1
|
de Oliveira IA, dos Reis LDNA, Fonseca MEDN, Melo FFS, Boiteux LS, Pereira-Carvalho RDC. Geminiviridae and Alphasatellitidae Diversity Revealed by Metagenomic Analysis of Susceptible and Tolerant Tomato Cultivars across Distinct Brazilian Biomes. Viruses 2024; 16:899. [PMID: 38932191 PMCID: PMC11209153 DOI: 10.3390/v16060899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
The diversity of Geminiviridae and Alphasatellitidae species in tomatoes was assessed via high-throughput sequencing of 154 symptomatic foliar samples collected from 2002 to 2017 across seven Brazilian biomes. The first pool (BP1) comprised 73 samples from the North (13), Northeast (36), and South (24) regions. Sixteen begomoviruses and one Topilevirus were detected in BP1. Four begomovirus-like contigs were identified as putative novel species (NS). NS#1 was reported in the semi-arid (Northeast) region and NS#2 and NS#4 in mild subtropical climates (South region), whereas NS#3 was detected in the warm and humid (North) region. The second pool (BP2) comprised 81 samples from Southeast (39) and Central-West (42) regions. Fourteen viruses and subviral agents were detected in BP2, including two topileviruses, a putative novel begomovirus (NS#5), and two alphasatellites occurring in continental highland areas. The five putative novel begomoviruses displayed strict endemic distributions. Conversely, tomato mottle leaf curl virus (a monopartite species) displayed the most widespread distribution occurring across the seven sampled biomes. The overall diversity and frequency of mixed infections were higher in susceptible (16 viruses + alphasatellites) in comparison to tolerant (carrying the Ty-1 or Ty-3 introgressions) samples, which displayed 9 viruses. This complex panorama reinforces the notion that the tomato-associated Geminiviridae diversity is yet underestimated in Neotropical regions.
Collapse
Affiliation(s)
- Izaías Araújo de Oliveira
- Department of Plant Pathology, University of Brasília (UnB), Brasília 70910-900, DF, Brazil; (I.A.d.O.); (L.d.N.A.d.R.); (F.F.S.M.)
| | | | | | - Felipe Fochat Silva Melo
- Department of Plant Pathology, University of Brasília (UnB), Brasília 70910-900, DF, Brazil; (I.A.d.O.); (L.d.N.A.d.R.); (F.F.S.M.)
| | - Leonardo Silva Boiteux
- Department of Plant Pathology, University of Brasília (UnB), Brasília 70910-900, DF, Brazil; (I.A.d.O.); (L.d.N.A.d.R.); (F.F.S.M.)
- Embrapa Vegetable Crops (Hortaliças), National Center for Vegetable Crops Research (CNPH),Brasília 70275-970, DF, Brazil;
| | - Rita de Cássia Pereira-Carvalho
- Department of Plant Pathology, University of Brasília (UnB), Brasília 70910-900, DF, Brazil; (I.A.d.O.); (L.d.N.A.d.R.); (F.F.S.M.)
| |
Collapse
|
2
|
Dos Reis LDNA, Boiteux LS, Fonseca MEN, Rojas MR, Gilbertson RL, Pereira-Carvalho RDC. Tomato golden net virus and tomato yellow net virus: two novel New World begomoviruses with monopartite genomes. Arch Virol 2023; 168:235. [PMID: 37642719 DOI: 10.1007/s00705-023-05836-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/13/2023] [Indexed: 08/31/2023]
Abstract
Two novel tomato-infecting begomoviruses were discovered via high-throughput sequencing in Brazil. Both viruses were also Sanger-sequenced and displayed DNA-A components phylogenetically related to New World bipartite begomoviruses. The names tomato golden net virus (ToGNV) and tomato yellow net virus (ToYNV) were proposed. The majority of the New World begomoviruses has bipartite genomes. However, extensive analyses revealed that ToGNV and ToYNV have monopartite genomes, because no cognate DNA-B components were detected. Hence, they may comprise a unique group of monopartite New World begomoviruses, which have enormous biological, molecular, and plant breeding interest.
