1
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Mbewe W, Mukasa S, Ochwo-Ssemakula M, Sseruwagi P, Tairo F, Ndunguru J, Duffy S. Cassava brown streak virus evolves with a nucleotide-substitution rate that is typical for the family Potyviridae. Virus Res 2024; 346:199397. [PMID: 38750679 PMCID: PMC11145536 DOI: 10.1016/j.virusres.2024.199397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/08/2024] [Accepted: 05/12/2024] [Indexed: 05/25/2024]
Abstract
The ipomoviruses (family Potyviridae) that cause cassava brown streak disease (cassava brown streak virus [CBSV] and Uganda cassava brown streak virus [UCBSV]) are damaging plant pathogens that affect the sustainability of cassava production in East and Central Africa. However, little is known about the rate at which the viruses evolve and when they emerged in Africa - which inform how easily these viruses can host shift and resist RNAi approaches for control. We present here the rates of evolution determined from the coat protein gene (CP) of CBSV (Temporal signal in a UCBSV dataset was not sufficient for comparable analysis). Our BEAST analysis estimated the CBSV CP evolves at a mean rate of 1.43 × 10-3 nucleotide substitutions per site per year, with the most recent common ancestor of sampled CBSV isolates existing in 1944 (95% HPD, between years 1922 - 1963). We compared the published measured and estimated rates of evolution of CPs from ten families of plant viruses and showed that CBSV is an average-evolving potyvirid, but that members of Potyviridae evolve more quickly than members of Virgaviridae and the single representatives of Betaflexiviridae, Bunyaviridae, Caulimoviridae and Closteroviridae.
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Affiliation(s)
- Willard Mbewe
- Department of Biological Sciences, Malawi University of Science and Technology, P. O. Box 5196, Limbe, Malawi.
| | - Settumba Mukasa
- School of Agriculture and Environmental Science, Department of Agricultural Production, P. O. Box 7062, Makerere University, Kampala, Uganda
| | - Mildred Ochwo-Ssemakula
- School of Agriculture and Environmental Science, Department of Agricultural Production, P. O. Box 7062, Makerere University, Kampala, Uganda
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Fred Tairo
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Slaam, Tanzania
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, United States.
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2
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Torralba B, Blanc S, Michalakis Y. Reassortments in single-stranded DNA multipartite viruses: Confronting expectations based on molecular constraints with field observations. Virus Evol 2024; 10:veae010. [PMID: 38384786 PMCID: PMC10880892 DOI: 10.1093/ve/veae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/23/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Single-stranded DNA multipartite viruses, which mostly consist of members of the genus Begomovirus, family Geminiviridae, and all members of the family Nanoviridae, partly resolve the cost of genomic integrity maintenance through two remarkable capacities. They are able to systemically infect a host even when their genomic segments are not together in the same host cell, and these segments can be separately transmitted by insect vectors from host to host. These capacities potentially allow such viruses to reassort at a much larger spatial scale, since reassortants could arise from parental genotypes that do not co-infect the same cell or even the same host. To assess the limitations affecting reassortment and their implications in genome integrity maintenance, the objective of this review is to identify putative molecular constraints influencing reassorted segments throughout the infection cycle and to confront expectations based on these constraints with empirical observations. Trans-replication of the reassorted segments emerges as the major constraint, while encapsidation, viral movement, and transmission compatibilities appear more permissive. Confronting the available molecular data and the resulting predictions on reassortments to field population surveys reveals notable discrepancies, particularly a surprising rarity of interspecific natural reassortments within the Nanoviridae family. These apparent discrepancies unveil important knowledge gaps in the biology of ssDNA multipartite viruses and call for further investigation on the role of reassortment in their biology.
