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Abe J, Wang Y, Yamada T, Sato M, Ono T, Atsumi G, Abe J, Hajimorad MR, Nakahara KS. Recessive Resistance Governed by a Major Quantitative Trait Locus Restricts Clover Yellow Vein Virus in Mechanically but Not Graft-Inoculated Cultivated Soybeans. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1026-1037. [PMID: 30830836 DOI: 10.1094/mpmi-12-18-0331-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Clover yellow vein virus (ClYVV) infects and causes disease in legume plants. However, here, we found that ClYVV isolate No. 30 (ClYVV-No.30) inefficiently multiplied or spread via cell-to-cell movement in mechanically inoculated leaves of a dozen soybean (Glycine max) cultivars and resulted in failure to spread systemically. Soybean plants also had a similar resistance phenotype against additional ClYVV isolates. In contrast, all but one of 24 tested accessions of wild soybeans (G. soja) were susceptible to ClYVV-No.30. Graft inoculation of cultivated soybean TK780 with ClYVV-No.30-infected wild soybean B01167 scion resulted in systemic infection of the cultivated soybean rootstock. This suggests that, upon mechanical inoculation, the cultivated soybean inhibits ClYVV-No.30, at infection steps prior to the systemic spread of the virus, via vascular systems. Systemic infection of all F1 plants from crossing between TK780 and B01167 and of 68 of 76 F2 plants with ClYVV-No.30 indicated recessive inheritance of the resistance. Further genetic analysis using 64 recombinant inbred lines between TK780 and B01167 detected one major quantitative trait locus, designated d-cv, for the resistance that was positioned in the linkage group D1b (chromosome 2). The mapped region on soybean genome suggests that d-cv is not an allele of the known resistance genes against soybean mosaic virus.
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Affiliation(s)
- Junya Abe
- 1Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yongzhi Wang
- 2Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, U.S.A
- 3Jilin Academy of Agricultural Sciences, 1363 Caiyu Street, Changchun 130033, Jilin, China
| | - Tetsuya Yamada
- 1Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Masako Sato
- 1Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Takuya Ono
- 1Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Go Atsumi
- 4National Institute of Advanced Industrial Science and Technology, Sapporo, Hokkaido, Japan
| | - Jun Abe
- 1Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - M R Hajimorad
- 2Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, U.S.A
| | - Kenji S Nakahara
- 1Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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Mao Y, Sun X, Shen J, Gao F, Qiu G, Wang T, Nie X, Zhang W, Gao Y, Bai Y. Molecular Evolutionary Analysis of Potato Virus Y Infecting Potato Based on the VPg Gene. Front Microbiol 2019; 10:1708. [PMID: 31402905 PMCID: PMC6676787 DOI: 10.3389/fmicb.2019.01708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/10/2019] [Indexed: 11/21/2022] Open
Abstract
Potato virus Y (PVY) is an important plant pathogen infecting solanaceous crops, causing significant losses to global potato and tobacco production. Some aspects of the plant pathology and molecular biology of PVY have been studied intensively, but the evolutionary dynamics of this virus are poorly understood. Here, we performed a comprehensive set of rigorous evolutionary analyses using 177 nucleotide sequences of the viral genome linked protein (VPg) gene, which interacts with the plant eukaryotic translation initiation factor 4E (eIF4E). Our Bayesian analysis reveals that the VPg gene of PVY has been evolving at a rate of 5.60 × 10–4 subs/site/year (95% credibility interval 3.35 × 10–4–8.17 × 10–4), which is equivalent to those of other plant-infecting RNA viruses. We identified different evolutionary constraints on the two clades of PVY, clade N and clade O, whose diverge time were estimated at the year 1861 CE (95% credibility interval 1750–1948 CE). We also found that genetic variations were correlated with geographic regions, suggesting that the evolution of this pathogen is strongly affected by geographical associated factors. Taken together, the results of our study have potential implications for the control strategies of PVY.
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Affiliation(s)
- Yanzhi Mao
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xuhong Sun
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jianguo Shen
- Inspection and Quarantine Technology Center, Fujian Exit-Entry, Inspection and Quarantine Bureau, Fuzhou, China
| | - Fangluan Gao
- Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guangwei Qiu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Teng Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xianzhou Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Wei Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yanling Gao
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yanju Bai
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
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Fuentes S, Jones RAC, Matsuoka H, Ohshima K, Kreuze J, Gibbs AJ. Potato virus Y; the Andean connection. Virus Evol 2019; 5:vez037. [PMID: 31559020 PMCID: PMC6755682 DOI: 10.1093/ve/vez037] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Potato virus Y (PVY) causes disease in potatoes and other solanaceous crops. The appearance of its necrogenic strains in the 1980s made it the most economically important virus of potatoes. We report the isolation and genomic sequences of 32 Peruvian isolates of PVY which, together with 428 published PVY genomic sequences, gave an alignment of 460 sequences. Of these 190 (41%) were non-recombinant, and 162 of these provided a dated phylogeny, that corresponds well with the likely history of PVY, and show that PVY originated in South America which is where potatoes were first domesticated. The most basal divergences of the PVY population produced the N and C: O phylogroups; the origin of the N phylogroup is clearly Andean, but that of the O and C phylogroups is unknown, although they may have been first to establish in European crops. The current PVY population originated around 156 CE. PVY was probably first taken from South America to Europe in the 16th century in tubers. Most of the present PVY diversity emerged in the second half of the 19th century, after the Phytophthora infestans epidemics of the mid-19th century destroyed the European crop and stimulated potato breeding. Imported breeding lines were shared, and there was no quarantine. The early O population was joined later by N phylogroup isolates and their recombinants generated the R1 and R2 populations of damaging necrogenic strains. Our dating study has confirmed that human activity has dominated the phylodynamics of PVY for the last two millennia.
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Affiliation(s)
- Segundo Fuentes
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Roger A C Jones
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA
| | - Hiroki Matsuoka
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, Australia
| | - Kazusato Ohshima
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, Australia
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Adrian J Gibbs
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, Japan
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Fribourg CE, Gibbs AJ, Adams IP, Boonham N, Jones RAC. Biological and Molecular Properties of Wild potato mosaic virus Isolates from Pepino ( Solanum muricatum). PLANT DISEASE 2019; 103:1746-1756. [PMID: 31082318 DOI: 10.1094/pdis-12-18-2164-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In 1976, a virus with flexuous, filamentous virions typical of the family Potyviridae was isolated from symptomatic pepino (Solanum muricatum) plants growing in two valleys in Peru's coastal desert region. In 2014, a virus with similar-shaped virions was isolated from asymptomatic fruits obtained from pepino plants growing in six coastal valleys and a valley in Peru's Andean highlands. Both were identified subsequently as Wild potato mosaic virus (WPMV) by serology or high-throughput sequencing (HTS). The symptoms caused by two old and seven new isolates from pepino were examined in indicator plants. Infected solanaceous hosts varied considerably in their sensitivities to infection and individual isolates varied greatly in virulence. All seven new isolates caused quick death of infected Nicotiana benthamiana plants and more than half of them killed infected plants of Physalis floridana and S. chancayense. These three species were the most sensitive to infection. The most virulent isolate was found to be BA because it killed five of eight solanaceous host species whereas CA was the least severe because it only killed N. benthamiana. Using HTS, complete genomic sequences of six isolates were obtained, with one isolate (FE) showing evidence of recombination. The distances between individual WPMV isolates in phylogenetic trees and the geographical distances between their collection sites were found to be unrelated. The individual WPMV isolates displayed nucleotide sequence identities of 80.9-99.8%, whereas the most closely related virus, Potato virus V (PVV), was around 75% identical to WPMV. WPMV, PVV, and Peru tomato virus formed clusters of similar phylogenetic diversity, and were found to be distinct but related viruses within the overall Potato virus Y lineage. WPMV infection seems widespread and of likely economic significance to pepino producers in Peru's coastal valleys. Because it constitutes the fifth virus found infecting pepino and this crop is entirely vegetatively propagated, development of healthy pepino stock programs is advocated.
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Affiliation(s)
- Cesar E Fribourg
- 1 Departamento de Fitopatologia, Universidad Nacional Agraria, La Molina, Lima, Peru
| | - Adrian J Gibbs
- 2 Emeritus Faculty, Australian National University, Canberra, ACT, Australia
| | | | - Neil Boonham
- 4 Institute for Agrifood Research Innovations, Newcastle University, Newcastle upon Tyne, U.K
| | - Roger A C Jones
- 5 Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA, Australia, and Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, Australia
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Hamid A, Zhai Y, Ramesh SV, Pappu HR. Complete genome characterization and population dynamics of potato virus Y-NTN strain from India. Virusdisease 2019; 30:252-260. [PMID: 31179364 DOI: 10.1007/s13337-019-00526-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/18/2019] [Indexed: 11/28/2022] Open
Abstract
Potato virus Y (PVY) is a major threat to potato cultivation worldwide. PVY exists as biologically and genetically distinct strains and causes varying degrees of pathogenicity and a wide range of symptoms in potato. Knowledge of the nature of PVY strains is essential for breeding PVY resistant cultivars that are durable against a wide range of strains. We report the complete genome of a PVY potato isolate (JK12) characterised from the potato production areas of Jammu and Kashmir, India. Nucleotide sequence comparisons and phylogenetic analysis with known PVY strains revealed that the isolate belongs to the NTN strain of PVY. At the whole genome sequence level, the JK12 isolate shared the highest identity (99.42%) with PVY-NTN strains reported from Germany, followed by those from United Kingdom (99.34%) and Japan (99.33%). Recombination detection analysis identified two recombination break points and JK12 appeared to have originated from a recombination event between a PVY-N strain from Belgium as a major parent and a PVY-O strain from China as the minor parent. Our results suggest possible mutation and recombination could be the basis for the evolution and the subsequent establishment of NTN in this region. Furthermore, a global evolutionary lineage analysis of all the known PVY strains showed relatively low nucleotide diversity among the PVY-NTN strains. Neutrality tests showed that all the genotypes of PVY are undergoing purifying selection suggesting population expansion of PVY. This is the first report of complete genomic characterization of an NTN strain of PVY isolated from commercial potato fields in India. The implications of the emergence of this strain in the Indian context are discussed.