Collapse
Affiliation(s)
| | - Leonardo S Boiteux
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Brasília, DF, Brazil
- Embrapa Vegetable Crops, National Center for Vegetable Crops Research (CNPH), Brasília, DF, Brazil
| | - Maria Esther N Fonseca
- Embrapa Vegetable Crops, National Center for Vegetable Crops Research (CNPH), Brasília, DF, Brazil
| | | | | | | |
Collapse
|
3
|
How To Be a Successful Monopartite Begomovirus in a Bipartite-Dominated World: Emergence and Spread of Tomato Mottle Leaf Curl Virus in Brazil. J Virol 2022; 96:e0072522. [PMID: 36043875 PMCID: PMC9517693 DOI: 10.1128/jvi.00725-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Begomoviruses are members of the family Geminiviridae, a large and diverse group of plant viruses characterized by a small circular single-stranded DNA genome encapsidated in twinned quasi-icosahedral virions. Cultivated tomato (Solanum lycopersicum L.) is particularly susceptible and is infected by >100 bipartite and monopartite begomoviruses worldwide. In Brazil, 25 tomato-infecting begomoviruses have been described, most of which are bipartite. Tomato mottle leaf curl virus (ToMoLCV) is one of the most important of these and was first described in the late 1990s but has not been fully characterized. Here, we show that ToMoLCV is a monopartite begomovirus with a genomic DNA similar in size and genome organization to those of DNA-A components of New World (NW) begomoviruses. Tomato plants agroinoculated with the cloned ToMoLCV genomic DNA developed typical tomato mottle leaf curl disease symptoms, thereby fulfilling Koch's postulates and confirming the monopartite nature of the ToMoLCV genome. We further show that ToMoLCV is transmitted by whiteflies, but not mechanically. Phylogenetic analyses placed ToMoLCV in a distinct and strongly supported clade with other begomoviruses from northeastern Brazil, designated the ToMoLCV lineage. Genetic analyses of the complete sequences of 87 ToMoLCV isolates revealed substantial genetic diversity, including five strain groups and seven subpopulations, consistent with a long evolutionary history. Phylogeographic models generated with partial or complete sequences predicted that the ToMoLCV emerged in northeastern Brazil >700 years ago, diversifying locally and then spreading widely in the country. Thus, ToMoLCV emerged well before the introduction of MEAM1 whiteflies, suggesting that the evolution of NW monopartite begomoviruses was facilitated by local whitefly populations and the highly susceptible tomato host. IMPORTANCE Worldwide, diseases of tomato caused by whitefly-transmitted geminiviruses (begomoviruses) cause substantial economic losses and a reliance on insecticides for management. Here, we describe the molecular and biological properties of tomato mottle leaf curl virus (ToMoLCV) from Brazil and establish that it is a NW monopartite begomovirus indigenous to northeastern Brazil. This answered a long-standing question regarding the genome of this virus, and it is part of an emerging group of these viruses in Latin America. This appears to be driven by widespread planting of the highly susceptible tomato and by local and exotic whiteflies. Our extensive phylogenetic studies placed ToMoLCV in a distinct strongly supported clade with other begomoviruses from northeastern Brazil and revealed new insights into the origin of Brazilian begomoviruses. The novel phylogeographic analysis indicated that ToMoLCV has had a long evolutionary history, emerging in northeastern Brazil >700 years ago. Finally, the tools used here (agroinoculation system and ToMoLCV-specific PCR test) and information on the biology of the virus (host range and whitefly transmission) will be useful in developing and implementing integrated pest management (IPM) programs targeting ToMoLCV.