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Affiliation(s)
- Babil Torralba
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Stéphane Blanc
- PHIM, Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Avenue du Campus d’Agropolis - ZAC de Baillarguet, Montpellier 34980, France
| | - Yannis Michalakis
- MIVEGEC, Université Montpellier, CNRS, IRD, 911, Avenue Agropolis, Montpellier 34394, France
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3
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Ohshima K, Kawakubo S, Muraoka S, Gao F, Ishimaru K, Kayashima T, Fukuda S. Genomic Epidemiology and Evolution of Scallion Mosaic Potyvirus From Asymptomatic Wild Japanese Garlic. Front Microbiol 2021; 12:789596. [PMID: 34956155 PMCID: PMC8692251 DOI: 10.3389/fmicb.2021.789596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/11/2021] [Indexed: 11/30/2022] Open
Abstract
Scallion mosaic virus (ScaMV) belongs to the turnip mosaic virus phylogenetic group of potyvirus and is known to infect domestic scallion plants (Allium chinense) in China and wild Japanese garlic (Allium macrostemon Bunge) in Japan. Wild Japanese garlic plants showing asymptomatic leaves were collected from different sites in Japan during 2012–2015. We found that 73 wild Japanese garlic plants out of 277 collected plants were infected with ScaMV, identified by partial genomic nucleotide sequences of the amplified RT-PCR products using potyvirus-specific primer pairs. Sixty-three ScaMV isolates were then chosen, and those full genomic sequences were determined. We carried out evolutionary analyses of the complete polyprotein-coding sequences and four non-recombinogenic regions of partial genomic sequences. We found that 80% of ScaMV samples have recombination-like genome structure and identified 12 recombination-type patterns in the genomes of the Japanese ScaMV isolates. Furthermore, we found two non-recombinant-type patterns in the Japanese population. Because the wild plants and weeds may often serve as reservoirs of viruses, it is important to study providing the exploratory investigation before emergence in the domestic plants. This is possibly the first epidemiological and evolutionary study of a virus from asymptomatic wild plants.
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Affiliation(s)
- Kazusato Ohshima
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan.,Institute of Wild Onion Science, Saga University, Saga, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Shusuke Kawakubo
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan
| | - Satoshi Muraoka
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan
| | - Fangluan Gao
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kanji Ishimaru
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan.,Institute of Wild Onion Science, Saga University, Saga, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan
| | - Tomoko Kayashima
- Institute of Wild Onion Science, Saga University, Saga, Japan.,Department of School Education Course, Faculty of Education, Saga University, Saga, Japan
| | - Shinji Fukuda
- Department of Biological Resource Science, Faculty of Agriculture, Saga University, Saga, Japan.,Institute of Wild Onion Science, Saga University, Saga, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.,Saga University Center for Education and Research in Agricultural Innovation, Faculty of Agriculture, Saga University, Saga, Japan
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4
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Genomic analysis of the brassica pathogen turnip mosaic potyvirus reveals its spread along the former trade routes of the Silk Road. Proc Natl Acad Sci U S A 2021; 118:2021221118. [PMID: 33741737 PMCID: PMC8000540 DOI: 10.1073/pnas.2021221118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Our article presents the most comprehensive reconstruction of the evolutionary and phylogeographic history of a major plant pathogen of brassica vegetables in Eurasia. Sampling across such a large landmass poses considerable challenges, and our study attempts to describe the spatial and temporal patterns of migration for a plant pathogen on a large scale. Our phylogeographic and molecular clock analyses show that the migration pathways of turnip mosaic potyvirus retrace some of the historical trade arteries of the Silk Road. This study demonstrates how a comprehensive genetic analysis can provide a large-scale view of the epidemiology and human-mediated spread of a plant pathogen across centuries of evolutionary history. Plant pathogens have agricultural impacts on a global scale and resolving the timing and route of their spread can aid crop protection and inform control strategies. However, the evolutionary and phylogeographic history of plant pathogens in Eurasia remains largely unknown because of the difficulties in sampling across such a large landmass. Here, we show that turnip mosaic potyvirus (TuMV), a significant pathogen of brassica crops, spread from west to east across Eurasia from about the 17th century CE. We used a Bayesian phylogenetic approach to analyze 579 whole genome sequences and up to 713 partial sequences of TuMV, including 122 previously unknown genome sequences from isolates that we collected over the past five decades. Our phylogeographic and molecular clock analyses showed that TuMV isolates of the Asian-Brassica/Raphanus (BR) and basal-BR groups and world-Brassica3 (B3) subgroup spread from the center of emergence to the rest of Eurasia in relation to the host plants grown in each country. The migration pathways of TuMV have retraced some of the major historical trade arteries in Eurasia, a network that formed the Silk Road, and the regional variation of the virus is partly characterized by different type patterns of recombinants. Our study presents a complex and detailed picture of the timescale and major transmission routes of an important plant pathogen.