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Affiliation(s)
- Aflaq Hamid
- 1Department of Plant Pathology, Washington State University, Pullman, WA USA.,2Department of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K India
| | - Ying Zhai
- 1Department of Plant Pathology, Washington State University, Pullman, WA USA
| | - S V Ramesh
- 3ICAR-Central Plantation Crops Research Institute, Kasaragod, Kasaragod, Kerala India
| | - Hanu R Pappu
- 1Department of Plant Pathology, Washington State University, Pullman, WA USA
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Maina S, Barbetti MJ, Edwards OR, Minemba D, Areke MW, Jones RAC. Zucchini yellow mosaic virus Genomic Sequences from Papua New Guinea: Lack of Genetic Connectivity with Northern Australian or East Timorese Genomes, and New Recombination Findings. PLANT DISEASE 2019; 103:1326-1336. [PMID: 30995424 DOI: 10.1094/pdis-09-18-1666-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) isolates were obtained in Papua New Guinea (PNG) from cucumber (Cucumis sativus) or pumpkin (Cucurbita spp.) plants showing mosaic symptoms growing at Kongop in the Mount Hagen District, Western Highlands Province, or Zage in the Goroka District, Eastern Highlands Province. The samples were blotted onto FTA cards, which were sent to Australia, where they were subjected to high-throughput sequencing. When the coding regions of the nine new ZYMV genomic sequences found were compared with those of 64 other ZYMV sequences from elsewhere, they grouped together, forming new minor phylogroup VII within ZYMV's major phylogroup A. Genetic connectivity was lacking between ZYMV genomic sequences from PNG and its neighboring countries, Australia and East Timor; the closest match between a PNG and any other genomic sequence was a 92.8% nucleotide identity with a sequence in major phylogroup A's minor phylogroup VI from Japan. When the RDP5.2 recombination analysis program was used to compare 66 ZYMV sequences, evidence was obtained of 30 firm recombination events involving 41 sequences, and all isolates from PNG were recombinants. There were 21 sequences without recombination events in major phylogroup A, whereas there were only 4 such sequences within major phylogroup B. ZYMV's P1, Cl, N1a-Pro, P3, CP, and NIb regions contained the highest evidence of recombination breakpoints. Following removal of recombinant sequences, seven minor phylogroups were absent (I, III, IV, V, VI, VII, and VIII), leaving only minor phylogroups II and IX. By contrast, when a phylogenetic tree was constructed using recombinant sequences with their recombinationally derived tracts removed before analysis, five previous minor phylogroups remained unchanged within major phylogroup A (II, III, IV, V, and VII) while four formed two new merged phylogroups (I/VI and VIII/IX). Absence of genetic connectivity between PNG, Australian, and East Timorese ZYMV sequences, and the 92.8% nucleotide identity between a PNG sequence and the closest sequence from elsewhere, suggest that a single introduction may have occurred followed by subsequent evolution to adapt to the PNG environment. The need for enhanced biosecurity measures to protect against potentially damaging virus movements crossing the seas separating neighboring countries in this region of the world is discussed.
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Affiliation(s)
- Solomon Maina
- 1 School of Agriculture and Environment, Faculty of Science, and
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
| | - Martin J Barbetti
- 1 School of Agriculture and Environment, Faculty of Science, and
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
| | - Owain R Edwards
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- 4 Commonwealth Scientific and Industrial Research Organisation Land and Water, Floreat Park, WA 6014, Australia
| | - David Minemba
- 1 School of Agriculture and Environment, Faculty of Science, and
- 5 The National Agricultural Research Institute, PO Box 4415, Lae, Morobe Province, Papua New Guinea
| | - Michael W Areke
- 6 National Agriculture Quarantine and Inspection Authority, PO Box 741, Port Moresby, National Capital District, Papua New Guinea; and
| | - Roger A C Jones
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, Australian Capital Territory, Australia
- 7 Department of Primary Industries and Regional Development, South Perth, WA, Australia
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Temporal analysis and adaptive evolution of the global population of potato virus M. INFECTION GENETICS AND EVOLUTION 2019; 73:167-174. [PMID: 31054922 DOI: 10.1016/j.meegid.2019.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/24/2022]
Abstract
Potato virus M (PVM), which is a member of the genus Carlavirus in the family Betaflexviridae, causes critical economic losses of nightshade crops. PVM is transmitted by aphids in a non-persistent manner, by sap inoculation and also transmitted in tubers. Previously, several reports described the genetic structure of PVM. However, the evolutionary rate, timescale, spread and adaptation evolution of the virus have not been examined. In this study, we investigated the phylodynamics of PVM using 145 nucleotide sequences of the coat protein gene and 117 sequences of the cysteine-rich nucleic acid-binding protein (NABP) gene, which were sampled between 1985 and 2013. We found that at least three lineages with isolates that were defined geographically but not by the original host were clustered. The evolutionary rate of the NABP (1.06 × 10-2) was faster than that of the CP (4.12 × 10-3). The time to the most recent common ancestors (TMRCAs) is similar between CP (CIs 31-110) and NABP (CIs 28-33) genes. Based on CP and NABP genes, PVM migrated from China to Canada, Iran, India and European countries, and it circulated within China. Our study is the first attempt to evaluate the evolutionary rates, timescales and migration dynamics of PVM.
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58
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Eş I, Gavahian M, Marti-Quijal FJ, Lorenzo JM, Mousavi Khaneghah A, Tsatsanis C, Kampranis SC, Barba FJ. The application of the CRISPR-Cas9 genome editing machinery in food and agricultural science: Current status, future perspectives, and associated challenges. Biotechnol Adv 2019; 37:410-421. [DOI: 10.1016/j.biotechadv.2019.02.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/19/2019] [Accepted: 02/13/2019] [Indexed: 12/26/2022]
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Maina S, Barbetti MJ, Edwards OR, Minemba D, Areke MW, Jones RAC. Genetic Connectivity Between Papaya Ringspot Virus Genomes from Papua New Guinea and Northern Australia, and New Recombination Insights. PLANT DISEASE 2019; 103:737-747. [PMID: 30856073 DOI: 10.1094/pdis-07-18-1136-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isolates of papaya ringspot virus (PRSV) were obtained from plants of pumpkin (Cucurbita spp.) or cucumber (Cucumis sativus) showing mosaic symptoms growing at Zage in Goroka District in the Eastern Highland Province of Papua New Guinea (PNG) or Bagl in the Mount Hagen District, Western Highlands Province. The samples were sent to Australia on FTA cards where they were subjected to High Throughput Sequencing (HTS). When the coding regions of the six new PRSV genomic sequences obtained via HTS were compared with those of 54 other complete PRSV sequences from other parts of the world, all six grouped together with the 12 northern Australian sequences within major phylogroup B minor phylogroup I, the Australian sequences coming from three widely dispersed locations spanning the north of the continent. Notably, none of the PNG isolates grouped with genomic sequences from the nearby country of East Timor in phylogroup A. The closest genetic match between Australian and PNG sequences was a nucleotide (nt) sequence identity of 96.9%, whereas between PNG and East Timorese isolates it was only 83.1%. These phylogenetic and nt identity findings demonstrate genetic connectivity between PRSV populations from PNG and Australia. Recombination analysis of the 60 PRSV sequences available revealed evidence of 26 recombination events within 18 isolates, only four of which were within major phylogroup B and none of which were from PNG or Australia. Within the recombinant genomes, the P1, Cl, NIa-Pro, NIb, 6K2, and 5'UTR regions contained the highest numbers of recombination breakpoints. After removal of nonrecombinant sequences, four minor phylogroups were lost (IV, VII, VIII, XV), only one of which was in phylogroup B. When genome regions from which recombinationally derived tracts of sequence were removed from recombinants prior to alignment with nonrecombinant genomes, seven previous minor phylogroups within major phylogroup A, and two within major phylogroup B, merged either partially or entirely forming four merged minor phylogroups. The genetic connectivity between PNG and northern Australian isolates and absence of detectable recombination within either group suggests that PRSV isolates from East Timor, rather than PNG, might pose a biosecurity threat to northern Australian agriculture should they prove more virulent than those already present.
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Affiliation(s)
- Solomon Maina
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
| | - Martin J Barbetti
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
| | - Owain R Edwards
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
- 4 CSIRO Land and Water, Floreat Park, WA6014, Australia
| | - David Minemba
- 1 School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 5 The National Agriculture Research Institute, P.O. Box 4415, Lae, Morobe Province, Papua New Guinea
| | - Michael W Areke
- 6 National Agriculture Quarantine and Inspection Authority, P.O. Box 741, Port Moresby, National Capital District, Papua New Guinea; and
| | - Roger A C Jones
- 2 UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley, WA, Australia
- 3 Cooperative Research Centre for Plant Biosecurity, Canberra, ACT, Australia
- 7 Department of Primary Industries and Rural Development Food Western Australia, South Perth, WA, Australia
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Pepper veinal mottle virus in Japan is closely related to isolates from other Asian countries, but more distantly to most of those from Africa. Virus Genes 2019; 55:347-355. [PMID: 30895438 DOI: 10.1007/s11262-019-01656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/11/2019] [Indexed: 10/27/2022]
Abstract
Pepper veinal mottle virus (PVMV) is known to infect chilli pepper and belongs to the Chilli veinal mottle virus phylogroup of potyviruses. PVMV has recently appeared in Japan. In this study, we report six complete genomic sequences of PVMV isolates from chilli pepper (i.e. Capsicum annuum) in Okinawa Islands in Japan, and we determined the evolutionary relationships between Japanese isolates and the isolates reported earlier from African and Asian countries. Complete genomic sequences of the six Japanese PVMV isolates were 9760 nucleotides in length, excluding the nucleotide primer sequences used for amplifying 5' end of the genomes. The major findings of this study are as follows: (1) all the Japanese isolates of PVMV have similar biological and molecular characteristics, indicating the presence of only one population in Japan; (2) there are at least three major phylogenetic groups of PVMV worldwide; (3) PVMV probably originated in East Africa; and (4) all the Asian isolates are closely related to the Ghanaian isolate.
