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Norberg A, Susi H, Sallinen S, Baran P, Clark NJ, Laine AL. Direct and indirect viral associations predict coexistence in wild plant virus communities. Curr Biol 2023; 33:1665-1676.e4. [PMID: 37019108 DOI: 10.1016/j.cub.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/17/2023] [Accepted: 03/08/2023] [Indexed: 04/07/2023]
Abstract
Viruses are a vastly underestimated component of biodiversity that occur as diverse communities across hierarchical scales from the landscape level to individual hosts. The integration of community ecology with disease biology is a powerful, novel approach that can yield unprecedented insights into the abiotic and biotic drivers of pathogen community assembly. Here, we sampled wild plant populations to characterize and analyze the diversity and co-occurrence structure of within-host virus communities and their predictors. Our results show that these virus communities are characterized by diverse, non-random coinfections. Using a novel graphical network modeling framework, we demonstrate how environmental heterogeneity influences the network of virus taxa and how the virus co-occurrence patterns can be attributed to non-random, direct statistical virus-virus associations. Moreover, we show that environmental heterogeneity changed virus association networks, especially through their indirect effects. Our results highlight a previously underestimated mechanism of how environmental variability can influence disease risks by changing associations between viruses that are conditional on their environment.
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Affiliation(s)
- Anna Norberg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland; Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, 7034 Trondheim, Norway.
| | - Hanna Susi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Suvi Sallinen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Pezhman Baran
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
| | - Nicholas J Clark
- School of Veterinary Science, Faculty of Science, University of Queensland, Gatton, QL 4343, Australia
| | - Anna-Liisa Laine
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, 8057 Zürich, Switzerland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 65 00014, Helsinki, Finland
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Phylogenetic and Evolutionary Studies of Grapevine Pinot Gris Virus Isolates from Canada. Viruses 2023; 15:v15030735. [PMID: 36992444 PMCID: PMC10057519 DOI: 10.3390/v15030735] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
This study investigated the phylogenetic relationship of grapevine Pinot gris virus (GPGV) isolates from Canada with GPGV isolates reported worldwide. Full-length genomes of 25 GPGV isolates representing the main four grape-growing regions in Canada (British Columbia, Ontario, Nova Scotia and Quebec) were sequenced and compared to genomes of 43 GPGV isolates representing eight countries and three continents. Phylogenetic analysis based on full genome sequences revealed an unambiguous separation of North American GPGV isolates with isolates from Europe and Asia. Within the North American clade, GPGV isolates from the USA segregated into a distinct subclade, whereas the relationships amongst GPGV isolates from different regions of Canada were not clearly defined. The phylogenetic analysis of the overlapping regions of MP and CP genes involving 169 isolates from 14 countries resulted in two distinctive clades, which were seemingly independent of their country of origin. Clade 1 included the majority of asymptomatic isolates (81% asymptomatic), whereas clade 2 was predominantly formed of symptomatic isolates (78% symptomatic). This research is the first study focused on the genetic variability and origin of GPGV in Canada.
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Molecular Detection of Southern Tomato Amalgavirus Prevalent in Tomatoes and Its Genomic Characterization with Global Evolutionary Dynamics. Viruses 2022; 14:v14112481. [PMID: 36366579 PMCID: PMC9693158 DOI: 10.3390/v14112481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from Solanum lycopersicum L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.
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Wild Radish (Raphanus raphanistrum L.) Is a Potential Reservoir Host of Cucurbit Chlorotic Yellows Virus. Viruses 2022; 14:v14030593. [PMID: 35337000 PMCID: PMC8950442 DOI: 10.3390/v14030593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 02/04/2023] Open
Abstract
Cucurbit chlorotic yellows virus (CCYV) belongs to the genus Crinivirus and is part of a complex of whitefly-transmitted viruses that cause yellowing disease in cucurbits. In the southeastern USA, heavy incidences of CCYV have been observed on all cucurbits grown in the fall. CCYV was detected from wild radish (Raphanus raphanistrum L.), a common weed that grows in the southeastern USA by high-throughput sequencing as well as RT-PCR. CCYV sequence from wild radish was 99.90% and 99.95%, identical to RNA 1 and RNA 2 of cucurbit isolates of CCYV from the region. Transmission assays using whiteflies demonstrated that wild radish is a good host for CCYV. Whiteflies were also able to acquire CCYV from wild radish and transmit the virus to cucurbit hosts, which developed typical symptoms associated with CCYV. Using quantitative PCR, the titer of CCYV in wild radish was also estimated to be on par with that of cucurbit hosts of the virus. Whitefly bioassays revealed that wild radish is an acceptable feeding and reproductive host plant. These results indicate that wild radish could serve as a reservoir host for CCYV in the USA and other parts of the world where similar conditions exist.