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5
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Ahsan M, Ashfaq M, Riaz H, Khan Z, Hamza MZ, Asad Z. Genetic diversity and molecular characterization of Cucumber mosaic cucumovirus (CMV) subgroup II infecting Spinach (Spinacia oleracea) and Pea (Pisum sativum) in Pothwar region of Pakistan. BRAZ J BIOL 2021; 83:e245865. [PMID: 34495149 DOI: 10.1590/1519-6984.245865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/13/2021] [Indexed: 11/22/2022] Open
Abstract
Cucumber mosaic virus (CMV) is a tremendous threat to vegetables across the globe, including in Pakistan. The present work was conducted to investigate the genetic variability of CMV isolates infecting pea and spinach vegetables in the Pothwar region of Pakistan. Serological-based surveys during 2016-2017 revealed 31.70% overall CMV disease incidence from pea and spinach crops. Triple-antibody sandwich enzyme-linked immunosorbent assay (TAS-ELISA) revealed that all the positive isolates belong to CMV subgroup II. Two selected cDNA from ELISA-positive samples representing each pea and spinach crops were PCR-amplified (ca.1100 bp) and sequenced corresponding to the CMV CP gene which shared 93.7% nucleotide identity with each other. Both the sequences of CMV pea (AAHAP) and spinach (AARS) isolates from Pakistan were submitted to GenBank as accession nos. MH119071 and MH119073, respectively. BLAST analysis revealed 93.4% sequence identity of AAHAP isolate with SpK (KC763473) from Iran while AARS isolate shared maximum identity (94.5%) with the strain 241 (AJ585519) from Australia and clustered with some reference isolates of CMV subgroup II from UK (Z12818) and USA (AF127976) in a Neighbour-joining phylogenetic reconstruction. A total of 59 polymorphic (segregating) sites (S) with nucleotide diversity (π) of 0.06218 was evident while no INDEL event was observed in Pakistani isolates. The evolutionary distance of Pakistani CMV isolates was recorded as 0.0657 with each other and 0.0574-0.2964 with other CMV isolates reported elsewhere in the world. A frequent gene flow (Fst = 0.30478 <0.33) was observed between Pakistani and earlier reported CMV isolates. In genetic differentiation analysis, the value of three permutation-based statistical tests viz; Z (84.3011), Snn (0.82456), and Ks* (4.04042) were non-significant. The statistical analysis revealed the values 2.02535, 0.01468, and 0.71862 of Tajima's D, Fu, & Li's F* and D* respectively, demonstrating that the CMV population is under balancing selection.
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Affiliation(s)
- M Ahsan
- PMAS-Arid Agriculture University, Department of Plant Pathology, Rawalpindi, Pakistan
| | - M Ashfaq
- MNS-University of Agriculture, Institute of Plant Protection, Plant Pathology, Multan, Pakistan
| | - H Riaz
- MNS-University of Agriculture, Institute of Plant Protection, Plant Pathology, Multan, Pakistan
| | - Z Khan
- MNS-University of Agriculture, Institute of Plant Breeding and Biotechnology, Multan, Pakistan
| | - M Z Hamza
- MNS-University of Agriculture, Institute of Plant Protection, Plant Pathology, Multan, Pakistan
| | - Z Asad
- PMAS-Arid Agriculture University, Department of Plant Pathology, Rawalpindi, Pakistan
- MNS-University of Agriculture, Institute of Plant Protection, Plant Pathology, Multan, Pakistan
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6
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Xavier CAD, Godinho MT, Mar TB, Ferro CG, Sande OFL, Silva JC, Ramos-Sobrinho R, Nascimento RN, Assunção I, Lima GSA, Lima ATM, Murilo Zerbini F. Evolutionary dynamics of bipartite begomoviruses revealed by complete genome analysis. Mol Ecol 2021; 30:3747-3767. [PMID: 34021651 DOI: 10.1111/mec.15997] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 12/17/2022]
Abstract
Several key evolutionary events marked the evolution of geminiviruses, culminating with the emergence of divided (bipartite) genomes represented by viruses classified in the genus Begomovirus. This genus represents the most abundant group of multipartite viruses, contributing significantly to the observed abundance of multipartite species in the virosphere. Although aspects related to virus-host interactions and evolutionary dynamics have been extensively studied, the bipartite nature of these viruses has been little explored in evolutionary studies. Here, we performed a parallel evolutionary analysis of the DNA-A and DNA-B segments of New World begomoviruses. A total of 239 full-length DNA-B sequences obtained in this study, combined with 292 DNA-A and 76 DNA-B sequences retrieved from GenBank, were analysed. The results indicate that the DNA-A and DNA-B respond differentially to evolutionary processes, with the DNA-B being more permissive to variation and more prone to recombination than the DNA-A. Although a clear geographic segregation was observed for both segments, differences in the genetic structure between DNA-A and DNA-B were also observed, with cognate segments belonging to distinct genetic clusters. DNA-B coding regions evolve under the same selection pressures than DNA-A coding regions. Together, our results indicate an interplay between reassortment and recombination acting at different levels across distinct subpopulations and segments.