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Nigam D, LaTourrette K, Souza PFN, Garcia-Ruiz H. Genome-Wide Variation in Potyviruses. FRONTIERS IN PLANT SCIENCE 2019; 10:1439. [PMID: 31798606 PMCID: PMC6863122 DOI: 10.3389/fpls.2019.01439] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/16/2019] [Indexed: 05/07/2023]
Abstract
Potyviruses (family Potyviridae, genus Potyvirus) are the result of an initial radiation event that occurred 6,600 years ago. The genus currently consists of 167 species that infect monocots or dicots, including domesticated and wild plants. Potyviruses are transmitted in a non-persistent way by more than 200 species of aphids. As indicated by their wide host range, worldwide distribution, and diversity of their vectors, potyviruses have an outstanding capacity to adapt to new hosts and environments. However, factors that confer adaptability are poorly understood. Viral RNA-dependent RNA polymerases introduce nucleotide substitutions that generate genetic diversity. We hypothesized that selection imposed by hosts and vectors creates a footprint in areas of the genome involved in host adaptation. Here, we profiled genomic and polyprotein variation in all species in the genus Potyvirus. Results showed that the potyviral genome is under strong negative selection. Accordingly, the genome and polyprotein sequence are remarkably stable. However, nucleotide and amino acid substitutions across the potyviral genome are not randomly distributed and are not determined by codon usage. Instead, substitutions preferentially accumulate in hypervariable areas at homologous locations across potyviruses. At a frequency that is higher than that of the rest of the genome, hypervariable areas accumulate non-synonymous nucleotide substitutions and sites under positive selection. Our results show, for the first time, that there is correlation between host range and the frequency of sites under positive selection. Hypervariable areas map to the N terminal part of protein P1, N and C terminal parts of helper component proteinase (HC-Pro), the C terminal part of protein P3, VPg, the C terminal part of NIb (RNA-dependent RNA polymerase), and the N terminal part of the coat protein (CP). Additionally, a hypervariable area at the NIb-CP junction showed that there is variability in the sequence of the NIa protease cleavage sites. Structural alignment showed that the hypervariable area in the CP maps to the N terminal flexible loop and includes the motif required for aphid transmission. Collectively, results described here show that potyviruses contain fixed hypervariable areas in key parts of the genome which provide mutational robustness and are potentially involved in host adaptation.
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62
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Aman R, Mahas A, Butt H, Aljedaani F, Mahfouz M. Engineering RNA Virus Interference via the CRISPR/Cas13 Machinery in Arabidopsis. Viruses 2018; 10:E732. [PMID: 30572690 PMCID: PMC6315463 DOI: 10.3390/v10120732] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 12/09/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are key immune mechanisms helping prokaryotic species fend off RNA and DNA viruses. CRISPR/Cas9 has broad applications in basic research and biotechnology and has been widely used across eukaryotic species for genome engineering and functional analysis of genes. The recently developed CRISPR/Cas13 systems target RNA rather than DNA and thus offer new potential for transcriptome engineering and combatting RNA viruses. Here, we used CRISPR/LshCas13a to stably engineer Arabidopsis thaliana for interference against the RNA genome of Turnip mosaic virus (TuMV). Our data demonstrate that CRISPR RNAs (crRNAs) guiding Cas13a to the sequences encoding helper component proteinase silencing suppressor (HC-Pro) or GFP target 2 (GFP-T2) provide better interference compared to crRNAs targeting other regions of the TuMV RNA genome. This work demonstrates the exciting potential of CRISPR/Cas13 to be used as an antiviral strategy to obstruct RNA viruses, and encourages the search for more robust and effective Cas13 variants or CRISPR systems that can target RNA.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Fatimah Aljedaani
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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Bhushan K. CRISPR/Cas13a targeting of RNA virus in plants. PLANT CELL REPORTS 2018; 37:1707-1712. [PMID: 29779095 DOI: 10.1007/s00299-018-2297-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 05/11/2018] [Indexed: 06/08/2023]
Abstract
KEY MESSAGE This approach is quite promising to control plant viral diseases and create synthetic networks to better understand the structure/function relationship in RNA and proteins. Plant viruses are obligate intracellular parasites which causes enormous losses in crop yield worldwide. These viruses replicate into infected cells by highjacking host cellular machinery. Over the last two decades, diverse approaches such as conventional breeding, transgenic approach and gene silencing strategies have been used to control RNA viruses, but escaped due to high rate of mutation. Recently, a novel CRISPR enzyme, called Cas13a, has been used engineered to confer RNA viruses resistance in plants. Here, we summarize the recent breakthrough of CRISPR/Cas13a and its applications in RNA biology.
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Affiliation(s)
- Kul Bhushan
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Xu T, Lei L, Shi J, Wang X, Chen J, Xue M, Sun S, Zhan B, Xia Z, Jiang N, Zhou T, Lai J, Fan Z. Characterization of maize translational responses to sugarcane mosaic virus infection. Virus Res 2018; 259:97-107. [PMID: 30355529 DOI: 10.1016/j.virusres.2018.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/14/2018] [Accepted: 10/18/2018] [Indexed: 10/28/2022]
Abstract
Sugarcane mosaic virus (SCMV) frequently causes dramatic losses in maize production as the main pathogen of maize dwarf mosaic disease. It is important to understand the translational responses in maize to SCMV infection since viruses have to recruit host translation apparatus to express their proteins. However, due to technical limitations, research on virus translation lags far behind that on transcription. Here, we studied the relationship between systemic symptom expression and virus accumulation and found that both SCMV RNA and proteins accumulated rapidly during the systemic infection process in which varying degrees of chlorosis to mosaic symptoms developed on non-inoculated leaves. In addition, we applied ribosome profiling, which couples polysomal mRNA isolation with high-throughput sequencing, on the symptomatic leaves infected with SCMV to unravel the translational responses of maize to viral infection on a genome-wide scale. The results showed that only the genomic positive-stranded RNA of SCMV was involved in translation, and SCMV only occupied a small amount of translational resources of host plant at the early stage of infection. Further analyses on a global gene expression and gene ontology (GO) enrichment revealed that photosynthesis and metabolism were dramatically repressed at both transcriptional and translational levels. Altogether, our results laid a foundation for dissecting the molecular mechanism of plant translational responses to viral infection.
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Affiliation(s)
- Tengzhi Xu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Lei Lei
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China; Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Junpeng Shi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Xin Wang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Mingshuo Xue
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Silong Sun
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Binhui Zhan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Zihao Xia
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Na Jiang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Tao Zhou
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Zaifeng Fan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China.
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Cordero T, Rosado A, Majer E, Jaramillo A, Rodrigo G, Daròs JA. Boolean Computation in Plants Using Post-translational Genetic Control and a Visual Output Signal. ACS Synth Biol 2018; 7:2322-2330. [PMID: 30212620 DOI: 10.1021/acssynbio.8b00214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Due to autotrophic growing capacity and extremely rich secondary metabolism, plants should be preferred targets of synthetic biology. However, developments in plants usually run below those in other taxonomic groups. In this work we engineered genetic circuits capable of logic YES, OR and AND Boolean computation in plant tissues with a visual output signal. The circuits, which are deployed by means of Agrobacterium tumefaciens, perform with the conditional activity of the MYB transcription factor Rosea1 from Antirrhinum majus inducing the accumulation of anthocyanins, plant endogenous pigments that are directly visible to the naked eye or accurately quantifiable by spectrophotometric analysis. The translational fusion of Rosea1 to several viral proteins, such as potyvirus NIb or fragments thereof, rendered the transcription factor inactive. However, anthocyanin accumulation could be restored by inserting protease cleavage sites between both moieties of the fusion and by coexpressing specific proteases, such as potyvirus nuclear inclusion a protease.
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Affiliation(s)
- Teresa Cordero
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022 Valencia, Spain
| | - Arantxa Rosado
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022 Valencia, Spain
- Institute for Integrative Systems Biology, Universitat de València-CSIC, 46980 Paterna, Spain
| | - Eszter Majer
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022 Valencia, Spain
| | - Alfonso Jaramillo
- Institute for Integrative Systems Biology, Universitat de València-CSIC, 46980 Paterna, Spain
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K
- Institute of Systems and Synthetic Biology, Université d’Évry Val d’Essonne-CNRS, F-91000 Évry, France
| | - Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022 Valencia, Spain
- Institute for Integrative Systems Biology, Universitat de València-CSIC, 46980 Paterna, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, 46022 Valencia, Spain
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Maina S, Barbetti MJ, Martin DP, Edwards OR, Jones RAC. New Isolates of Sweet potato feathery mottle virus and Sweet potato virus C: Biological and Molecular Properties, and Recombination Analysis Based on Complete Genomes. PLANT DISEASE 2018; 102:1899-1914. [PMID: 30136885 DOI: 10.1094/pdis-12-17-1972-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sweet potato feathery mottle virus (SPFMV) and Sweet potato virus C (SPVC) isolates were obtained from sweetpotato shoot or tuberous root samples from three widely separated locations in Australia's tropical north (Cairns, Darwin, and Kununurra). The samples were planted in the glasshouse and scions obtained from the plants were graft inoculated to Ipomoea setosa plants. Virus symptoms were recorded in the field in Kununurra and in glasshouse-grown sweetpotato and I. setosa plants. RNA extracts from I. setosa leaf samples were subjected to high-throughput sequencing. New complete SPFMV (n = 17) and SPVC (n = 6) genomic sequences were obtained and compared with 47 sequences from GenBank. Phylogenetic analysis revealed that the 17 new SPFMV genomes all fitted within either major phylogroup A, minor phylogroup II, formerly O; or major phylogroup B, formerly RC. Major phylogroup A's minor phylogroup I, formerly EA, only appeared when recombinants were included. Numbers of SPVC genomes were insufficient to subdivide it into phylogroups. Within phylogroup A's minor phylogroup II, the closest genetic match between an Australian and a Southeast Asian SPFMV sequence was the 97.4% nucleotide identity with an East Timorese sequence. Recombination analysis of the 43 SPFMV and 27 SPVC sequences revealed evidence of 44 recombination events, 16 of which involved interspecies sequence transfers between SPFMV and SPVC and 28 intraspecies transfers, 17 in SPFMV and 11 in SPVC. Within SPFMV, 11 intraspecies recombination events were between different major phylogroups and 6 were between members of the same major phylogroup. Phylogenetic analysis accounting for the detected recombination events within SPFMV sequences yielded evidence of minor phylogroup II and phylogroup B but the five sequences from minor phylogroup I were distributed in two separate groups among the sequences of minor phylogroup II. For the SPVC sequences, phylogenetic analysis accounting for the detected recombination events revealed three major phylogroups (A, B, and C), with major phylogroup A being further subdivided into two minor phylogroups. Within the recombinant genomes of both viruses, their PI, NIa-Pro, NIb, and CP genes contained the highest numbers of recombination breakpoints. The high frequency of interspecies and interphylogroup recombination events reflects the widespread occurrence of mixed SPVC and SPFMV infections within sweetpotato plants. The prevalence of infection in northern Australian sweetpotato samples reinforces the need for improved virus testing in healthy sweetpotato stock programs. Furthermore, evidence of genetic connectivity between Australian and East Timorese SPFMV genomes emphasizes the need for improved biosecurity measures to protect against potentially damaging international virus movements.