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5
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Challenges and opportunities for plant viruses under a climate change scenario. Adv Virus Res 2022. [DOI: 10.1016/bs.aivir.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Liu H, Zhao F, Qiao Q, Zhang D, Wang Y, Wang S, Tian Y, Zhang Z. Complete genome sequence of a divergent sweet potato chlorotic stunt virus isolate infecting Calystegia hederacea in China. Arch Virol 2021; 166:2037-2040. [PMID: 33900471 DOI: 10.1007/s00705-021-05076-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/11/2021] [Indexed: 11/25/2022]
Abstract
Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus, family Closteroviridae) is one of the most destructive viruses infecting sweet potatoes. In this study, we determined the complete genome sequence of an SPCSV-like isolate (CH) from Calystegia hederacea Wall. (Convolvulaceae), a weed species related to sweet potato, by combining next-generation sequencing and rapid amplification of cDNA ends. Comparisons of genome sequences and organization confirmed the classification of CH as SPCSV. However, the sequences and phylogenetic data revealed substantial genetic divergence between CH and all known SPCSV isolates. The amino acid sequence identity between the putative proteins in SPCSV-CH and the corresponding proteins in other known SPCSV isolates in each case was less than 85.0%. Phylogenetic analysis indicated that SPCSV-CH is separate from the groups of the known SPCSV isolates. Additionally, SPCSV-CH RNA1 lacks a p22 gene. A 10.1-kDa putative protein (p10) encoded by a sequence in the 5'-terminal region of RNA2 in SPCSV-CH is much larger than the corresponding protein in all known SPCSV isolates.
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Affiliation(s)
- Huihua Liu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, China.,IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China
| | - Fumei Zhao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, China.,IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China
| | - Qi Qiao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, China.,IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China
| | - Desheng Zhang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, China.,IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China
| | - Yongjiang Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, China.,IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China
| | - Shuang Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, China.,IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China
| | - Yuting Tian
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China.,Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, China.,IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China
| | - Zhenchen Zhang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Postgraduate T&R Base of Zhengzhou University, Zhengzhou, 450002, China. .,Henan Key Laboratory of Crop Pest Control, Zhengzhou, 450002, China. .,IPM Key Laboratory in Southern Part of North China for Ministry of Agriculture, Zhengzhou, 450002, China.
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7
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Xing Y, Hernandez Nopsa JF, Andersen KF, Andrade-Piedra JL, Beed FD, Blomme G, Carvajal-Yepes M, Coyne DL, Cuellar WJ, Forbes GA, Kreuze JF, Kroschel J, Kumar PL, Legg JP, Parker M, Schulte-Geldermann E, Sharma K, Garrett KA. Global Cropland Connectivity: A Risk Factor for Invasion and Saturation by Emerging Pathogens and Pests. Bioscience 2020; 70:744-758. [PMID: 32973407 PMCID: PMC7498352 DOI: 10.1093/biosci/biaa067] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The geographic pattern of cropland is an important risk factor for invasion and saturation by crop-specific pathogens and arthropods. Understanding cropland networks supports smart pest sampling and mitigation strategies. We evaluate global networks of cropland connectivity for key vegetatively propagated crops (banana and plantain, cassava, potato, sweet potato, and yam) important for food security in the tropics. For each crop, potential movement between geographic location pairs was evaluated using a gravity model, with associated uncertainty quantification. The highly linked hub and bridge locations in cropland connectivity risk maps are likely priorities for surveillance and management, and for tracing intraregion movement of pathogens and pests. Important locations are identified beyond those locations that simply have high crop density. Cropland connectivity risk maps provide a new risk component for integration with other factors-such as climatic suitability, genetic resistance, and global trade routes-to inform pest risk assessment and mitigation.
