lee E, Vansia R, Phelan J, Lofano A, Smith A, Wang A, Bilodeau GJ, Pernal SF, Guarna MM, Rott M, Griffiths JS. Area Wide Monitoring of Plant and Honey Bee ( Apis mellifera) Viruses in Blueberry ( Vaccinium corymbosum) Agroecosystems Facilitated by Honey Bee Pollination. Viruses 2023; 15:v15051209. [PMID: 37243295 DOI: 10.3390/v15051209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 05/28/2023] Open
Abstract
Healthy agroecosystems are dependent on a complex web of factors and inter-species interactions. Flowers are hubs for pathogen transmission, including the horizontal or vertical transmission of plant-viruses and the horizontal transmission of bee-viruses. Pollination by the European honey bee (Apis mellifera) is critical for industrial fruit production, but bees can also vector viruses and other pathogens between individuals. Here, we utilized commercial honey bee pollination services in blueberry (Vaccinium corymbosum) farms for a metagenomics-based bee and plant virus monitoring system. Following RNA sequencing, viruses were identified by mapping reads to a reference sequence database through the bioinformatics portal Virtool. In total, 29 unique plant viral species were found at two blueberry farms in British Columbia (BC). Nine viruses were identified at one site in Ontario (ON), five of which were not identified in BC. Ilarviruses blueberry shock virus (BlShV) and prune dwarf virus (PDV) were the most frequently detected viruses in BC but absent in ON, while nepoviruses tomato ringspot virus and tobacco ringspot virus were common in ON but absent in BC. BlShV coat protein (CP) nucleotide sequences were nearly identical in all samples, while PDV CP sequences were more diverse, suggesting multiple strains of PDV circulating at this site. Ten bee-infecting viruses were identified, with black queen cell virus frequently detected in ON and BC. Area-wide bee-mediated pathogen monitoring can provide new insights into the diversity of viruses present in, and the health of, bee-pollination ecosystems. This approach can be limited by a short sampling season, biased towards pollen-transmitted viruses, and the plant material collected by bees can be very diverse. This can obscure the origin of some viruses, but bee-mediated virus monitoring can be an effective preliminary monitoring approach.
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Affiliation(s)
- Eunseo Lee
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
| | - Raj Vansia
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - James Phelan
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Andrea Lofano
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
| | - Adam Smith
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3, Canada
| | - Guillaume J Bilodeau
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, 3851 Fallowfield Rd., Ottawa, ON K2J 4S1, Canada
| | - Stephen F Pernal
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - M Marta Guarna
- Beaverlodge Research Farm, Agriculture and Agri-Food Canada, P.O. Box 29, Beaverlodge, AB T0H 0C0, Canada
| | - Michael Rott
- Sidney Laboratory, Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Rd., North Saanich, BC V8L 1H3, Canada
| | - Jonathan S Griffiths
- London Research and Development Centre, Agriculture and Agri-Food Canada, 4902 Victoria Ave N, Vineland Station, ON L0R 2E0, Canada
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
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Hao X, Zhang W, Zhao F, Liu Y, Qian W, Wang Y, Wang L, Zeng J, Yang Y, Wang X. Discovery of Plant Viruses From Tea Plant ( Camellia sinensis (L.) O. Kuntze) by Metagenomic Sequencing. Front Microbiol 2018; 9:2175. [PMID: 30254625 PMCID: PMC6141721 DOI: 10.3389/fmicb.2018.02175] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 08/24/2018] [Indexed: 12/23/2022] Open
Abstract
The tea plant (Camellia sinensis (L.) O. Kuntze) is an economically important woody species. In this study, we collected 26 tea plant samples with typical discoloration symptoms from different tea gardens and performed metagenomic analysis based on next-generation sequencing. Homology annotation and PCR sequencing validation finally identified seven kinds of plant viruses from tea plant. Based on abundance distribution analysis, the two most abundant plant viruses were highlighted. Genetic characterization suggested that they are two novel virus species with relatively high homology to Blueberry necrotic ring blotch virus and American plum line pattern virus. We named the newly discovered viruses tea plant necrotic ring blotch virus (TPNRBV) and tea plant line pattern virus (TPLPV). Evolutionary relationship analysis indicated that TPNRBV and TPLPV should be grouped into the Blunervirus and the Ilarvirus genera, respectively. TPLPV might have same genome activation process with known ilarviruses based on sequence analysis. Moreover, specific primers for both viruses detection were designed and validated. The symptoms and ultrastructure of TPNRBV infected leaves were first recorded. Virus detections in the symptomatic and asymptomatic tissues from field plants showing tea plant necrotic ring blotch disease suggest that TPNRBV has a systemic movement feature. In summary, we first identified seven kinds of putative plant viruses by metagenomic analysis and report two novel viruses being latent pathogens to tea plant. The results will advance our understanding of tea plant virology and have significance for the genetic breeding of tea plants in the future.