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Affiliation(s)
- César A D Xavier
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Márcio T Godinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Talita B Mar
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Camila G Ferro
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Osvaldo F L Sande
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - José C Silva
- Dep. de Bioquímica e Biologia Molecular/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Roberto Ramos-Sobrinho
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Renato N Nascimento
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Iraildes Assunção
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Gaus S A Lima
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, Alagoas, Brazil
| | - Alison T M Lima
- Instituto de Ciências Agrárias, Universidade Federal de Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - F Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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7
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Molecular analysis of Greek isolates of cucumber mosaic virus from vegetables shows a low prevalence of satellite RNAs and suggests the presence of host-associated virus strains. Arch Virol 2021; 166:2199-2208. [PMID: 34057609 DOI: 10.1007/s00705-021-05115-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/06/2021] [Indexed: 01/27/2023]
Abstract
Cucumber mosaic virus (CMV) is a generalist pathogen that infects many economically important crops in Greece. The present study was designed to evaluate the genetic variability of Greek CMV isolates in combination with their satellite RNAs (satRNAs). To achieve this goal, 77 CMV isolates were collected from symptomatic Greek vegetables, mainly tomatoes and cucurbits, alongside their neighboring crops, during a four-year period from 2015 to 2018. Phylogenetic analysis of a partial coat protein (CP) gene segment revealed that all of the isolates belong to CMV subgroups IA and IB and that they are closely related to previously reported Greek isolates. It should be noted, however, that the latter mainly included tomato isolates. Network analysis of the evolutionary relationships among the CP sequences of the Greek isolates in comparison to the corresponding sequences obtained from the GenBank database indicated two predominant common ancestors and at least three differentiated peripherals, and possibly host-associated (tomatoes, legumes, cucurbits) haplogroups (strain groups). More specifically, host-adaptive evolution can be postulated regarding the tomato isolates in subgroup IB. Necrogenic or non-necrogenic satRNAs were detected in four samples from tomato and melon, and this is the first report of non-necrogenic satRNAs in CMV in Greece.
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8
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Heo KJ, Kwon SJ, Kim MK, Kwak HR, Han SJ, Kwon MJ, Rao ALN, Seo JK. Newly emerged resistance-breaking variants of cucumber mosaic virus represent ongoing host-interactive evolution of an RNA virus. Virus Evol 2020; 6:veaa070. [PMID: 33240527 PMCID: PMC7673075 DOI: 10.1093/ve/veaa070] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Understanding the evolutionary history of a virus and the mechanisms influencing the direction of its evolution is essential for the development of more durable strategies to control the virus in crop fields. While the deployment of host resistance in crops is the most efficient means to control various viruses, host resistance itself can act as strong selective pressure and thus play a critical role in the evolution of virus virulence. Cucumber mosaic virus (CMV), a plant RNA virus with high evolutionary capacity, has caused endemic disease in various crops worldwide, including pepper (Capsicum annuum L.), because of frequent emergence of resistance-breaking variants. In this study, we examined the molecular and evolutionary characteristics of recently emerged, resistance-breaking CMV variants infecting pepper. Our population genetics analysis revealed that the high divergence capacity of CMV RNA1 might have played an essential role in the host-interactive evolution of CMV and in shaping the CMV population structure in pepper. We also demonstrated that nonsynonymous mutations in RNA1 encoding the 1a protein enabled CMV to overcome the deployed resistance in pepper. Our findings suggest that resistance-driven selective pressures on RNA1 might have contributed in shaping the unique evolutionary pattern of CMV in pepper. Therefore, deployment of a single resistance gene may reduce resistance durability against CMV and more integrated approaches are warranted for successful control of CMV in pepper.