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Affiliation(s)
- Yanru Xing
- Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute at University of Florida, Gainesville, USA
- Yanru Xing and John F. Hernandez Nopsa contributed equally to this work
| | - John F Hernandez Nopsa
- Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Mosquera-Bogota, Colombia
- Yanru Xing and John F. Hernandez Nopsa contributed equally to this work
| | - Kelsey F Andersen
- Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute at University of Florida, Gainesville, USA
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Jorge L Andrade-Piedra
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Fenton D Beed
- Plant Production and Protection Division, Food and Agriculture Organization, United Nations (FAO), 00153 Roma, Italy
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Guy Blomme
- Bioversity International, c/o ILRI, Addis Ababa, Ethiopia
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Mónica Carvajal-Yepes
- International Center for Tropical Agriculture (CIAT), AA6713, Cali, Colombia
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Danny L Coyne
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Wilmer J Cuellar
- International Center for Tropical Agriculture (CIAT), AA6713, Cali, Colombia
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Gregory A Forbes
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Jan F Kreuze
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Jürgen Kroschel
- International Potato Center (CIP), P.O. Box 1558, Lima 12, Peru
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - James P Legg
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Monica Parker
- International Potato Center (CIP), Nairobi, Kenya
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Elmar Schulte-Geldermann
- International Potato Center (CIP), Nairobi, Kenya
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Kalpana Sharma
- International Potato Center (CIP), Nairobi, Kenya
- CGIAR Research Program on Roots, Tubers, and Bananas
| | - Karen A Garrett
- Plant Pathology Department, Institute for Sustainable Food Systems, and Emerging Pathogens Institute at University of Florida, Gainesville, USA
- CGIAR Research Program on Roots, Tubers, and Bananas
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8
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Gautam S, Gadhave KR, Buck JW, Dutta B, Coolong T, Adkins S, Srinivasan R. Virus-virus interactions in a plant host and in a hemipteran vector: Implications for vector fitness and virus epidemics. Virus Res 2020; 286:198069. [PMID: 32574679 DOI: 10.1016/j.virusres.2020.198069] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 10/24/2022]
Abstract
Mixed virus infection in host plants can differentially alter the plant phenotype, influence vector fitness, and affect virus acquisition and inoculation by vectors than single-virus infection. Vector acquisition of multiple viruses from multiple host plants could also differentially affect vector fitness and virus inoculation than acquisition of one virus. Whitefly-virus pathosystems in the southern United States include both the above-stated facets. For the first facet, this study examined the effects of single and mixed infection of cucurbit leaf crumple virus (CuLCrV, a begomovirus) and cucurbit yellow stunting disorder virus (CYSDV, a crinivirus) infecting squash on whitefly (Bemisia tabaci Gennadius MEAM1) host preference and fitness. Mixed infection of CuLCrV and CYSDV in squash plants severely altered their phenotype than single infection. The CYSDV load was reduced in mixed-infected squash plants than in singly-infected plants. Consequently, whiteflies acquired reduced amounts of CYSDV from mixed-infected plants than singly-infected plants. No differences in CuLCrV load were found between singly- and mixed-infected squash plants, and acquisition of CuLCrV by whiteflies did not vary between singly- and mixed-infected squash plants. Both singly- and mixed-infected plants similarly affected whitefly preference, wherein non-viruliferous and viruliferous (CuLCrV and/or CYSDV) whiteflies preferred non-infected plants over infected plants. The fitness study involving viruliferous and non-viruliferous whiteflies revealed no differences in developmental time and fecundity. For the second facet, this study evaluated the effects of individual or combined acquisition of tomato-infecting tomato yellow leaf curl virus (TYLCV, a begomovirus) and squash-infecting CuLCrV on whitefly host preference and fitness. Whiteflies that acquired both CuLCrV and TYLCV had significantly lower CuLCrV load than whiteflies that acquired CuLCrV alone, whereas TYLCV load remained unaltered when acquired individually or in conjunction with CuLCrV. Whitefly preference was not affected following individual or combined virus acquisition. Viruliferous (CuLCrV and/or TYLCV) whiteflies preferred to settle on non-infected tomato and squash plants. The mere presence of CuLCrV and/or TYLCV in whiteflies did not affect their fitness. Taken together, these results indicate that mixed infection of viruses in host plants and acquisition of multiple viruses by the vector could have implications for virus accumulation, virus acquisition, vector preference, and epidemics that sometimes are different from single-virus infection or acquisition.