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Affiliation(s)
- Solomon Maina
- School of Agriculture and Environment and the University of Western Australia (UWA) Institute of Agriculture, Faculty of Science, UWA, Crawley, WA 6009, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617, Australia
| | - Martin J Barbetti
- School of Agriculture and Environment and UWA Institute of Agriculture, Faculty of Science, UWA
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, Cape Town 7549, South Africa
| | - Owain R Edwards
- CSIRO Land and Water, Floreat Park, WA 6014, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617, Australia
| | - Roger A C Jones
- Department of Primary Industries and Rural Development, South Perth, WA 6151, Australia; UWA Institute of Agriculture, Faculty of Science, UWA
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Hubei poty-like virus 1 is likely an interspecies recombinant of sugarcane mosaic virus and putative bean yellow mosaic virus. Arch Virol 2018; 164:261-265. [DOI: 10.1007/s00705-018-4047-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/16/2018] [Indexed: 10/28/2022]
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68
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Wu M, Wu WP, Liu CC, Liu YN, Wu XY, Ma FF, Zhu AQ, Yang JY, Wang B, Chen JQ. A bean common mosaic virus (BCMV)-resistance gene is fine-mapped to the same region as Rsv1-h in the soybean cultivar Suweon 97. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1851-1860. [PMID: 29909526 DOI: 10.1007/s00122-018-3117-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 05/14/2018] [Indexed: 05/11/2023]
Abstract
KEY MESSAGE In the soybean cultivar Suweon 97, BCMV-resistance gene was fine-mapped to a 58.1-kb region co-localizing with the Soybean mosaic virus (SMV)-resistance gene, Rsv1-h raising a possibility that the same gene is utilized against both viral pathogens. Certain soybean cultivars exhibit resistance against soybean mosaic virus (SMV) or bean common mosaic virus (BCMV). Although several SMV-resistance loci have been reported, the understanding of the mechanism underlying BCMV resistance in soybean is limited. Here, by crossing a resistant cultivar Suweon 97 with a susceptible cultivar Williams 82 and inoculating 220 F2 individuals with a BCMV strain (HZZB011), we observed a 3:1 (resistant/susceptible) segregation ratio, suggesting that Suweon 97 possesses a single dominant resistance gene against BCMV. By performing bulked segregant analysis with 186 polymorphic simple sequence repeat (SSR) markers across the genome, the resistance gene was determined to be linked with marker BARSOYSSR_13_1109. Examining the genotypes of nearby SSR markers on all 220 F2 individuals then narrowed down the gene between markers BARSOYSSR_13_1109 and BARSOYSSR_13_1122. Furthermore, 14 previously established F2:3 lines showing crossovers between the two markers were assayed for their phenotypes upon BCMV inoculation. By developing six more SNP (single nucleotide polymorphism) markers, the resistance gene was finally delimited to a 58.1-kb interval flanked by BARSOYSSR_13_1114 and SNP-49. Five genes were annotated in this interval of the Williams 82 genome, including a characteristic coiled-coil nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR, CNL)-type of resistance gene, Glyma13g184800. Coincidentally, the SMV-resistance allele Rsv1-h was previously mapped to almost the same region, thereby suggesting that soybean Suweon 97 likely relies on the same CNL-type R gene to resist both viral pathogens.
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Affiliation(s)
- Mian Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Wen-Ping Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Cheng-Chen Liu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Ying-Na Liu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Xiao-Yi Wu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Fang-Fang Ma
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - An-Qi Zhu
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China
| | - Jia-Yin Yang
- Huaiyin Institute of Agricultural Sciences of Xuhuai Region in Jiangsu, Huai'an, 223001, Jiangsu Province, China.
| | - Bin Wang
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
| | - Jian-Qun Chen
- Laboratory of Plant Genetics and Molecular Evolution, School of Life Sciences, Nanjing University, 163 XianLin Avenue, Nanjing, 210023, China.
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69
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Wu Z, Mo C, Zhang S, Li H. Characterization of Papaya ringspot virus isolates infecting transgenic papaya 'Huanong No.1' in South China. Sci Rep 2018; 8:8206. [PMID: 29844514 PMCID: PMC5974079 DOI: 10.1038/s41598-018-26596-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/15/2018] [Indexed: 11/09/2022] Open
Abstract
In 2006, the release and cultivation of the genetically modified papaya cultivar 'Huanong No.1' successfully controlled the destructive papaya ringspot disease caused by Papaya ringspot virus (PRSV) in South China. However, some transgenic papaya plants from Guangdong and Hainan are found infected by PRSV. In this study, Field investigation was carried out and susceptible transgenic papaya samples were collected during 2012-2016. Twenty representative isolates were artificially inoculated into Cucurbita pepo and commercialised 'Huanong No.1' papaya, and results indicated that the plants showed obvious disease symptoms. Phylogenetic analysis of CP genes of 120 PRSV-infected isolates showed that PRSV can be divided into three groups. Isolates from Guangdong and Hainan belong to Group III, which is further divided into two subgroups. The isolates collected in this study have greatly diverged from the previously reported dominant strains Ys, Vb and Sm in South China, indicating that they belong to a new lineage. Further analysis showed a highly genetic differentiation between isolates, and 27.1% of the isolates were identified as recombinants on the basis of CP nucleotide sequences. These results indicate that the genetic variation of PRSV and the formation of the new virus lineage may explain the loss of transgenic papaya resistance in South China.
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Affiliation(s)
- Zilin Wu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Cuiping Mo
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Shuguang Zhang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Huaping Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
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70
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Arous S, Harmon CL, Capobianco HM, Polston JE. Comparison of genus-specific primers in RT-PCR for the broad-spectrum detection of viruses in the genus Potyvirus by plant diagnostic laboratories. J Virol Methods 2018; 258:29-34. [PMID: 29753708 DOI: 10.1016/j.jviromet.2018.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 03/14/2018] [Accepted: 05/06/2018] [Indexed: 11/28/2022]
Abstract
The Potyvirus genus is one of the largest genera of plant viruses and encompasses many economically important pathogens. While a number of degenerate primers for use in broad spectrum RT-PCR assays have been published, it is not clear which of these primers would be the most useful for use by plant diagnostic laboratories. Twelve sets of primers were tested for their ability to detect nine potyviruses in a two-step RT-PCR. Viruses were extracted from different host backgrounds and were selected to represent eight clades plus one species between clades (sensu Gibbs and Ohshima, 2010). Results of this study indicated that the primers CIFor/CIRev produced easily detectable amplicons from all nine potyviruses without non-specific amplification, false positives, or false negatives. CIFor/CIRev produced single amplicons from potyvirus-infected tissues which could be sequenced directly without gel purification to identify the virus to species.
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Affiliation(s)
- S Arous
- Dept. of Plant Pathology, University of Florida, Gainesville, FL, 32611, United States; Higher Institute of Biotechnology Sidi Thabet, University of Manouba, Biotechpole Sidi Thabet, 2020, Tunisia.
| | - C L Harmon
- Plant Diagnostic Center, Dept. of Plant Pathology, University of Florida, Gainesville, FL, 32611, United States.
| | - H M Capobianco
- Dept. of Plant Pathology, University of Florida, Gainesville, FL, 32611, United States.
| | - J E Polston
- Dept. of Plant Pathology, University of Florida, Gainesville, FL, 32611, United States.
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71
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Sardaru P, Sinausía L, López‐González S, Zindovic J, Sánchez F, Ponz F. The apparent non-host resistance of Ethiopian mustard to a radish-infecting strain of Turnip mosaic virus is largely determined by the C-terminal region of the P3 viral protein. MOLECULAR PLANT PATHOLOGY 2018; 19:1984-1994. [PMID: 29517848 PMCID: PMC6638043 DOI: 10.1111/mpp.12674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 05/22/2023]
Abstract
Two different isolates of Turnip mosaic virus (TuMV: UK 1 and JPN 1) belonging to different virus strains were tested on three different Brassica species, namely turnip (Brassica rapa L.), Indian mustard (Brassica juncea L.) and Ethiopian mustard (Brassica carinata A. Braun). Although all three hosts were readily infected by isolate UK 1, isolate JPN 1 was able to establish a visible systemic infection only in the first two. Ethiopian mustard plants showed no local or systemic symptoms, and no virus antigens could be detected by enzyme-linked immunosorbent assay (ELISA). Thus, this species looks like a non-host for JPN 1, an apparent situation of non-host resistance (NHR). Through an experimental approach involving chimeric viruses made by gene interchange between two infectious clones of both virus isolates, the genomic region encoding the C-terminal domain of viral protein P3 was found to bear the resistance determinant, excluding any involvement of the viral fusion proteins P3N-PIPO and P3N-ALT in the resistance. A further determinant refinement identified two adjacent positions (1099 and 1100 of the viral polyprotein) as the main determinants of resistance. Green fluorescent protein (GFP)-tagged viruses showed that the resistance of Ethiopian mustard to isolate JPN 1 is only apparent, as virus-induced fluorescence could be found in discrete areas of both inoculated and non-inoculated leaves. In comparison with other plant-virus combinations of extreme resistance, we propose that Ethiopian mustard shows an apparent NHR to TuMV JPN 1, but not complete immunity or extreme resistance.