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Affiliation(s)
| | - Sun-Jung Kwon
- Institutes of Green Bio Science and Technology, Seoul National University, 1447 Pyeongchang-ro, Pyeongchang 25354, Republic of Korea
| | - Mi-Kyeong Kim
- Department of Plant Medicine, Chungbuk National University, 1 Chungdae-ro, Cheongju 28644, Republic of Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, 300 Nongsaengmyeong-ro, Wanju 55365, Republic of Korea
| | - Soo-Jung Han
- Department of International Agricultural Technology
| | - Min-Jun Kwon
- Department of International Agricultural Technology
| | - A L N Rao
- Department of Microbiology and Plant Pathology, University of California, Boyce Hall 1463, 900 University Ave, Riverside, CA 92521, USA
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9
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Desbiez C, Wipf-Scheibel C, Millot P, Berthier K, Girardot G, Gognalons P, Hirsch J, Moury B, Nozeran K, Piry S, Schoeny A, Verdin E. Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area. Virus Res 2020; 286:198042. [PMID: 32504705 DOI: 10.1016/j.virusres.2020.198042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/19/2020] [Accepted: 05/31/2020] [Indexed: 12/20/2022]
Abstract
Plant viral diseases represent a significant burden to plant health, and their highest impact in Mediterranean agriculture is on vegetables grown under intensive horticultural practices. In order to understand better virus evolution and emergence, the most prevalent viruses were mapped in the main cucurbitaceous (melon, squashes) and solanaceous (tomato, pepper) crops and in some wild hosts in the French Mediterranean area, and virus diversity, evolution and population structure were studied through molecular epidemiology approaches. Surveys were performed in summer 2016 and 2017, representing a total of 1530 crop samples and 280 weed samples. The plant samples were analysed using serological and molecular approaches, including high-throughput sequencing (HTS). The viral species and their frequency in crops were quite similar to those of surveys conducted ten years before in the same areas. Contrary to other Mediterranean countries, aphid-transmitted viruses remain the most prevalent in France whereas whitefly-transmitted ones have not yet emerged. However, HTS analysis of viral evolution revealed the appearance of undescribed viral variants, especially for watermelon mosaic virus (WMV) in cucurbits, or variants not present in France before, as for cucumber mosaic virus (CMV) in solanaceous crops. Deep sequencing also revealed complex virus populations within individual plants with frequent recombination or reassortment. The spatial genetic structure of cucurbit aphid-borne yellows virus (CABYV) was related to the landscape structure, whereas in the case of WMV, the recurrence of introduction events and probable human exchanges of plant material resulted in complex spatial pattern of genetic variation.
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Affiliation(s)
| | | | | | | | | | | | - Judith Hirsch
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | - Benoît Moury
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
| | | | - Sylvain Piry
- INRAE, Pathologie Végétale, F-84140, Montfavet, France; CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, Montpellier, France
| | | | - Eric Verdin
- INRAE, Pathologie Végétale, F-84140, Montfavet, France
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10
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Evolutionary timescale and geographical movement of cucumber mosaic virus, with focus on Iranian strains. Arch Virol 2019; 165:185-192. [PMID: 31637514 DOI: 10.1007/s00705-019-04439-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 09/16/2019] [Indexed: 10/25/2022]
Abstract
Cucumber mosaic virus (CMV) is a geographically widespread plant virus with a very broad host range. The virus has been detected in diverse crops all over Iran. In this study, we estimated the timescale of the evolution of CMV subgroup I and the geographical movement of the virus with a focus on Iranian strains. Analyses using the MP and CP genes and their concatenation revealed that the CMV population within subgroup I had a single ancestor dating back to about 450-550 years ago. The Iranian strains formed three clusters in a maximum-clade-credibility phylogenetic tree. It was found that the most recent common ancestor of the Iranian strains within each cluster dates back to less than 100 years ago. Our results also suggest that both short- and long-distance migration of Iranian CMV strains has occurred in the last 100 years.
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11
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Petrzik K. Evolutionary forces at work in partitiviruses. Virus Genes 2019; 55:563-573. [PMID: 31230256 DOI: 10.1007/s11262-019-01680-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023]
Abstract
The family Partitiviridae consists of dsRNA viruses with genome separated into two segments and encoding replicase and capsid protein only. We examined the nucleotide diversity expressed as the ratio dN/dS of nonsynonymous and synonymous substitutions, which has been calculated for 12 representative viruses of all five genera of partitiviruses. We can state that strong purifying selection works on both the RdRp and CP genes and propose that putative positive selection occurs also on the RdRp genes in two viruses. Among the 95 evaluated viruses, wherein both segments had been sequenced, 8 viruses in betapartitiviruses and 9 in alphapartitiviruses were identified as reassortment candidates because they differ extremely in their CP identity even as they are related in terms of RdRp. Furthermore, there are indications that reassortants are present among isolates of different viruses.