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Affiliation(s)
- Saurabh Gautam
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA, 30223, USA
| | - Kiran R Gadhave
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA, 30223, USA
| | - James W Buck
- Department of Plant Pathology, University of Georgia, 1109 Experiment St., Griffin, GA, 30223, USA
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, 3250 Rainwater Road, Tifton, GA, 31793, USA
| | - Tim Coolong
- Department of Horticulture, University of Georgia, 3250 Rainwater Road, Tifton, GA, 31793, USA
| | - Scott Adkins
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL, 34945, USA
| | - Rajagopalbabu Srinivasan
- Department of Entomology, University of Georgia, 1109 Experiment Street, Griffin, GA, 30223, USA.
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9
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Abstract
The pathological importance of mixed viral infections in plants might be underestimated except for a few well-characterized synergistic combinations in certain crops. Considering that the host ranges of many viruses often overlap and that most plant species can be infected by several unrelated viruses, it is not surprising to find more than one virus simultaneously in the same plant. Furthermore, dispersal of the majority of plant viruses relies on efficient transmission mechanisms mediated by vector organisms, mainly but not exclusively insects, which can contribute to the occurrence of multiple infections in the same plant. Recent work using different experimental approaches has shown that mixed viral infections can be remarkably frequent, up to the point that they could be considered the rule more than the exception. The purpose of this review is to describe the impact of multiple infections not only on the participating viruses themselves but also on their vectors and on the common host. From this standpoint, mixed infections arise as complex events that involve several cross-interacting players, and they consequently require a more general perspective than the analysis of single-virus/single-host approaches for a full understanding of their relevance.
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Affiliation(s)
- Ana Beatriz Moreno
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
| | - Juan José López-Moya
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Spain
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Domingo-Calap ML, Moreno AB, Díaz Pendón JA, Moreno A, Fereres A, López-Moya JJ. Assessing the Impact on Virus Transmission and Insect Vector Behavior of a Viral Mixed Infection in Melon. PHYTOPATHOLOGY 2020; 110:174-186. [PMID: 31502517 DOI: 10.1094/phyto-04-19-0126-fi] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mixed viral infections in plants are common, and can result in synergistic or antagonistic interactions. Except in complex diseases with severe symptoms, mixed infections frequently remain unnoticed, and their impact on insect vector transmission is largely unknown. In this study, we considered mixed infections of two unrelated viruses commonly found in melon plants, the crinivirus cucurbit yellow stunting disorder virus (CYSDV) and the potyvirus watermelon mosaic virus (WMV), and evaluated their vector transmission by whiteflies and aphids, respectively. Their dynamics of accumulation was analyzed until 60 days postinoculation (dpi) in mixed-infected plants, documenting reduced titers of WMV and much higher titers of CYSDV compared with single infections. At 24 dpi, corresponding to the peak of CYSDV accumulation, similar whitefly transmission rates were obtained when comparing either individual or mixed-infected plants as CYSDV sources, although its secondary dissemination was slightly biased toward plants previously infected with WMV, regardless of the source plant. However, at later time points, mixed-infected plants partially recovered from the initially severe symptoms, and CYSDV transmission became significantly higher. Interestingly, aphid transmission rates both at early and late time points were unaltered when WMV was acquired from mixed-infected plants despite its reduced accumulation. This lack of correlation between WMV accumulation and transmission could result from compensatory effects observed in the analysis of the aphid feeding behavior by electrical penetration graphs. Thus, our results showed that mixed-infected plants could provide advantages for both viruses, directly favoring CYSDV dissemination while maintaining WMV transmission.