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Affiliation(s)
- Papaiah Sardaru
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
- Present address:
Department of Virology, College of SciencesSri Venkateswara UniversityTirupati 517502India
| | - Laura Sinausía
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
- Present address:
Celgene Institute for Translational Research Europe, Parque Científico y Tecnológico Cartuja 93, Centro de Empresas Pabellón de Italia, C/. Isaac Newton, 441092 SevillaSpain
| | - Silvia López‐González
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
| | - Jelena Zindovic
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
- Present address:
On leave of absence from Biotechnical Faculty, University of Montenegro, Mihajla Lalica 181000 PodgoricaMontenegro
| | - Flora Sánchez
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
| | - Fernando Ponz
- Centro de Biotecnología y Genómica de Plantas (UPM‐INIA), Campus Montegancedo28223 MadridSpain
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72
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An Iranian genomic sequence of Beet mosaic virus provides insights into diversity and evolution of the world population. Virus Genes 2018; 54:272-279. [DOI: 10.1007/s11262-018-1533-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 01/03/2018] [Indexed: 11/26/2022]
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73
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Aman R, Ali Z, Butt H, Mahas A, Aljedaani F, Khan MZ, Ding S, Mahfouz M. RNA virus interference via CRISPR/Cas13a system in plants. Genome Biol 2018; 19:1. [PMID: 29301551 PMCID: PMC5755456 DOI: 10.1186/s13059-017-1381-1] [Citation(s) in RCA: 382] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/13/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND CRISPR/Cas systems confer immunity against invading nucleic acids and phages in bacteria and archaea. CRISPR/Cas13a (known previously as C2c2) is a class 2 type VI-A ribonuclease capable of targeting and cleaving single-stranded RNA (ssRNA) molecules of the phage genome. Here, we employ CRISPR/Cas13a to engineer interference with an RNA virus, Turnip Mosaic Virus (TuMV), in plants. RESULTS CRISPR/Cas13a produces interference against green fluorescent protein (GFP)-expressing TuMV in transient assays and stable overexpression lines of Nicotiana benthamiana. CRISPR RNA (crRNAs) targeting the HC-Pro and GFP sequences exhibit better interference than those targeting other regions such as coat protein (CP) sequence. Cas13a can also process pre-crRNAs into functional crRNAs. CONCLUSIONS Our data indicate that CRISPR/Cas13a can be used for engineering interference against RNA viruses, providing a potential novel mechanism for RNA-guided immunity against RNA viruses and for other RNA manipulations in plants.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Zahir Ali
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Fatimah Aljedaani
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Muhammad Zuhaib Khan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shouwei Ding
- Center for Plant Cell Biology, Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Magdy Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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74
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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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Perotto MC, Pozzi EA, Celli MG, Luciani CE, Mitidieri MS, Conci VC. Identification and characterization of a new potyvirus infecting cucurbits. Arch Virol 2017; 163:719-724. [PMID: 29196817 DOI: 10.1007/s00705-017-3660-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/20/2017] [Indexed: 11/25/2022]
Abstract
A new potyvirus, tentatively named cucurbit vein banding virus (CVBV), was identified in crops of cucurbits in San Pedro (Buenos Aires, Argentina). The complete genome sequences of two isolates of CVBV were obtained by next-generation sequencing (Illumina). The genomic RNA consisted of 9968 and 9813 nucleotides, respectively, and displayed typical potyvirus organization. The percentage identity for these two genome sequences, using BLASTn, was 77% to sweet potato virus c and 73% to tomato necrotic stunt virus. BLASTx analysis of the complete polyprotein showed that the most closely related virus is plum pox virus, with 48% amino acid sequence identity for both isolates. Sequence comparisons and phylogenetic analyses indicate that CVBV belongs to a previously undescribed species in genus Potyvirus.
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Affiliation(s)
- M C Perotto
- Instituto de Patología Vegetal (IPAVE-CIAP-INTA), Camino 60 cuadras km 5,5, Córdoba, X5020ICA, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Camino 60 cuadras km 5,5, Córdoba, X5020ICA, Argentina.
| | - E A Pozzi
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Camino 60 cuadras km 5,5, Córdoba, X5020ICA, Argentina
| | - M G Celli
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Camino 60 cuadras km 5,5, Córdoba, X5020ICA, Argentina
| | - C E Luciani
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Camino 60 cuadras km 5,5, Córdoba, X5020ICA, Argentina
| | - M S Mitidieri
- Estación Experimental Agropecuaria San Pedro (EEA San Pedro-INTA), Ruta 9, km 170, 2930, San Pedro, Buenos Aires, Argentina
| | - V C Conci
- Instituto de Patología Vegetal (IPAVE-CIAP-INTA), Camino 60 cuadras km 5,5, Córdoba, X5020ICA, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Camino 60 cuadras km 5,5, Córdoba, X5020ICA, Argentina
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Lan P, Zhao J, Zhou Y, Li Y, Shen D, Liao Q, Li R, Li F. Complete genome sequence of Paris mosaic necrosis virus, a distinct member of the genus Potyvirus. Arch Virol 2017; 163:787-790. [PMID: 29188364 DOI: 10.1007/s00705-017-3649-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 10/05/2017] [Indexed: 11/28/2022]
Abstract
The complete genomic sequence of a novel potyvirus was determined from Paris polyphylla var. yunnanensis. Its genomic RNA consists of 9,660 nucleotides (nt) excluding the 3'-terminal poly (A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a putative large polyprotein of 3030 amino acids. The virus shares 53.9-70.1% nt sequence identity and 43.9-73.2% amino acid sequence identity with other viruses classified within the genus Potyvirus. Proteolytic cleavage sites and conserved motifs of the potyviruses were identified in the polyprotein and within individual proteins. Phylogenetic analysis indicated that the virus is most closely related to members of the BCMV subgroup. The results suggest that the virus should be classified as a novel species within the genus Potyvirus, which we tentatively name "Paris mosaic necrosis virus".
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Affiliation(s)
- Pingxiu Lan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jurun Zhao
- Dendrobium Institute of Longling, Longling, 678300, Yunnan, China
| | - Yalin Zhou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Yueyue Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Dingcai Shen
- Dendrobium Institute of Longling, Longling, 678300, Yunnan, China
| | - Qinchan Liao
- Dendrobium Institute of Longling, Longling, 678300, Yunnan, China
| | - Ruhui Li
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA.
| | - Fan Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China.
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Kaur C, Raj R, Srivastava A, Kumar S, Raj SK. Sequence analysis of six full-length bean yellow mosaic virus genomes reveals phylogenetic diversity in India strains, suggesting subdivision of phylogenetic group-IV. Arch Virol 2017; 163:235-242. [PMID: 29052788 DOI: 10.1007/s00705-017-3609-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
We report the complete genome sequence of five bean yellow mosaic virus (BYMV) isolates (CK-GL1, CK-GL3, CK-GL4, CK-GL5 and Vfaba2) that share 74.6-98.9% (nucleotide) and 81.5-99.1% (amino acid) identity with globally available BYMV sequences. Phylogenetic analysis clustered them specifically in BYMV phylogenetic group-IV within the existing nine groups. The CK-GL1, CK-GL2, CK-GL4 and CK-GL5 isolates formed a discrete cluster within group-IV. The present study suggests subdivision of group-IV into subgroup-IVa and IVb. Moreover, infectivity assays using in vitro RNA transcripts from subgroup-IVa (CK-GL3 isolate) and IVb (CK-GL1 isolate) showed distinct biological differences between the isolates supporting subdivision.
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Affiliation(s)
- Charanjeet Kaur
- Plant Molecular Virology Laboratory, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh, 226 001, India
| | - Rashmi Raj
- Plant Molecular Virology Laboratory, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh, 226 001, India.,Department of Plant Microbe Interactions, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh, 226 001, India
| | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University, Sector 125, Noida, Uttar Pradesh, 201 313, India
| | - Susheel Kumar
- Plant Molecular Virology Laboratory, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh, 226 001, India. .,Department of Plant Microbe Interactions, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh, 226 001, India.
| | - Shri Krishna Raj
- Plant Molecular Virology Laboratory, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, Uttar Pradesh, 226 001, India.
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Gao R, Xu Y, Candresse T, He Z, Li S, Ma Y, Lu M. Further insight into genetic variation and haplotype diversity of Cherry virus A from China. PLoS One 2017; 12:e0186273. [PMID: 29020049 PMCID: PMC5636130 DOI: 10.1371/journal.pone.0186273] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 09/28/2017] [Indexed: 02/03/2023] Open
Abstract
Cherry virus A (CVA) infection appears to be prevalent in cherry plantations worldwide. In this study, the diversity of CVA isolates from 31 cherry samples collected from different orchards around Bohai Bay in northeastern China was analyzed. The complete genome of one of these isolates, ChYT52, was found to be 7,434 nt in length excluding the poly (A) tail. It shares between 79.9-98.7% identity with CVA genome sequences in GenBank, while its RdRp core is more divergent (79.1-90.7% nt identity), likely as a consequence of a recombination event. Phylogenetic analysis of ChYT52 genome with CVA genomes in Genbank resulted in at least 7 major clusters plus additional 5 isolates alone at the end of long branches suggesting the existence of further phylogroups diversity in CVA. The genetic diversity of Chinese CVA isolates from 31 samples and GenBank sequences were analyzed in three genomic regions that correspond to the coat protein, the RNA-dependent RNA polymerase core region, and the movement protein genes. With few exceptions likely representing further recombination impact, the trees various trees are largely congruent, indicating that each region provides valuable phylogenetic information. In all cases, the majority of the Chinese CVA isolates clustering in phylogroup I, together with the X82547 reference sequence from Germany. Statistically significant negative values were obtained for Tajima's D in the three genes for phylogroup I, suggesting that it may be undergoing a period of expansion. There was considerable haplotype diversity in the individual samples and more than half samples contained genetically diverse haplotypes belonging to different phylogroups. In addition, a number of statistically significant recombination events were detected in CVA genomes or in the partial genomic sequences indicating an important contribution of recombination to CVA evolution. This work provides a foundation for elucidation of the epidemiological characteristics and evolutionary history of CVA populations.