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Affiliation(s)
- Xinyuan Hao
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Weifu Zhang
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Fumei Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Ying Liu
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Wenjun Qian
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Yuchun Wang
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Lu Wang
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Jianming Zeng
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Yajun Yang
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
| | - Xinchao Wang
- National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, China
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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] [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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Galipienso L, Martínez C, Willemsen A, Alfaro-Férnandez A, Ambrosio IFS, Davino S, Rubio L. Genetic variability and evolutionary analysis of parietaria mottle virus: role of selection and genetic exchange. Arch Virol 2015; 160:2611-6. [PMID: 26234185 DOI: 10.1007/s00705-015-2550-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 07/21/2015] [Indexed: 10/23/2022]
Abstract
The genetic variability and evolution of parietaria mottle virus (PMoV) of the genus Ilarvirus was studied by analyzing nucleotide sequences of 2b and CP genes from isolates collected in different countries. Phylogenetic analysis showed that PMoV isolates clustered in different clades: one (clade I) composed of only Italian isolates and three clades (clades II-IV) including the Spanish isolates. The Greek isolate GrT-1 used in this study was in clade IV for the CP phylogenetic tree whereas it formed a separate branch in the 2b phylogenetic tree. The nucleotide sequence diversity of both the 2b and CP genes was low (0.062 ± 0.006 and 0.063 ± 0.006 for 2b and CP, respectively) but higher than those of other ilarviruses. Distribution of synonymous and nonsynonymous substitutions revealed that 2b and CP proteins are under purifying selection, with some positions under diversifying selection. Genetic exchange among Spanish isolates was also detected.
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Affiliation(s)
- Luis Galipienso
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain. .,Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139, Palermo, Italy.
| | - Carolina Martínez
- Programa de Biología y Biotecnología Vegetal, Universidad Autónoma de Barcelona (UAB), 08193, Bellaterra, Barcelona, Spain
| | - Anouk Willemsen
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Valencia, Spain
| | - Ana Alfaro-Férnandez
- Grupo de Virología, Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain
| | - Isabel Font-San Ambrosio
- Grupo de Virología, Instituto Agroforestal Mediterráneo, Universidad Politécnica de Valencia (UPV), 46022, Valencia, Spain
| | - Salvatore Davino
- Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139, Palermo, Italy.,Department of Agricultural and Forestry Science, University of Palermo, 90128, Palermo, Italy
| | - Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.,Euro-Mediterranean Institute of Science and Technology (IEMEST), 90139, Palermo, Italy
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Bergua M, Luis-Arteaga M, Escriu F. Genetic Diversity, Reassortment, and Recombination in Alfalfa mosaic virus Population in Spain. PHYTOPATHOLOGY 2014; 104:1241-1250. [PMID: 24779352 DOI: 10.1094/phyto-11-13-0309-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The variability and genetic structure of Alfalfa mosaic virus (AMV) in Spain was evaluated through the molecular characterization of 60 isolates collected from different hosts and different geographic areas. Analysis of nucleotide sequences in four coding regions--P1, P2, movement protein (MP), and coat protein (CP)--revealed a low genetic diversity and different restrictions to variation operating on each coding region. Phylogenetic analysis of Spanish isolates along with previously reported AMV sequences showed consistent clustering into types I and II for P1 and types I, IIA, and IIB for MP and CP regions. No clustering was observed for the P2 region. According to restriction fragment length polymorphism analysis, the Spanish AMV population consisted of seven haplotypes, including two haplotypes generated by reassortment and one involving recombination. The most frequent haplotypes (types for P1, MP, and CP regions, respectively) were I-I-I (37%), II-IIB-IIB (30%), and one of the reassortants, II-I-I (17%). Distribution of haplotypes was not uniform, indicating that AMV population was structured according to the geographic origin of isolates. Our results suggest that agroecological factors are involved in the maintenance of AMV genetic types, including the reassortant one, and in their geographic distribution.