Collapse
|
4
|
Xavier CAD, Nogueira AM, Bello VH, Watanabe LFM, Barbosa TMC, Alves Júnior M, Barbosa L, Beserra-Júnior JEA, Boari A, Calegario R, Gorayeb ES, Honorato Júnior J, Koch G, Lima GSDA, Lopes C, de Mello RN, Pantoja K, Silva FN, Ramos Sobrinho R, Santana EN, da Silva JWP, Krause-Sakate R, Zerbini FM. Assessing the diversity of whiteflies infesting cassava in Brazil. PeerJ 2021; 9:e11741. [PMID: 34316398 PMCID: PMC8286705 DOI: 10.7717/peerj.11741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Background The necessity of a competent vector for transmission is a primary ecological factor driving the host range expansion of plant arthropod-borne viruses, with vectors playing an essential role in disease emergence. Cassava begomoviruses severely constrain cassava production in Africa. Curiously, begomoviruses have never been reported in cassava in South America, the center of origin for this crop. It has been hypothesized that the absence of a competent vector in cassava is the reason why begomoviruses have not emerged in South America. Methods We performed a country-wide whitefly diversity study in cassava in Brazil. Adults and/or nymphs of whiteflies were collected from sixty-six cassava fields in the main agroecological zones of the country. A total of 1,385 individuals were genotyped based on mitochondrial cytochrome oxidase I sequences. Results A high species richness was observed, with five previously described species and two putative new ones. The prevalent species were Tetraleurodes acaciae and Bemisia tuberculata, representing over 75% of the analyzed individuals. Although we detected, for the first time, the presence of Bemisia tabaci Middle East-Asia Minor 1 (BtMEAM1) colonizing cassava in Brazil, it was not prevalent. The species composition varied across regions, with fields in the Northeast region showing a higher diversity. These results expand our knowledge of whitefly diversity in cassava and support the hypothesis that begomovirus epidemics have not occurred in cassava in Brazil due to the absence of competent vector populations. However, they indicate an ongoing adaptation process of BtMEAM1 to cassava, increasing the likelihood of begomovirus emergence in this crop.
Collapse
Affiliation(s)
- Cesar A D Xavier
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | | | | | | | | | - Miguel Alves Júnior
- Faculdade de Engenharia Agronômica, Universidade Federal do Pará, Altamira, PA, Brazil
| | - Leonardo Barbosa
- Instituto Federal do Sudeste de Minas Gerais, Rio Pomba, MG, Brazil
| | | | | | - Renata Calegario
- Dep. de Fitotecnia e Fitossanidade, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Silva Gorayeb
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Jaime Honorato Júnior
- Centro Multidisciplinar do Campus de Barra, Universidade Federal do Oeste da Bahia, Barra, BA, Brazil
| | - Gabriel Koch
- Dep. de Fitotecnia e Fitossanidade, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | | | - Cristian Lopes
- Instituto Federal do Sudeste de Minas Gerais, Rio Pomba, MG, Brazil
| | | | | | - Fábio Nascimento Silva
- Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Lages, SC, Brazil
| | - Roberto Ramos Sobrinho
- Centro de Ciências Agrárias/Fitossanidade, Universidade Federal de Alagoas, Rio Largo, AL, Brazil
| | | | | | | | - Francisco M Zerbini
- Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| |
Collapse
|
5
|
Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Kutnjak D. Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing. Front Microbiol 2021; 12:671925. [PMID: 34093492 PMCID: PMC8175903 DOI: 10.3389/fmicb.2021.671925] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/12/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.
Collapse
Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,School for Viticulture and Enology, University of Nova Gorica, Nova Gorica, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| |
Collapse
|
6
|
Krause-Sakate R, Watanabe LFM, Gorayeb ES, da Silva FB, Alvarez DDL, Bello VH, Nogueira AM, de Marchi BR, Vicentin E, Ribeiro-Junior MR, Marubayashi JM, Rojas-Bertini CA, Muller C, Bueno RCODF, Rosales M, Ghanim M, Pavan MA. Population Dynamics of Whiteflies and Associated Viruses in South America: Research Progress and Perspectives. INSECTS 2020; 11:insects11120847. [PMID: 33260578 PMCID: PMC7760982 DOI: 10.3390/insects11120847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/30/2020] [Accepted: 11/26/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary Whiteflies are one of the most important and widespread pests in the world. In South America, the currently most important species occurring are Bemisia afer,Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. The present review compiles information from several studies conducted in South America regarding these insects, providing data related to the dynamics and distribution of whiteflies, the associated viruses, and the management strategies to keep whiteflies under the economic damage threshold. Abstract By having an extensive territory and suitable climate conditions, South America is one of the most important agricultural regions in the world, providing different kinds of vegetable products to different regions of the world. However, such favorable conditions for plant production also allow the development of several pests, increasing production costs. Among them, whiteflies (Hemiptera: Aleyrodidae) stand out for their potential for infesting several crops and for being resistant to insecticides, having high rates of reproduction and dispersal, besides their efficient activity as virus vectors. Currently, the most important species occurring in South America are Bemisia afer, Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. In this review, a series of studies performed in South America were compiled in an attempt to unify the advances that have been developed in whitefly management in this continent. At first, a background of the current whitefly distribution in South American countries as well as factors affecting them are shown, followed by a background of the whitefly transmitted viruses in South America, addressing their location and association with whiteflies in each country. Afterwards, a series of management strategies are proposed to be implemented in South American fields, including cultural practices and biological and chemical control, finalizing with a section containing future perspectives and directions for further research.