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Affiliation(s)
- Rui Gao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunxiao Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuxin Ma
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon Cedex, France
| | - Meiguang Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Genetic diversity of potato virus Y (PVY): sequence analyses reveal ten novel PVY recombinant structures. Arch Virol 2017; 163:23-32. [DOI: 10.1007/s00705-017-3568-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/16/2017] [Indexed: 01/27/2023]
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81
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Phylogenetic study of recombinant strains of Potato virus Y. Virology 2017; 507:40-52. [DOI: 10.1016/j.virol.2017.03.018] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 11/19/2022]
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Maina S, Coutts BA, Edwards OR, de Almeida L, Kehoe MA, Ximenes A, Jones RAC. Zucchini yellow mosaic virus Populations from East Timorese and Northern Australian Cucurbit Crops: Molecular Properties, Genetic Connectivity, and Biosecurity Implications. PLANT DISEASE 2017; 101:1236-1245. [PMID: 30682959 DOI: 10.1094/pdis-11-16-1672-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) isolates from cucurbit crops growing in northern Australia and East Timor were investigated to establish possible genetic connectivity between crop viruses in Australia and Southeast Asia. Leaves from symptomatic plants of pumpkin (Cucurbita moschata and C. maxima), melon (Cucumis melo), and zucchini (C. pepo) were sampled near Broome, Darwin, and Kununurra in northern Australia. Leaves from symptomatic plants of cucumber (C. sativus) and pumpkin sampled in East Timor were sent to Australia on FTA cards. These samples were subjected to high-throughput sequencing and 15 complete new ZYMV genomic sequences obtained. When their nucleotide sequences were compared with those of 48 others from GenBank, the East Timorese and Kununurra sequences (three per location) and single earlier sequences from Singapore and Reunion Island were all in major phylogroup B. The seven Broome and two Darwin sequences were in minor phylogroups I and II, respectively, within larger major phylogroup A. When coat protein (CP) nucleotide sequences from the 15 new genomes and 47 Australian isolates sequenced previously were compared with 331 other CP sequences, the closest genetic match for a sequence from Kununurra was with an East Timorese sequence (95.5% nucleotide identity). Analysis of the 63 complete genomes found firm recombination events in 12 (75%) and 2 (4%) sequences from northern Australia or Southeast Asia versus the rest of the world, respectively; therefore, the formers' high recombination frequency might reflect adaptation to tropical conditions. Both parents of the recombinant Kununurra sequence were East Timorese. Phylogenetic analysis, nucleotide sequence identities, and recombination analysis provided clear evidence of genetic connectivity between sequences from Kununurra and East Timor. Inoculation of a Broome isolate to zucchini and watermelon plants reproduced field symptoms observed in northern Australia. This research has important biosecurity implications over entry of damaging viral crop pathogens not only into northern Australia but also moving between Australia's different agricultural regions.
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Affiliation(s)
- Solomon Maina
- School of Agriculture and Environment and the UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia; and Cooperative Research Centre for Plant Biosecurity, Canberra, ACT 2617, Australia
| | - Brenda A Coutts
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, WA 6151, Australia
| | - Owain R Edwards
- Commonwealth Scientific and Industrial Research Organisation, Land and Water, Floreat Park, WA 6014, Australia, and Cooperative Research Centre for Plant Biosecurity, Canberra
| | - Luis de Almeida
- Seeds of Life Project, Ministry Agriculture and Fisheries, PO Box 221, Dili, East Timor
| | - Monica A Kehoe
- Department of Agriculture and Food Western Australia, South Perth
| | - Abel Ximenes
- DNQB-Plant Quarantine International Airport Nicolau Lobato Comoro, Dili, East Timor
| | - Roger A C Jones
- Department of Agriculture and Food Western Australia, South Perth; UWA Institute of Agriculture, Faculty of Science, The University of Western Australia, Crawley; and Australia and Cooperative Research Centre for Plant Biosecurity, Canberra
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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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Mbewe W, Tairo F, Sseruwagi P, Ndunguru J, Duffy S, Mukasa S, Benesi I, Sheat S, Koerbler M, Winter S. Variability in P1 gene redefines phylogenetic relationships among cassava brown streak viruses. Virol J 2017; 14:118. [PMID: 28637472 PMCID: PMC5480109 DOI: 10.1186/s12985-017-0790-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/16/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cassava brown streak disease is emerging as the most important viral disease of cassava in Africa, and is consequently a threat to food security. Two distinct species of the genus Ipomovirus (family Potyviridae) cause the disease: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). To understand the evolutionary relationships among the viruses, 64 nucleotide sequences from the variable P1 gene from major cassava producing areas of east and central-southern Africa were determined. METHODS We sequenced an amplicon of the P1 region of 31 isolates from Malawi and Tanzania. In addition to these, 33 previously reported sequences of virus isolates from Uganda, Kenya, Tanzania, Malawi and Mozambique were added to the analysis. RESULTS Phylogenetic analyses revealed three major P1 clades of Cassava brown streak viruses (CBSVs): in addition to a clade of most CBSV and a clade containing all UCBSV, a novel, intermediate clade of CBSV isolates which has been tentatively called CBSV-Tanzania (CBSV-TZ). Virus isolates of the distinctive CBSV-TZ had nucleotide identities as low as 63.2 and 63.7% with other members of CBSV and UCBSV respectively. CONCLUSIONS Grouping of P1 gene sequences indicated for distinct sub-populations of CBSV, but not UCBSV. Representatives of all three clades were found in both Tanzania and Malawi.
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Affiliation(s)
- Willard Mbewe
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901 USA
- School of Agriculture and Environmental Science, Department of Agricultural Production, Makerere University, P. O. Box, 7062 Kampala, Uganda
| | - Fred Tairo
- Mikocheni Agricultural Research Institute, P. O. Box 6226, Dar es Salaam, PO Tanzania
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P. O. Box 6226, Dar es Salaam, PO Tanzania
| | - Joseph Ndunguru
- Mikocheni Agricultural Research Institute, P. O. Box 6226, Dar es Salaam, PO Tanzania
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901 USA
| | - Ssetumba Mukasa
- School of Agriculture and Environmental Science, Department of Agricultural Production, Makerere University, P. O. Box, 7062 Kampala, Uganda
| | - Ibrahim Benesi
- Chitedze Agricultural Research Station, P. O. Box, 153 Lilongwe, Malawi
| | - Samar Sheat
- Leibniz Institute - DSMZ Plant Virus Department, Braunschweig, Germany
| | - Marianne Koerbler
- Leibniz Institute - DSMZ Plant Virus Department, Braunschweig, Germany
| | - Stephan Winter
- Leibniz Institute - DSMZ Plant Virus Department, Braunschweig, Germany
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Ksenofontov AL, Dobrov EN, Fedorova NV, Serebryakova MV, Prusov AN, Baratova LA, Paalme V, Järvekülg L, Shtykova EV. Isolated Potato Virus A coat protein possesses unusual properties and forms different short virus-like particles. J Biomol Struct Dyn 2017; 36:1728-1738. [DOI: 10.1080/07391102.2017.1333457] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Alexander L. Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Eugeny N. Dobrov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Natalia V. Fedorova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Marina V. Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Andrei N. Prusov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Ludmila A. Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
| | - Viiu Paalme
- Department of Chemistry and Biotechnology, Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618, Estonia
| | - Lilian Järvekülg
- Department of Chemistry and Biotechnology, Tallinn University of Technology , Akadeemia tee 15, Tallinn 12618, Estonia
| | - Eleonora V. Shtykova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University , Moscow 119234, Russia
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics”, Russian Academy of Sciences , Moscow, Russia
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Moradi Z, Nazifi E, Mehrvar M. Occurrence and Evolutionary Analysis of Coat Protein Gene Sequences of Iranian Isolates of Sugarcane mosaic virus. THE PLANT PATHOLOGY JOURNAL 2017; 33:296-306. [PMID: 28592948 PMCID: PMC5461048 DOI: 10.5423/ppj.oa.10.2016.0219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 05/31/2023]
Abstract
Sugarcane mosaic virus (SCMV) is one of the most damaging viruses infecting sugarcane, maize and some other graminaceous species around the world. To investigate the genetic diversity of SCMV in Iran, the coat protein (CP) gene sequences of 23 SCMV isolates from different hosts were determined. The nucleotide sequence identity among Iranian isolates was more than 96%. They shared nucleotide identities of 75.5-99.9% with those of other SCMV isolates available in GenBank, the highest with the Egyptian isolate EGY7-1 (97.5-99.9%). The results of phylogenetic analysis suggested five divergent evolutionary lineages that did not completely reflect the geographical origin or host plant of the isolates. Population genetic analysis revealed greater between-group than within-group evolutionary divergence values, further supporting the results of the phylogenetic analysis. Our results indicated that natural selection might have contributed to the evolution of isolates belonging to the five identified SCMV groups, with infrequent genetic exchanges occurring between them. Phylogenetic analyses and the estimation of genetic distance indicated that Iranian isolates have low genetic diversity. No recombination was found in the CP cistron of Iranian isolates and the CP gene was under negative selection. These findings provide a comprehensive analysis of the population structure and driving forces for the evolution of SCMV with implications for global exchange of sugarcane germplasm. Gene flow, selection and somehow homologous recombination were found to be the important evolutionary factors shaping the genetic structure of SCMV populations.