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Abstract
Ilarviruses were among the first 16 groups of plant viruses approved by ICTV. Like Alfalfa mosaic virus (AMV), bromoviruses, and cucumoviruses they are isometric viruses and possess a single-stranded, tripartite RNA genome. However, unlike these other three groups, ilarviruses were recognized as being recalcitrant subjects for research (their ready lability is reflected in the sigla used to create the group name) and were renowned as unpromising subjects for the production of antisera. However, it was recognized that they shared properties with AMV when the phenomenon of genome activation, in which the coat protein (CP) of the virus is required to be present to initiate infection, was demonstrated to cross group boundaries. The CP of AMV could activate the genome of an ilarvirus and vice versa. Development of the molecular information for ilarviruses lagged behind the knowledge available for the more extensively studied AMV, bromoviruses, and cucumoviruses. In the past 20 years, genomic data for most known ilarviruses have been developed facilitating their detection and allowing the factors involved in the molecular biology of the genus to be investigated. Much information has been obtained using Prunus necrotic ringspot virus and the more extensively studied AMV. A relationship between some ilarviruses and the cucumoviruses has been defined with the recognition that members of both genera encode a 2b protein involved in RNA silencing and long distance viral movement. Here, we present a review of the current knowledge of both the taxonomy and the molecular biology of this genus of agronomically and horticulturally important viruses.
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Pallas V, Aparicio F, Herranz MC, Amari K, Sanchez-Pina MA, Myrta A, Sanchez-Navarro JA. Ilarviruses of Prunus spp.: a continued concern for fruit trees. PHYTOPATHOLOGY 2012; 102:1108-1120. [PMID: 23148725 DOI: 10.1094/phyto-02-12-0023-rvw] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Prunus spp. are affected by a large number of viruses, causing significant economic losses through either direct or indirect damage, which results in reduced yield and fruit quality. Among these viruses, members of the genus Ilarvirus (isometric labile ringspot viruses) occupy a significant position due to their distribution worldwide. Although symptoms caused by these types of viruses were reported early in the last century, their molecular characterization was not achieved until the 1990s, much later than for other agronomically relevant viruses. This was mainly due to the characteristic liability of virus particles in tissue extracts. In addition, ilarviruses, together with Alfalfa mosaic virus, are unique among plant viruses in that they require a few molecules of the coat protein in the inoculum in order to be infectious, a phenomenon known as genome activation. Another factor that has made the study of this group of viruses difficult is that infectious clones have been obtained only for the type member of the genus, Tobacco streak virus. Four ilarviruses, Prunus necrotic ringspot virus, Prune dwarf virus, Apple mosaic virus, and American plum line pattern virus, are pathogens of the main cultivated fruit trees. As stated in the 9th Report of the International Committee on Taxonomy of Viruses, virions of this genus are "unpromising subjects for the raising of good antisera." With the advent of molecular approaches for their detection and characterization, it has been possible to get a more precise view of their prevalence and genome organization. This review updates our knowledge on the incidence, genome organization and expression, genetic diversity, modes of transmission, and diagnosis, as well as control of this peculiar group of viruses affecting fruit trees.
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Affiliation(s)
- V Pallas
- Instituto de Biologia Celular y Molecular de Plantas, Universidad Politécnica de Valencia-Consejo, Spain.