Collapse
Affiliation(s)
- Renate Krause-Sakate
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
- Correspondence: ; Tel.: +55-14-3880-7487
| | - Luís Fernando Maranho Watanabe
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Eduardo Silva Gorayeb
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | - Felipe Barreto da Silva
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Daniel de Lima Alvarez
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Vinicius Henrique Bello
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Angélica Maria Nogueira
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | | | - Eduardo Vicentin
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Marcos Roberto Ribeiro-Junior
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Julio Massaharu Marubayashi
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Claudia Andrea Rojas-Bertini
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | | | - Regiane Cristina Oliveira de Freitas Bueno
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| | - Marlene Rosales
- Facultad de Agronomía e Ingeniería, Pontificia Universidad Católica de Chile, Forestal, Vicuña Mackena, 4860, Macul, Santiago 7820436, Chile; (C.A.R.-B.); (M.R.)
| | - Murad Ghanim
- Department of Entomology, Institute of Plant Protection, The Volcani Center, Rishon LeZion 7505101, Israel;
| | - Marcelo Agenor Pavan
- Department of Plant Protection, Universidade Estadual Paulista “Julio de Mesquita Filho” (UNESP), Botucatu 18610-034, Brazil; (L.F.M.W.); (E.S.G.); (F.B.d.S.); (D.d.L.A.); (V.H.B.); (A.M.N.); (E.V.); (M.R.R.-J.); (J.M.M.); (R.C.O.d.F.B.); (M.A.P.)
| |
Collapse
|
7
|
Diversity of tomato-infecting begomoviruses and spatiotemporal dynamics of an endemic viral species of the Brazilian Atlantic rain forest biome. Virus Genes 2020; 57:83-93. [PMID: 33236238 DOI: 10.1007/s11262-020-01812-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/17/2020] [Indexed: 10/22/2022]
Abstract
Yield losses induced by a complex of begomoviruses are observed across all major tomato-producing areas in Brazil. Tomato severe rugose virus (ToSRV) is the most widespread begomovirus in the country. Conversely, tomato common mosaic virus (ToCmMV) displays a more restricted geographical distribution to areas associated with the Atlantic Rain Forest (ARF) biome, encompassing the States of Espírito Santo-ES, Minas Gerais-MG, and Rio de Janeiro-RJ. Here, we characterized 277 tomato-infecting isolates collected in fields located within the ARF biome from 2006 to 2018. ToSRV displayed the highest prevalence (n = 157), followed by ToCmMV (n = 95) and tomato interveinal chlorosis virus (n = 14). Four other begomoviruses were also detected, but with very low incidences. ToCmMV was the predominant begomovirus in the ARF biome up to 2014-2015 with very low ToSRV incidence. Subsequently, ToSRV became the most prevalent species in ES and RJ, but ToCmMV was still predominating in the "Zona da Mata" meso-region in MG. Due to the remarkable endemic distribution of ToCmMV, we carried out phylogeographical studies of this virus using information from all 28 available isolates with complete DNA-A sequences. The closest common ancestor of ToCmMV was more likely originated around Coimbra-MG area ≈ 25 years before the formal report of this viral species. So far, all surveys indicated tomatoes as the only natural hosts of ToCmMV with outbreaks occurring mainly (but not exclusively) in highland areas. ToSRV shows a more widespread incidence across both highland and lowland areas of the ARF biome.