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Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
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12
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Giakountis A, Tsarmpopoulos I, Chatzivassiliou EK. Cucumber mosaic virus Isolates from Greek Legumes are Associated with Satellite RNAs that are Necrogenic for Tomato. PLANT DISEASE 2018; 102:2268-2276. [PMID: 30189158 DOI: 10.1094/pdis-08-17-1259-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Worldwide, Cucumber mosaic virus (CMV) is the causal agent of many economically important diseases. Based on immunological or molecular analysis, three distinct subgroups of CMV isolates can be identified (IA, IB, and II). In addition, some CMV isolates are associated with satellite RNAs (satRNAs), a type of noncoding transcript that may alter the symptoms of CMV infections. This study presents an analysis of CMV isolates occurring in legumes in Greece in respect to their genetic diversity, and the presence and diversity of their satRNA. Phylogenetic analysis of the CMV coat protein sequence of 18 legume and 5 tomato CMV isolates collected throughout Greece classified them within subgroups IA and IB, with a limited genetic diversity. The CMV satRNAs found in nine field legumes exhibiting mild symptoms and in one tomato with a necrotic syndrome contained a functional necrogenic motif; therefore, they were grouped within the necrogenic group of CMV-satRNAs. The necrotic phenotype was expressed in all legume CMV isolates containing necrogenic satRNAs when mechanically inoculated onto tomato plants. To our knowledge, this is the first observation that legumes host necrogenic CMV-satRNAs. The possible role of legumes in the epidemiology of CMV and necrogenic satRNA complex is discussed.
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Affiliation(s)
- Antonis Giakountis
- Agricultural University of Athens, School of Agricultural Production, Infrastructure and Environment, Department of Crop Science, Plant Pathology Laboratory, Iera Odos 75, Votanikos, 11855 Athens, Greece
| | - Iason Tsarmpopoulos
- Agricultural University of Athens, School of Agricultural Production, Infrastructure and Environment, Department of Crop Science, Plant Pathology Laboratory, Iera Odos 75, Votanikos, 11855 Athens, Greece
| | - Elisavet K Chatzivassiliou
- Agricultural University of Athens, School of Agricultural Production, Infrastructure and Environment, Department of Crop Science, Plant Pathology Laboratory, Iera Odos 75, Votanikos, 11855 Athens, Greece
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Pagán I. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view. INFECTION GENETICS AND EVOLUTION 2018; 65:187-199. [PMID: 30055330 DOI: 10.1016/j.meegid.2018.07.033] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/24/2018] [Accepted: 07/24/2018] [Indexed: 10/28/2022]
Abstract
During the past four decades, the scientific community has seen an exponential advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of plant virus populations. Predating these advances, the field of Phylogenetics has significantly contributed to understand important aspects of plant virus evolution. This review aims at summarizing the impact of Phylogenetics in the current knowledge on three major aspects of plant virus evolution that have benefited from the development of phylogenetic inference: (1) The identification and classification of plant virus diversity. (2) The mechanisms and forces shaping the evolution of plant virus populations. (3) The understanding of the interaction between plant virus evolution, epidemiology and ecology. The work discussed here highlights the important role of phylogenetic approaches in the study of the dynamics of plant virus populations.
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Affiliation(s)
- Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA, E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid 28223, Spain.
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Shi J, Yu L, Song B. Proteomics analysis of Xiangcaoliusuobingmi-treated Capsicum annuum L. infected with Cucumber mosaic virus. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2018; 149:113-122. [PMID: 30033007 DOI: 10.1016/j.pestbp.2018.06.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/22/2018] [Accepted: 06/13/2018] [Indexed: 05/24/2023]
Abstract
Among different viruses, Cucumber mosaic virus (CMV) has the most extensive host range, being capable of infecting over 1200 species, and causes severe damage worldwide. Xiangcaoliusuobingmi (B1), a candidate plant immune activator drug, exhibited significant protective effects against CMV. However, its potential mechanism is still unknown. In this study, we found the defensive enzyme activities of peroxidase (POD), phenylalanine ammonia lyase (PAL), superoxide dismutase (SOD) and catalase (CAT) can be enhanced by B1. Meanwhile, we found RT-qPCR assay results of the defensive gene expression can be improved by B1 in capsicum. Moreover, we analyze the result of label-free proteomics, B1 could trigger abscisic acid (ABA) pathway. All data provide a more understanding about the response to infect CMV capsicum activeted by B1 in the level of the plant physiology and biochemistry, gene and protein.