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Affiliation(s)
- Maria Luisa Domingo-Calap
- Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas (CSIC)-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
| | - Ana Beatriz Moreno
- Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas (CSIC)-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
| | - Juan Antonio Díaz Pendón
- Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-UMA-CSIC), Algarrobo-Costa, Málaga, Spain
| | - Aranzazu Moreno
- Institute of Agricultural Sciences, ICA, CSIC, Madrid, Spain
| | - Alberto Fereres
- Institute of Agricultural Sciences, ICA, CSIC, Madrid, Spain
| | - Juan José López-Moya
- Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas (CSIC)-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
- CSIC, Barcelona, Spain
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11
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Shi J, Zhao L, Yan B, Zhu Y, Ma H, Chen W, Ruan S. Comparative Transcriptome Analysis Reveals the Transcriptional Alterations in Growth- and Development-Related Genes in Sweet Potato Plants Infected and Non-Infected by SPFMV, SPV2, and SPVG. Int J Mol Sci 2019; 20:ijms20051012. [PMID: 30813603 PMCID: PMC6429102 DOI: 10.3390/ijms20051012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 01/31/2019] [Accepted: 02/10/2019] [Indexed: 11/16/2022] Open
Abstract
Field co-infection of multiple viruses results in considerable losses in the yield and quality of storage roots in sweet potato. However, little is known about the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses. Here, a comparative transcriptomic analysis was performed to reveal the transcriptional alterations in sweet potato plants infected (VCSP) and non-infected (VFSP) by Sweet potato mild mottle virus (SPFMV), Sweet potato virus Y (SPV2) and Sweet potato virus G (SPVG). A total of 1580 and 12,566 differentially expressed genes (DEGs) were identified in leaves and storage roots of VFSP and VCSP plants, respectively. In leaves, 707 upregulated and 773 downregulated genes were identified, whereas 5653 upregulated and 6913 downregulated genes were identified in storage roots. Gene Ontology (GO) classification and pathway enrichment analysis showed that the expression of genes involved in chloroplast and photosynthesis and brassinosteroid (BR) biosynthesis in leaves and the vitamin biosynthetic process in storage roots was inhibited by co-infection of three viruses: SPFMV, SPV2, and SPVG. This was likely closely related to better photosynthesis and higher contents of Vitamin C (Vc) in storage roots of VFSP than that of VCSP. While some genes involved in ribosome and secondary metabolite-related pathways in leaves and alanine, aspartate, and glutamate metabolism in storage roots displayed higher expression in VCSP than in VFSP. Quantitative real-time PCR analysis demonstrated that the expression patterns of 26 DEGs, including 16 upregulated genes and 10 downregulated genes were consistent with the RNA-seq data from VFSP and VCSP. Taken together, this study integrates the results of morphology, physiology, and comparative transcriptome analyses in leaves and storage roots of VCSP and VFSP to reveal transcriptional alterations in growth- and development-related genes, providing new insight into the molecular mechanisms underlying developmental disorders of sweet potato subjected to co-infection by multiple viruses.
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Affiliation(s)
- Jiang Shi
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
| | - Lin Zhao
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
| | - Baiyuan Yan
- Jiande Seed Management Station, Hangzhou 311600, China.
| | - Yueqing Zhu
- Linan District Forestry and Agriculture Bureau, Hangzhou 311300, China.
| | - Huasheng Ma
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
| | - Wenyue Chen
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
| | - Songlin Ruan
- Institute of Crop Science, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
- Laboratory of Plant Molecular Biology & Proteomics, Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China.