Collapse
|
8
|
Dos Reis LDNA, Boiteux LS, Fonseca MEN, Pereira-Carvalho RDC. Tomato yellow vein streak virus and Tomato golden vein virus: a reappraisal of the classification status of two South American Begomovirus species based upon genome-wide pairwise identity of multiple isolates. Virus Genes 2020; 57:127-131. [PMID: 33211226 DOI: 10.1007/s11262-020-01810-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/06/2020] [Indexed: 11/25/2022]
Abstract
Tomato yellow vein streak virus (ToYVSV) and tomato golden vein virus (TGVV) are begomoviruses reported infecting tomatoes and other hosts across South America. However, their close phylogenetic relationship has generated uncertainties about their taxonomic status and nomenclature. In fact, genomic DNA-A identity levels of isolates reported with an identical virus name may range from 89-100%. In view of the potential inaccuracy regarding the classification status of these viruses (strains vs. distinct species), we carried out a comprehensive set of analyses employing all 45 available isolates with complete DNA-A sequences with either ToYVSV or TGVV designation. Two clear-cut clusters were identified and they were consistent with the current criteria for Begomovirus species demarcation. Moreover, our reappraisal confirmed a large array of misnamed isolates and recognized a distinctive set of virus species-specific genomic, biological, and ecological features. Hence, the present work gives support to the notion that these viruses are closely-related, but they are distinct and valid Begomovirus species. From the breeding standpoint, this information will be useful in guiding germplasm screening strategies searching for sources of large-spectrum resistance to isolates of both viruses.
Collapse
Affiliation(s)
| | - Leonardo S Boiteux
- Departamento de Fitopatologia, Universidade de Brasília (UnB), Brasília-DF, Brazil
- National Center for Vegetable Crops Research (CNPH), Embrapa Vegetable Crops (Hortaliças), Brasília-DF, Brazil
| | - Maria Esther N Fonseca
- National Center for Vegetable Crops Research (CNPH), Embrapa Vegetable Crops (Hortaliças), Brasília-DF, Brazil
| | | |
Collapse
|
9
|
Souza TA, Silva JMF, Nagata T, Martins TP, Nakasu EYT, Inoue-Nagata AK. A Temporal Diversity Analysis of Brazilian Begomoviruses in Tomato Reveals a Decrease in Species Richness between 2003 and 2016. FRONTIERS IN PLANT SCIENCE 2020; 11:1201. [PMID: 32849745 PMCID: PMC7424291 DOI: 10.3389/fpls.2020.01201] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Understanding the molecular evolution and diversity changes of begomoviruses is crucial for predicting future outbreaks of the begomovirus disease in tomato crops. Thus, a molecular diversity study using high-throughput sequencing (HTS) was carried out on samples of infected tomato leaves collected between 2003 and 2016 from Central Brazil. DNA samples were subjected to rolling circle amplification and pooled in three batches, G1 (2003-2005, N = 107), G2 (2009-2011, N = 118), and G3 (2014-2016, N = 129) prior to HTS. Nineteen genome-sized geminivirus sequences were assembled, but only 17 were confirmed by PCR. In the G1 library, five begomoviruses and one capula-like virus were detected, but the number of identified viruses decreased to three begomoviruses in the G2 and G3 libraries. The bipartite begomovirus tomato severe rugose virus (ToSRV) and the monopartite tomato mottle leaf curl virus (ToMoLCV) were found to be the most prevalent begomoviruses in this survey. Our analyses revealed a significant increase in both relative abundance and genetic diversity of ToMoLCV from G1 to G3, and ToSRV from G1 to G2; however, both abundance and diversity decreased from G2 to G3. This suggests that ToMoLCV and ToSRV outcompeted other begomoviruses from G1 to G2 and that ToSRV was being outcompeted by ToMoLCV from G2 to G3. The possible evolutionary history of begomoviruses that were likely transferred from wild native plants and weeds to tomato crops after the introduction of the polyphagous vector Bemisia tabaci MEAM1 and the wide use of cultivars carrying the Ty-1 resistance gene are discussed, as well as the strengths and limitations of the use of HTS in identification and diversity analysis of begomoviruses.