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Affiliation(s)
- Jing Shi
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Lu Yu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, PR China.
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The genetic diversity of narcissus viruses related to turnip mosaic virus blur arbitrary boundaries used to discriminate potyvirus species. PLoS One 2018; 13:e0190511. [PMID: 29300751 PMCID: PMC5754079 DOI: 10.1371/journal.pone.0190511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/15/2017] [Indexed: 11/19/2022] Open
Abstract
Narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected from around Japan, and tested for virus infections using potyvirus-specific primers. Many were found to be infected with a macluravirus and mixtures of different potyviruses, one third of them narcissus yellow stripe virus (NYSV)-like viruses. Genomes of nine of the NYSV-like viruses were sequenced and, together with four already published, provided data for phylogenetic and pairwise identity analyses of their place in the turnip mosaic virus (TuMV) phylogenetic group. Using existing ICTV criteria for defining potyvirus species, the narcissus viruses in TuMV group were found to be from five species; the previously described NLSYV, and four new species we call narcissus virus 1 (NV-1) and narcissus yellow stripe-1 to -3 (NYSV-1, NYSV-2 and NYSV-3). However, as all are from a single host species, and natural recombinants with NV-1 and NYSV-3 'parents have been found in China and India, we also conclude that they could be considered to be members of a single mega-species, narcissus virus; the criteria for defining such a potyvirus species would then be that their polyprotein sequences have greater than 69% identical nucleotides and greater than 75% identical amino acids.
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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Yasaka R, Fukagawa H, Ikematsu M, Soda H, Korkmaz S, Golnaraghi A, Katis N, Ho SYW, Gibbs AJ, Ohshima K. The Timescale of Emergence and Spread of Turnip Mosaic Potyvirus. Sci Rep 2017; 7:4240. [PMID: 28652582 PMCID: PMC5484681 DOI: 10.1038/s41598-017-01934-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/05/2017] [Indexed: 11/16/2022] Open
Abstract
Plant viruses have important global impacts on crops, and identifying their centre and date of emergence is important for planning control measures. Turnip mosaic virus (TuMV) is a member of the genus Potyvirus in the family Potyviridae and is a major worldwide pathogen of brassica crops. For two decades, we have collected TuMV isolates, mostly from brassicas, in Turkey and neighbouring countries. This region is thought to be the centre of emergence of this virus. We determined the genomic sequences of 179 of these isolates and used these to estimate the timescale of the spread of this virus. Our Bayesian coalescent analyses used synonymous sites from a total of 417 novel and published whole-genome sequences. We conclude that TuMV probably originated from a virus of wild orchids in Germany and, while adapting to wild and domestic brassicas, spread via Southern Europe to Asia Minor no more than 700 years ago. The population of basal-B group TuMVs in Asia Minor is older than all other populations of this virus, including a newly discovered population in Iran. The timescale of the spread of TuMV correlates well with the establishment of agriculture in these countries.
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Affiliation(s)
- Ryosuke Yasaka
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan.,The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Kagoshima, 890-0065, Japan
| | - Hirofumi Fukagawa
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan
| | - Mutsumi Ikematsu
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan
| | - Hiroko Soda
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan
| | - Savas Korkmaz
- Department of Plant Protection, Faculty of Agriculture, University of Canakkale Onsekiz Mart, Canakkale, Turkey
| | - Alireza Golnaraghi
- Department of Plant Protection, College of Agriculture and Natural Resources, Science and Research Branch, Islamic Azad University, Tehran, P.O. Box 14515-775, Iran
| | - Nikolaos Katis
- Plant Pathology Laboratory, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, 540 06, Greece
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Adrian J Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, 840-8502, Japan. .,The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24, Kagoshima, 890-0065, Japan.