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Population structure of blackberry chlorotic ringspot virus in the United States. Arch Virol 2012; 158:667-72. [DOI: 10.1007/s00705-012-1523-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Accepted: 09/17/2012] [Indexed: 11/26/2022]
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Tromas N, Elena SF. The rate and spectrum of spontaneous mutations in a plant RNA virus. Genetics 2010; 185:983-9. [PMID: 20439778 PMCID: PMC2907213 DOI: 10.1534/genetics.110.115915] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 04/30/2010] [Indexed: 11/18/2022] Open
Abstract
Knowing mutation rates and the molecular spectrum of spontaneous mutations is important to understanding how the genetic composition of viral populations evolves. Previous studies have shown that the rate of spontaneous mutations for RNA viruses widely varies between 0.01 and 2 mutations per genome and generation, with plant RNA viruses always occupying the lower side of this range. However, this peculiarity of plant RNA viruses is based on a very limited number of studies. Here we analyze the spontaneous mutational spectrum and the mutation rate of Tobacco etch potyvirus, a model system of positive sense RNA viruses. Our experimental setup minimizes the action of purifying selection on the mutational spectrum, thus giving a picture of what types of mutations are produced by the viral replicase. As expected for a neutral target, we found that transitions and nonsynonymous (including a few stop codons and small deletions) mutations were the most abundant type. This spectrum was notably different from the one previously described for another plant virus. We have estimated that the spontaneous mutation rate for this virus was in the range 10(-6)-10(-5) mutations per site and generation. Our estimates are in the same biological ballpark that previous values reported for plant RNA viruses. This finding gives further support to the idea that plant RNA viruses may have lower mutation rates than their animal counterparts.
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Affiliation(s)
- Nicolas Tromas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, 46022 València, Spain and The Santa Fe Institute, Santa Fe, New Mexico 87501
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas–Universidad Politécnica de Valencia, 46022 València, Spain and The Santa Fe Institute, Santa Fe, New Mexico 87501
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Sanjuán R, Agudelo-Romero P, Elena SF. Upper-limit mutation rate estimation for a plant RNA virus. Biol Lett 2009; 5:394-6. [PMID: 19324646 DOI: 10.1098/rsbl.2008.0762] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
It is generally accepted that mutation rates of RNA viruses are inherently high due to the lack of proofreading mechanisms. However, direct estimates of mutation rate are surprisingly scarce, in particular for plant viruses. Here, based on the analysis of in vivo mutation frequencies in tobacco etch virus, we calculate an upper-bound mutation rate estimation of 3x10(-5) per site and per round of replication; a value which turns out to be undistinguishable from the methodological error. Nonetheless, the value is barely on the lower side of the range accepted for RNA viruses, although in good agreement with the only direct estimate obtained for other plant viruses. These observations suggest that, perhaps, differences in the selective pressures operating during plant virus evolution may have driven their mutation rates towards values lower than those characteristic of other RNA viruses infecting bacteria or animals.
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Affiliation(s)
- Rafael Sanjuán
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
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Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus. Arch Virol 2008; 153:909-19. [PMID: 18365129 DOI: 10.1007/s00705-008-0066-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 02/14/2008] [Indexed: 10/22/2022]
Abstract
Prunus necrotic ringspot virus (PNRSV) is distributed worldwide, but no molecular data have been previously reported from South American isolates. The nucleotide sequences corresponding to the movement (MP) and coat (CP) proteins of 23 isolates of PNRSV from Chile, Brazil, and Uruguay, and from different Prunus species, have been obtained. Phylogenetic analysis performed with full-length MP and CP sequences from all the PNRSV isolates confirmed the clustering of the isolates into the previously reported PV32-I, PV96-II and PE5-III phylogroups. No association was found between specific sequences and host, geographic origin or symptomatology. Comparative analysis showed that both MP and CP have phylogroup-specific amino acids and all of the motifs previously characterized for both proteins. The study of the distribution of synonymous and nonsynonymous changes along both open reading frames revealed that most amino acid sites are under the effect of negative purifying selection.
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