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Affiliation(s)
- Zohreh Moradi
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad 91779-1163,
Iran
| | - Ehsan Nazifi
- Department of Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar 47416-95447,
Iran
| | - Mohsen Mehrvar
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad 91779-1163,
Iran
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87
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Cordero T, Mohamed MA, López-Moya JJ, Daròs JA. A Recombinant Potato virus Y Infectious Clone Tagged with the Rosea1 Visual Marker (PVY-Ros1) Facilitates the Analysis of Viral Infectivity and Allows the Production of Large Amounts of Anthocyanins in Plants. Front Microbiol 2017; 8:611. [PMID: 28428782 PMCID: PMC5382215 DOI: 10.3389/fmicb.2017.00611] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/27/2017] [Indexed: 11/13/2022] Open
Abstract
Potato virus Y (PVY) is a major threat to the cultivation of potato and other solanaceous plants. By inserting a cDNA coding for the Antirrhinum majus Rosea1 transcription factor into a PVY infectious clone, we created a biotechnological tool (PVY-Ros1) that allows infection by this relevant plant virus to be tracked by the naked eye with no need for complex instrumentation. Rosea1 is an MYB-type transcription factor whose expression activates the biosynthesis of anthocyanin pigments in a dose-specific and cell-autonomous manner. Our experiments showed that the mechanical inoculation of solanaceous plants with PVY-Ros1 induced the formation of red infection foci in inoculated tissue and solid dark red pigmentation in systemically infected tissue, which allows disease progression to be easily monitored. By using silver nanoparticles, a nanomaterial with exciting antimicrobial properties, we proved the benefits of PVY-Ros1 to analyze novel antiviral treatments in plants. PVY-Ros1 was also helpful for visually monitoring the virus transmission process by an aphid vector. Most importantly, the anthocyanin analysis of infected tobacco tissues demonstrated that PVY-Ros1 is an excellent biotechnological tool for molecular farming because it induces the accumulation of larger amounts of anthocyanins, antioxidant compounds of nutritional, pharmaceutical and industrial interest, than those that naturally accumulate in some fruits and vegetables well known for their high anthocyanin content. Hence these results support the notion that the virus-mediated expression of regulatory factors and enzymes in plants facilitates easy quick plant metabolism engineering.
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Affiliation(s)
- Teresa Cordero
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia)Valencia, Spain
| | - Mohamed A. Mohamed
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia)Valencia, Spain
| | - Juan-José López-Moya
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas – Institut de Recerca i Tecnologia Agroalimentaries – Universitat Autònoma de Barcelona – Universitat de BarcelonaBarcelona, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia)Valencia, Spain
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88
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Gao F, Zou W, Xie L, Zhan J. Adaptive evolution and demographic history contribute to the divergent population genetic structure of Potato virus Y between China and Japan. Evol Appl 2017; 10:379-390. [PMID: 28352297 PMCID: PMC5367074 DOI: 10.1111/eva.12459] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/10/2017] [Indexed: 12/22/2022] Open
Abstract
Potato virus Y (PVY) is an important plant pathogen causing considerable economic loss to potato production. Knowledge of the population genetic structure and evolutionary biology of the pathogen, particularly at a transnational scale, is limited but vital in developing sustainable management schemes. In this study, the population genetic structure and molecular evolution of PVY were studied using 127 first protein (P1) and 137 coat protein (CP) sequences generated from isolates collected from potato in China and Japan. High genetic differentiation was found between the populations from the two countries, with higher nucleotide diversity in Japan than China in both genes and a KST value of .216 in the concatenated sequences of the two genes. Sequences from the two countries clustered together according to their geographic origin. Further analyses showed that spatial genetic structure in the PVY populations was likely caused by demographic dynamics of the pathogen and natural selection generated by habitat heterogeneity. Purifying selection was detected at the majority of polymorphic sites although some clade-specific codons were under positive selection. In past decades, PVY has undergone a population expansion in China, whereas in Japan, the population size of the pathogen has remained relatively constant.
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Affiliation(s)
- Fangluan Gao
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Wenchao Zou
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lianhui Xie
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiasui Zhan
- Fujian Key Laboratory of Plant VirologyInstitute of Plant VirologyFujian Agriculture and Forestry UniversityFuzhouChina
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89
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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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90
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Charon J, Theil S, Nicaise V, Michon T. Protein intrinsic disorder within the Potyvirus genus: from proteome-wide analysis to functional annotation. MOLECULAR BIOSYSTEMS 2016; 12:634-52. [PMID: 26699268 DOI: 10.1039/c5mb00677e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Within proteins, intrinsically disordered regions (IDRs) are devoid of stable secondary and tertiary structures under physiological conditions and rather exist as dynamic ensembles of inter-converting conformers. Although ubiquitous in all domains of life, the intrinsic disorder content is highly variable in viral genomes. Over the years, functional annotations of disordered regions at the scale of the whole proteome have been conducted for several animal viruses. But to date, similar studies applied to plant viruses are still missing. Based on disorder prediction tools combined with annotation programs and evolutionary studies, we analyzed the intrinsic disorder content in Potyvirus, using a 10-species dataset representative of this genus diversity. In this paper, we revealed that: (i) the Potyvirus proteome displays high disorder content, (ii) disorder is conserved during Potyvirus evolution, suggesting a functional advantage of IDRs, (iii) IDRs evolve faster than ordered regions, and (iv) IDRs may be associated with major biological functions required for the Potyvirus cycle. Notably, the proteins P1, Coat protein (CP) and Viral genome-linked protein (VPg) display a high content of conserved disorder, enriched in specific motifs mimicking eukaryotic functional modules and suggesting strategies of host machinery hijacking. In these three proteins, IDRs are particularly conserved despite their high amino acid polymorphism, indicating a link to adaptive processes. Through this comprehensive study, we further investigate the biological relevance of intrinsic disorder in Potyvirus biology and we propose a functional annotation of potyviral proteome IDRs.
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Affiliation(s)
- Justine Charon
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Sébastien Theil
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Valérie Nicaise
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
| | - Thierry Michon
- UMR Biologie du Fruit et Pathologie, INRA, Villenave d'Ornon cedex, France. and UMR Biologie du Fruit et Pathologie, Université de Bordeaux, Villenave d'Ornon cedex, France
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91
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Folch-Fortuny A, Bosque G, Picó J, Ferrer A, Elena SF. Fusion of genomic, proteomic and phenotypic data: the case of potyviruses. MOLECULAR BIOSYSTEMS 2016; 12:253-61. [PMID: 26593691 DOI: 10.1039/c5mb00507h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Data fusion has been widely applied to analyse different sources of information, combining all of them in a single multivariate model. This methodology is mandatory when different omic data sets must be integrated to fully understand an organism using a systems biology approach. Here, a data fusion procedure is presented to combine genomic, proteomic and phenotypic data sets gathered for Tobacco etch virus (TEV). The genomic data correspond to random mutations inserted in most viral genes. The proteomic data represent both the effect of these mutations on the encoded proteins and the perturbation induced by the mutated proteins to their neighbours in the protein-protein interaction network (PPIN). Finally, the phenotypic trait evaluated for each mutant virus is replicative fitness. To analyse these three sources of information a Partial Least Squares (PLS) regression model is fitted in order to extract the latent variables from data that explain (and relate) the significant variables to the fitness of TEV. The final output of this methodology is a set of functional modules of the PPIN relating topology and mutations with fitness. Throughout the re-analysis of these diverse TEV data, we generated valuable information on the mechanism of action of certain mutations and how they translate into organismal fitness. Results show that the effect of some mutations goes beyond the protein they directly affect and spreads on the PPIN to neighbour proteins, thus defining functional modules.
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Affiliation(s)
- A Folch-Fortuny
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, València, Spain.
| | - G Bosque
- Institut Universitari d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, València, Spain
| | - J Picó
- Institut Universitari d'Automàtica i Informàtica Industrial, Universitat Politècnica de València, València, Spain
| | - A Ferrer
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, València, Spain.
| | - S F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València, València, Spain and The Santa Fe Institute, Santa Fe, New Mexico, USA
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92
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Iranian johnsongrass mosaic virus: the complete genome sequence, molecular and biological characterization, and comparison of coat protein gene sequences. Virus Genes 2016; 53:77-88. [PMID: 27632283 DOI: 10.1007/s11262-016-1389-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 09/02/2016] [Indexed: 12/13/2022]
Abstract
Iranian johnsongrass mosaic virus (IJMV) is one of the most prevalent viruses causing maize mosaic disease in Iran. An IJMV isolate, Maz-Bah, was obtained from the maize showing mosaic symptoms in Mazandaran, north of Iran. The complete genomic sequence of Maz-Bah is 9544 nucleotides, excluding the poly(A) tail. It contains one single open reading frame of 9165 nucleotides and encodes a large polyprotein of 3054 amino acids, flanked by a 5'-untranslated region (UTR) of 143 nucleotides and a 3'-UTR of 236 nucleotides. The entire genomic sequence of Maz-Bah isolate shares identities of 84.9 and 94.2 % with the IJMV (Shz) isolate, the lone complete genome sequence available in the GenBank at the nucleotide (nt) and deduced amino acid (aa) levels, respectively. The whole genome sequences share identities of 51.5-69.8 and 44.9-74.3 % with those of other Sugarcane mosaic virus (SCMV) subgroup potyviruses at nt and aa levels, respectively. In phylogenetic trees based on the multiple alignments of the entire nt and aa sequences, IJMV isolates formed a separate sublineage of the tree with potyviruses infecting monocotyledons of cereals, indicating that IJMV is a member of SCMV subgroup of potyviruses. IJMV is most closely related to Sorghum mosaic virus and Maize dwarf mosaic virus and less closely related to the Johnsongrass mosaic virus and Cocksfoot streak virus. To further investigate the genetic relationship of IJMV, 9 other isolates from different hosts were cloned and sequenced. The identity of IJMV CP nt and aa sequences of 11 Iranian isolates ranged from 86.4 to 99.8 % and 90.5 to 99.7 %, respectively, indicating a high nt variability in CP gene. Furthermore, in the CP-based phylogenetic tree, IJMV isolates were clustered together with a maize potyvirus described as Zea mosaic virus from Israel (with 86-89 % nt identity), indicating that both isolates probably are the strains of the same virus.
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93
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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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94
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First Genome Sequence of Wild Onion Symptomless Virus, a Novel Member of Potyvirus in the Turnip Mosaic Virus Phylogenetic Group. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00851-16. [PMID: 27540073 PMCID: PMC4991718 DOI: 10.1128/genomea.00851-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The nearly complete genome sequence of a new species of potyvirus was obtained from the symptomless wild onion (Allium sp.) in Turkey. This virus has less than 67% nucleotide sequence identities over the polyprotein to other known potyviruses. We propose the name wild onion symptomless virus for this novel potyvirus.