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Gibbs AJ, Ohshima K, Yasaka R, Mohammadi M, Gibbs MJ, Jones RAC. The phylogenetics of the global population of potato virus Y and its necrogenic recombinants. Virus Evol 2017; 3:vex002. [PMID: 28458913 PMCID: PMC5399925 DOI: 10.1093/ve/vex002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Potato virus Y (PVY) is a major pathogen of potatoes and other solanaceous crops worldwide. It is most closely related to potyviruses first or only found in the Americas, and it almost certainly originated in the Andes, where its hosts were domesticated. We have inferred the phylogeny of the published genomic sequences of 240 PVY isolates collected since 1938 worldwide, but not the Andes. All fall into five groupings, which mostly, but not exclusively, correspond with groupings already devised using biological and taxonomic data. Only 42 percent of the sequences are not recombinant, and all these fall into one or other of three phylogroups; the previously named C (common), O (ordinary), and N (necrotic) groups. There are also two other distinct groups of isolates all of which are recombinant; the R-1 isolates have N (5' terminal minor) and O (major) parents, and the R-2 isolates have R-1 (major) and N (3' terminal minor) parents. Many isolates also have additional minor intra- and inter-group recombinant genomic regions. The complex interrelationships between the genomes were resolved by progressively identifying and removing recombinants using partitioned sequences of synonymous codons. Least squared dating and BEAST analyses of two datasets of gene sequences from non-recombinant heterochronously-sampled isolates (seventy-three non-recombinant major ORFs and 166 partial ORFs) found the 95% confidence intervals of the TMRCA estimates overlap around 1,000 CE (Common Era; AD). We attempted to identify the most accurate datings by comparing the estimated phylogenetic dates with historical events in the worldwide adoption of potato and other PVY hosts as crops, but found that more evidence from gene sequences of non-potato isolates, especially from South America, was required.
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Affiliation(s)
- Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Ryosuke Yasaka
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Musa Mohammadi
- Department of Plant Protection, Vali-e-asr University of Rafsanjan, Rafsanjan, Iran
| | | | - Roger A. C. Jones
- Department of Agriculture and Food Western Australia, Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- 3 Baron-Hay Court, South Perth, WA 6151, Australia
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Ohshima K, Nomiyama R, Mitoma S, Honda Y, Yasaka R, Tomimura K. Evolutionary rates and genetic diversities of mixed potyviruses in Narcissus. INFECTION GENETICS AND EVOLUTION 2016; 45:213-223. [PMID: 27590715 DOI: 10.1016/j.meegid.2016.08.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/12/2016] [Accepted: 08/29/2016] [Indexed: 01/09/2023]
Abstract
There is no attempt to evaluate evolutionary rates, timescales and diversities of viruses collected from mixedly infected hosts in nature. Plants of the genus Narcissus are a monocotyledon and are susceptible to several viruses. In this study, narcissus plants (Narcissus tazetta var. chinensis) showing mosaic or striping leaves were collected in Japan, and these were investigated for potyvirus infections using potyvirus-specific primers. Individual narcissus plants were found frequently to be mixedly infected with different potyviruses, different isolates and quasispecies of same virus. The viruses were potyviruses and a macluravirus in the family Potyviridae, namely Narcissus late season yellows virus (NLSYV), Narcissus yellow stripe virus (NYSV), Narcissus degeneration virus (NDV), Cyrtanthus elatus virus A (CyEVA) and Narcissus latent virus (NLV). Genetic diversities of coat protein coding region of different virus species were different; NYSV and CyEVA were most diverse whereas NDV was least. Evolutionary rates of all five narcissus viruses were 1.33-7.15×10-3nt/site/year and were similar. The most recent common ancestors (TMRCAs) varied between virus species; NYSV and CyEVA were the oldest whereas NDV was the youngest. Thus, the oldness of TMRCAs of the viruses correlated well with the greatness of nucleotide diversities.
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Affiliation(s)
- Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan; The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan.
| | - Rei Nomiyama
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Shinichiro Mitoma
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Yuki Honda
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan
| | - Ryosuke Yasaka
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan; The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kenta Tomimura
- Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO (National Agriculture and Food Research Organization), 485-6 Okitsu Nakacho, Shimizu, Shizuoka 424-0292, Japan
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Migration of plant viruses: Time correlations with the agriculture history and human immigration. Uirusu 2015; 65:229-238. [PMID: 27760921 DOI: 10.2222/jsv.65.229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this review, I made the phylodynamic comparisons of three plant viruses, Turnip mosaic virus (TuMV), Cauliflower mosaic virus (CaMV) and Cucumber mosaic virus (CMV), using the genomic sequences of a large numbers of isolates collected worldwide. We analyzed these genomic nucleotide sequences, in combination with published sequences, to estimate the timescale and rate of evolution of the individual genes of TuMV, CaMV and CMV. The main hosts of the viruses are Brassicaceae crops. We also compared these estimates from complete sequences with those from which non-synonymous and invariate codons had been removed. Our analyses provided a preliminary definition of the present geographical structure of three plant virus populations in the world, and showed that the time of migration of three plant viruses correlate well with agriculture history and human immigration.
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