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Kwak HR, Kim J, Kim M, Seo JK, Kim JS, Choi HS. Complete Genome Sequence Analysis of Two Divergent Groups of Sweet potato chlorotic fleck virus Isolates Collected from Korea. THE PLANT PATHOLOGY JOURNAL 2018; 34:451-457. [PMID: 30369855 PMCID: PMC6200045 DOI: 10.5423/ppj.nt.03.2018.0042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 06/10/2018] [Accepted: 07/29/2018] [Indexed: 06/08/2023]
Abstract
The Sweet potato chlorotic fleck virus (SPCFV), of the genus Carlavirus (family Betaflexiviridae), was first detected as one of several viruses infecting sweet potatoes (Ipomea batatas L.) in Korea. Out of 154 sweet potato samples collected in 2012 that were showing virus-like symptoms, 47 (31%) were infected with SPCFV, along with other viruses. The complete genome sequences of four SPCFV isolates were determined and analyzed using previously reported genome sequences. The complete genomes were found to contain 9,104-9,108 nucleotides, excluding the poly-A tail, containing six putative open reading frames (ORFs). Further, the SPCFV Korean isolates were divided into two groups (Group I and Group II) by phylogenetic analysis based on the complete nucleotide sequences; Group I and Group II had low nucleotide sequence identities of about 73%. For the first time, we determined the complete genome sequence for the Group II SPCFV isolates. The amino acid sequence identity in coat proteins (CP) between the two groups was over 90%, whereas the amino acid sequence identity in other proteins was less than 80%. In addition, SPCFV Korean isolates had a low amino acid sequence identity (61% CPs and 47% in the nucleotide- binding protein [NaBp] region) to that of Melon yellowing-associated virus (MYaV), a typical Carlavirus.
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Affiliation(s)
- Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365,
Korea
| | - Jaedeok Kim
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365,
Korea
| | - Mikyeong Kim
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365,
Korea
| | - Jang-Kyun Seo
- Graduate school of International Agricultural Technology, Seoul National University, Pyeongchang 25354,
Korea
| | - Jeong-Soo Kim
- Department of Plant Medicine, Andong National University, Andong 36729,
Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Science, Wanju 55365,
Korea
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Wainaina JM, Ateka E, Makori T, Kehoe MA, Boykin LM. Phylogenomic relationship and evolutionary insights of sweet potato viruses from the western highlands of Kenya. PeerJ 2018; 6:e5254. [PMID: 30038869 PMCID: PMC6054865 DOI: 10.7717/peerj.5254] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/24/2018] [Indexed: 11/20/2022] Open
Abstract
Sweet potato is a major food security crop within sub-Saharan Africa where 90% of Africa production occurs. One of the major limitations of sweet potato production are viral infections. In this study, we used a combination of whole genome sequences from a field isolate obtained from Kenya and those available in GenBank. Sequences of four sweet potato viruses: Sweet potato feathery mottle virus (SPFMV), Sweet potato virus C (SPVC), Sweet potato chlorotic stunt virus (SPCSV), Sweet potato chlorotic fleck virus (SPCFV) were obtained from the Kenyan sample. SPFMV sequences both from this study and from GenBank were found to be recombinant. Recombination breakpoints were found within the Nla-Pro, coat protein and P1 genes. The SPCSV, SPVC, and SPCFV viruses from this study were non-recombinant. Bayesian phylogenomic relationships across whole genome trees showed variation in the number of well-supported clades; within SPCSV (RNA1 and RNA2) and SPFMV two well-supported clades (I and II) were resolved. The SPCFV tree resolved three well-supported clades (I-III) while four well-supported clades were resolved in SPVC (I-IV). Similar clades were resolved within the coalescent species trees. However, there were disagreements between the clades resolved in the gene trees compared to those from the whole genome tree and coalescent species trees. However the coat protein gene tree of SPCSV and SPCFV resolved similar clades to the genome and coalescent species tree while this was not the case in SPFMV and SPVC. In addition, we report variation in selective pressure within sites of individual genes across all four viruses; overall all viruses were under purifying selection. We report the first complete genomes of SPFMV, SPVC, SPCFV, and a partial SPCSV from Kenya as a mixed infection in one sample. Our findings provide a snap shot on the evolutionary relationship of sweet potato viruses (SPFMV, SPVC, SPCFV, and SPCSV) from Kenya as well as assessing whether selection pressure has an effect on their evolution.