Collapse
Affiliation(s)
- Tadeu Araujo Souza
- Department of Plant Pathology, University of Brasilia, Brasilia, Brazil
- Laboratory of Virology, Embrapa Vegetables, Brasilia, Brazil
| | | | - Tatsuya Nagata
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | - Thaís Pereira Martins
- Laboratory of Virology, Embrapa Vegetables, Brasilia, Brazil
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | | | - Alice Kazuko Inoue-Nagata
- Department of Plant Pathology, University of Brasilia, Brasilia, Brazil
- Laboratory of Virology, Embrapa Vegetables, Brasilia, Brazil
| |
Collapse
|
10
|
Metagenomics of Neotropical Single-Stranded DNA Viruses in Tomato Cultivars with and without the Ty-1 Gene. Viruses 2020; 12:v12080819. [PMID: 32731641 PMCID: PMC7472167 DOI: 10.3390/v12080819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/17/2022] Open
Abstract
A complex of begomoviruses (Geminiviridae) can cause severe tomato yield losses in the neotropics. Here, next-generation sequencing was employed for large-scale assessment of single-stranded (ss)DNA virus diversity in tomatoes either harboring or lacking the large-spectrum begomovirus tolerance Ty-1 gene. Individual leaf samples exhibiting begomovirus-like symptoms (n = 107) were field-collected, circular DNA-enriched, subdivided into pools (with and without Ty-1), and Illumina-sequenced. Virus-specific PCR and Sanger dideoxy sequencing validations confirmed 15 distinct ssDNA virus/subviral agents (occurring mainly in mixed infections), which highlight the potential drawbacks of employing virus-specific resistance in tomato breeding. More viruses (14 versus 6 species) were observed in tomatoes without the Ty-1 gene. A gemycircularvirus (Genomoviridae), a new alpha-satellite, and two novel Begomovirus species were identified exclusively in samples without the Ty-1 gene. A novel begomovirus was found only in the Ty-1 pool, being the only species associated with severe symptoms in Ty-1 plants in our survey. Our work is the first step towards the elucidation of the potential begomovirus adaptation to Ty-1 and its specific filtering effects on a subset of ssDNA viral/subviral agents.
Collapse
|
11
|
García-Arenal F, Zerbini FM. Life on the Edge: Geminiviruses at the Interface Between Crops and Wild Plant Hosts. Annu Rev Virol 2019; 6:411-433. [PMID: 31180812 DOI: 10.1146/annurev-virology-092818-015536] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses constitute the largest group of emerging pathogens, and geminiviruses (plant viruses with circular, single-stranded DNA genomes) are the major group of emerging plant viruses. With their high potential for genetic variation due to mutation and recombination, their efficient spread by vectors, and their wide host range as a group, including both wild and cultivated hosts, geminiviruses are attractive models for the study of the evolutionary and ecological factors driving virus emergence. Studies on the epidemiological features of geminivirus diseases have traditionally focused primarily on crop plants. Nevertheless, knowledge of geminivirus infection in wild plants, and especially at the interface between wild and cultivated plants, is necessary to provide a complete view of their ecology, evolution, and emergence. In this review, we address the most relevant aspects of geminivirus variability and evolution in wild and crop plants and geminiviruses' potential to emerge in crops.