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95
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Zhu F, Sun Y, Wang Y, Pan H, Wang F, Zhang X, Zhang Y, Liu J. Molecular Characterization of the Complete Genome of Three Basal-BR Isolates of Turnip mosaic virus Infecting Raphanus sativus in China. Int J Mol Sci 2016; 17:E888. [PMID: 27271614 PMCID: PMC4926422 DOI: 10.3390/ijms17060888] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/16/2016] [Accepted: 05/27/2016] [Indexed: 11/23/2022] Open
Abstract
Turnip mosaic virus (TuMV) infects crops of plant species in the family Brassicaceae worldwide. TuMV isolates were clustered to five lineages corresponding to basal-B, basal-BR, Asian-BR, world-B and OMs. Here, we determined the complete genome sequences of three TuMV basal-BR isolates infecting radish from Shandong and Jilin Provinces in China. Their genomes were all composed of 9833 nucleotides, excluding the 3'-terminal poly(A) tail. They contained two open reading frames (ORFs), with the large one encoding a polyprotein of 3164 amino acids and the small overlapping ORF encoding a PIPO protein of 61 amino acids, which contained the typically conserved motifs found in members of the genus Potyvirus. In pairwise comparison with 30 other TuMV genome sequences, these three isolates shared their highest identities with isolates from Eurasian countries (Germany, Italy, Turkey and China). Recombination analysis showed that the three isolates in this study had no "clear" recombination. The analyses of conserved amino acids changed between groups showed that the codons in the TuMV out group (OGp) and OMs group were the same at three codon sites (852, 1006, 1548), and the other TuMV groups (basal-B, basal-BR, Asian-BR, world-B) were different. This pattern suggests that the codon in the OMs progenitor did not change but that in the other TuMV groups the progenitor sequence did change at divergence. Genetic diversity analyses indicate that the PIPO gene was under the highest selection pressure and the selection pressure on P3N-PIPO and P3 was almost the same. It suggests that most of the selection pressure on P3 was probably imposed through P3N-PIPO.
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Affiliation(s)
- Fuxiang Zhu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Ying Sun
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yan Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Fengting Wang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Xianghui Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Yanhua Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China.
| | - Jinliang Liu
- College of Plant Sciences, Jilin University, Changchun 130062, China.
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96
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Hamelin FM, Allen LJS, Prendeville HR, Hajimorad MR, Jeger MJ. The evolution of plant virus transmission pathways. J Theor Biol 2016; 396:75-89. [PMID: 26908348 DOI: 10.1016/j.jtbi.2016.02.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/30/2015] [Accepted: 02/12/2016] [Indexed: 01/12/2023]
Abstract
The evolution of plant virus transmission pathways is studied through transmission via seed, pollen, or a vector. We address the questions: under what circumstances does vector transmission make pollen transmission redundant? Can evolution lead to the coexistence of multiple virus transmission pathways? We restrict the analysis to an annual plant population in which reproduction through seed is obligatory. A semi-discrete model with pollen, seed, and vector transmission is formulated to investigate these questions. We assume vector and pollen transmission rates are frequency-dependent and density-dependent, respectively. An ecological stability analysis is performed for the semi-discrete model and used to inform an evolutionary study of trade-offs between pollen and seed versus vector transmission. Evolutionary dynamics critically depend on the shape of the trade-off functions. Assuming a trade-off between pollen and vector transmission, evolution either leads to an evolutionarily stable mix of pollen and vector transmission (concave trade-off) or there is evolutionary bi-stability (convex trade-off); the presence of pollen transmission may prevent evolution of vector transmission. Considering a trade-off between seed and vector transmission, evolutionary branching and the subsequent coexistence of pollen-borne and vector-borne strains is possible. This study contributes to the theory behind the diversity of plant-virus transmission patterns observed in nature.
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Affiliation(s)
- Frédéric M Hamelin
- Department of Ecology, Agrocampus Ouest, UMR1349 IGEPP, F-35042 Rennes, France.
| | - Linda J S Allen
- Department of Mathematics and Statistics, Texas Tech University, Lubbock, TX 79409-1042, USA
| | - Holly R Prendeville
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA
| | - M Reza Hajimorad
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996-4560, USA
| | - Michael J Jeger
- Division of Ecology and Evolution, Centre for Environmental Policy, Imperial College London, SL5 7PY, UK
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97
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Gao F, Jin J, Zou W, Liao F, Shen J. Geographically driven adaptation of chilli veinal mottle virus revealed by genetic diversity analysis of the coat protein gene. Arch Virol 2016; 161:1329-33. [PMID: 26831930 DOI: 10.1007/s00705-016-2761-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/11/2016] [Indexed: 11/26/2022]
Abstract
Chilli veinal mottle virus (ChiVMV) is an important plant pathogen with a wide host range. The genetic structure of ChiVMV was investigated by analyzing the coat protein (CP) genes of 87 ChiVMV isolates from seven Asian regions. Pairwise F ST values between ChiVMV populations ranged from 0.108 to 0.681, indicating a significant spatial structure for this pathogen. In phylogeny-trait association analysis, the viral isolates from the same region tended to group together, showing a distinct geographic feature. These results suggest that geographic driven adaptation may be an important determinant of the genetic diversity of ChiVMV.
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Affiliation(s)
- Fangluan Gao
- Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Jing Jin
- Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Wenchao Zou
- Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Furong Liao
- Inspection and Quarantine Technology Center, Xiamen Exit-Entry Inspection and Quarantine Bureau, Xiamen, 361012, People's Republic of China
| | - Jianguo Shen
- Inspection and Quarantine Technology Center, Fujian Exit-Entry, Inspection and Quarantine Bureau, Fuzhou, 350001, People's Republic of China.
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98
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Gao F, Lin W, Shen J, Liao F. Genetic diversity and molecular evolution of arabis mosaic virus based on the CP gene sequence. Arch Virol 2016; 161:1047-51. [PMID: 26758729 DOI: 10.1007/s00705-015-2729-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/14/2015] [Indexed: 11/24/2022]
Abstract
Arabis mosaic virus (ArMV) is a virus with a wide host range. In this study, the genetic diversity of ArMV and the molecular mechanisms underlying its evolution were investigated using the coat protein (CP) sequence. Of the 33 ArMV isolates studied, three were found to be recombinants. The other 30 recombination-free ArMV isolates could be separated into two major lineages with a significant F ST value (0.384) and tended to cluster according to their geographical origin. Different evolutionary constraints were detected for the two linages, pointing to a role of natural selection in the differentiation of ArMV.
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Affiliation(s)
- Fangluan Gao
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Wuzhen Lin
- Key Lab for Biopesticide and Chemical Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Jianguo Shen
- Inspection and Quarantine Technology Center, Fujian Exit-Entry, Inspection and Quarantine Bureau, Fuzhou, 350001, People's Republic of China
| | - Furong Liao
- Inspection and Quarantine Technology Center, Xiamen Exit-Entry Inspection and Quarantine Bureau, Xiamen, 361012, People's Republic of China.
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99
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Complete genome sequence of a Chinese isolate of pepper vein yellows virus and evolutionary analysis based on the CP, MP and RdRp coding regions. Arch Virol 2015; 161:677-83. [PMID: 26620586 DOI: 10.1007/s00705-015-2691-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/15/2015] [Indexed: 02/04/2023]
Abstract
The genome sequence of pepper vein yellows virus (PeVYV) (PeVYV-HN, accession number KP326573), isolated from pepper plants (Capsicum annuum L.) grown at the Hunan Vegetables Institute (Changsha, Hunan, China), was determined by deep sequencing of small RNAs. The PeVYV-HN genome consists of 6244 nucleotides, contains six open reading frames (ORFs), and is similar to that of an isolate (AB594828) from Japan. Its genomic organization is similar to that of members of the genus Polerovirus. Sequence analysis revealed that PeVYV-HN shared 92% sequence identity with the Japanese PeVYV genome at both the nucleotide and amino acid levels. Evolutionary analysis based on the coat protein (CP), movement protein (MP), and RNA-dependent RNA polymerase (RdRP) showed that PeVYV could be divided into two major lineages corresponding to their geographical origins. The Asian isolates have a higher population expansion frequency than the African isolates. Negative selection and genetic drift (founder effect) were found to be the potential drivers of the molecular evolution of PeVYV. Moreover, recombination was not the distinct cause of PeVYV evolution. This is the first report of a complete genomic sequence of PeVYV in China.
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Zhang S, Zhao Z, Zheng L, Liu J, Peng J, Yan F, Li F, Xie Y, Cheng Z, Zhou X, Zhang D, Liu Y. Complete genome analysis of a novel recombinant isolate of pepper veinal mottle virus from mainland China. Virol J 2015; 12:191. [PMID: 26573722 PMCID: PMC4647447 DOI: 10.1186/s12985-015-0419-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/08/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Pepper veinal mottle virus (PVMV) was well established in Africa, and also reported infecting pepper (Capsicum annuum L) in Taiwan and India. However, there is not available of PVMV in mainland China. Here, the first complete genome sequence of PVMV isolated from pepper in mainland China was reported. FINDING The complete genomic sequence of isolate PVMV-HN isolated from pepper in mainland China is reported in this study. The genome of PVMV-HN is 9793 nucleotides (nt) excluding the poly (A) tail, shares 98-99 % nucleotide sequence identity with those two PVMV isolates from Ghana and Taiwan. Recombinant analysis showed that PVMV-HN probably represents a novel recombinant of PVMV. The phylogenetic relationship of PVMV-HN isolate to other PVMV isolates and other potyviruses based on genome or polyprotein sequence level and CP gene level, was also analyzed in this study. CONCLUSION The current study will help to understand phylogenetic relationship of isolate PVMV-HN.
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Affiliation(s)
- Songbai Zhang
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
- Shaoyang University, Shaoyang, 422000, China
| | - Zibing Zhao
- Shaoyang University, Shaoyang, 422000, China
| | - Limin Zheng
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Jian Liu
- Longping Branch, Graduate College, Central South University, Changsha, 410125, China
| | - Jing Peng
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Fei Yan
- Virology and Biotechnology Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fan Li
- Key Laboratory of Agricultural Biodiversity for Pest Management of China Education Ministry, Yunnan Agricultural University, Kunming, 650201, China
| | - Yan Xie
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhaobang Cheng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 201014, China
| | - Xuguo Zhou
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Deyong Zhang
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China.
- Longping Branch, Graduate College, Central South University, Changsha, 410125, China.
| | - Yong Liu
- Key Laboratory of Pest Management of Horticultural Crop of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China.
- Longping Branch, Graduate College, Central South University, Changsha, 410125, China.
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