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Affiliation(s)
- James M. Wainaina
- School of Molecular Sciences/ARC CoE Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
| | - Elijah Ateka
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Timothy Makori
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Monica A. Kehoe
- Plant Pathology, Department of Primary Industries and Regional Development Diagnostic Laboratory Service, South Perth, WA, Australia
| | - Laura M. Boykin
- School of Molecular Sciences/ARC CoE Plant Energy Biology, The University of Western Australia, Crawley, WA, Australia
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Orfanidou CG, Baltzi A, Dimou NA, Katis NI, Maliogka VI. Cucurbit chlorotic yellows virus: Insights Into Its Natural Host Range, Genetic Variability, and Transmission Parameters. PLANT DISEASE 2017; 101:2053-2058. [PMID: 30677385 DOI: 10.1094/pdis-02-17-0164-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cucurbit chlorotic yellows virus (CCYV) (genus Crinivirus, family Closteroviridae) is implicated in cucurbit yellows disease (CYV), causing typical interveinal yellowing symptoms in leaves, and is transmitted by Bemisia tabaci Mediterranean (MED) and Middle East-Asia Minor 1 (MEAM1). Due to its recent report in cucurbit crops in Greece, field surveys were conducted during 2011-2016 to determine the presence of the virus in symptomatic cucurbits and alternative hosts among arable weed species. Results indicated the restricted spread of the virus and identified 13 weed species as CCYV hosts for the first time. Sequence analysis of the RNA-dependent RNA polymerase (RNA1) coat and minor coat proteins (RNA2) revealed very low genetic diversity (<0.1%) among the Greek isolates. Transmission experiments were also conducted using B. tabaci MED with retention determined at four days, whereas transmission efficiency was positively correlated with the number of adults used, features linked to the virus semipersistent mode of transmission.
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Affiliation(s)
- C G Orfanidou
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - A Baltzi
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - N A Dimou
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - N I Katis
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
| | - V I Maliogka
- Laboratory of Plant Pathology, Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, 54124, Thessaloniki, Greece
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Rodríguez-Nevado C, Montes N, Pagán I. Ecological Factors Affecting Infection Risk and Population Genetic Diversity of a Novel Potyvirus in Its Native Wild Ecosystem. FRONTIERS IN PLANT SCIENCE 2017; 8:1958. [PMID: 29184567 PMCID: PMC5694492 DOI: 10.3389/fpls.2017.01958] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
Increasing evidence indicates that there is ample diversity of plant virus species in wild ecosystems. The vast majority of this diversity, however, remains uncharacterized. Moreover, in these ecosystems the factors affecting plant virus infection risk and population genetic diversity, two traits intrinsically linked to virus emergence, are largely unknown. Along 3 years, we have analyzed the prevalence and diversity of plant virus species from the genus Potyvirus in evergreen oak forests of the Iberian Peninsula, the main wild ecosystem in this geographic region and in the entire Mediterranean basin. During this period, we have also measured plant species diversity, host density, plant biomass, temperature, relative humidity, and rainfall. Results indicated that potyviruses were always present in evergreen oak forests, with a novel virus species explaining the largest fraction of potyvirus-infected plants. We determined the genomic sequence of this novel virus and we explored its host range in natural and greenhouse conditions. Natural host range was limited to the perennial plant mountain rue (Ruta montana), commonly found in evergreen oak forests of the Iberian Peninsula. In this host, the virus was highly prevalent and was therefore provisionally named mediterranean ruda virus (MeRV). Focusing in this natural host-virus interaction, we analyzed the ecological factors affecting MeRV infection risk and population genetic diversity in its native wild ecosystem. The main predictor of virus infection risk was the host density. MeRV prevalence was the major factor determining genetic diversity and selection pressures in the virus populations. This observation supports theoretical predictions assigning these two traits a key role in parasite epidemiology and evolution. Thus, our analyses contribute both to characterize viral diversity and to understand the ecological determinants of virus population dynamics in wild ecosystems.
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Affiliation(s)
- Cristina Rodríguez-Nevado
- Centro de Biotecnología y Genómica de Plantas – Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Nuria Montes
- Plant Physiology, Pharmaceutical and Health Sciences Department, Faculty of Pharmacy, CEU-San Pablo University, Madrid, Spain
- Rheumatology Service, Hospital Universitario La Princesa, IIS-IP, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas – Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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