Collapse
Affiliation(s)
- Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28223 Pozuelo de Alarcón, Madrid, Spain;
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), and National Research Institute for Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Minas Gerais 36570-900, Brazil;
| |
Collapse
|
12
|
Silva RV, Teixeira AB, Diniz JFS, Plata-Rueda RA, Lima ÉFB, Fernandes FL. First record of thrips species and their damage to carrot in Alto Paranaíba. BRAZ J BIOL 2019; 80:194-196. [PMID: 31066768 DOI: 10.1590/1519-6984.206574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/18/2018] [Indexed: 11/21/2022] Open
Affiliation(s)
- R V Silva
- Laboratório de Manejo Integrado de Pragas, Instituto de Ciências Agrárias - IAP, Universidade Federal de Viçosa - UFV, Campus Rio Paranaíba, MG 230, Km 08, CEP 38810-000, Rio Paranaíba, MG, Brasil
| | - A B Teixeira
- Laboratório de Manejo Integrado de Pragas, Instituto de Ciências Agrárias - IAP, Universidade Federal de Viçosa - UFV, Campus Rio Paranaíba, MG 230, Km 08, CEP 38810-000, Rio Paranaíba, MG, Brasil
| | - J F S Diniz
- Laboratório de Manejo Integrado de Pragas, Instituto de Ciências Agrárias - IAP, Universidade Federal de Viçosa - UFV, Campus Rio Paranaíba, MG 230, Km 08, CEP 38810-000, Rio Paranaíba, MG, Brasil
| | - R A Plata-Rueda
- Laboratório de Manejo Integrado de Pragas, Instituto de Ciências Agrárias - IAP, Universidade Federal de Viçosa - UFV, Campus Rio Paranaíba, MG 230, Km 08, CEP 38810-000, Rio Paranaíba, MG, Brasil
| | - É F B Lima
- Departamento de Biologia, Centro de Ciências da Natureza, Universidade Federal do Piauí - UFPI, Campus Amílcar Ferreira Sobral, BR 343, Km 3.5, CEP 64808-605, Floriano, PI, Brasil
| | - F L Fernandes
- Laboratório de Manejo Integrado de Pragas, Instituto de Ciências Agrárias - IAP, Universidade Federal de Viçosa - UFV, Campus Rio Paranaíba, MG 230, Km 08, CEP 38810-000, Rio Paranaíba, MG, Brasil
| |
Collapse
|
13
|
Lee YJ, Kil EJ, Kwak HR, Kim M, Seo JK, Lee S, Choi HS. Phylogenetic Characterization of Tomato chlorosis virus Population in Korea: Evidence of Reassortment between Isolates from Different Origins. THE PLANT PATHOLOGY JOURNAL 2018; 34:199-207. [PMID: 29887776 PMCID: PMC5985646 DOI: 10.5423/ppj.oa.10.2017.0220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/22/2018] [Accepted: 02/16/2018] [Indexed: 05/29/2023]
Abstract
Tomato chlorosis virus (ToCV) is a whitefly-transmitted and phloem-limited crinivirus. In 2013, severe interveinal chlorosis and bronzing on tomato leaves, known symptoms of ToCV infection, were observed in greenhouses in Korea. To identify ToCV infection in symptomatic tomato plants, RT-PCR with ToCV-specific primers was performed on leaf samples collected from 11 tomato cultivating areas where ToCV-like symptoms were observed in 2013 and 2014. About half of samples (45.18%) were confirmed as ToCV-infected, and the complete genome of 10 different isolates were characterized. This is the first report of ToCV occurring in Korea. The phylogenetic relationship and genetic variation among ToCV isolates from Korea and other countries were also analysed. When RNA1 and RNA2 are analysed separately, ToCV isolates were clustered into three groups in phylogenetic trees, and ToCV Korean isolates were confirmed to belong to two groups, which were geographically separated. These results suggested that Korean ToCV isolates originated from two independent origins. However, the RNA1 and RNA2 sequences of the Yeonggwang isolate were confirmed to belong to different groups, which indicated that ToCV RNA1 and RNA2 originated from two different origins and were reassorted in Yeonggwang, which is the intermediate point of two geographically separated groups.
Collapse
Affiliation(s)
- Ye-Ji Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 16419,
Korea
- Dapartment of Seed Services, Foundation of Agricultural Technology Commercialization and Transfer, Iksan 54667,
Korea
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365,
Korea
| | - Eui-Joon Kil
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 16419,
Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365,
Korea
| | - Mikyeong Kim
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365,
Korea
| | - Jang-Kyun Seo
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365,
Korea
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354,
Korea
| | - Sukchan Lee
- Department of Genetic Engineering, Sungkyunkwan University, Suwon 16419,
Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju 55365,
Korea
| |
Collapse
|
14
|
Vaghi Medina CG, Teppa E, Bornancini VA, Flores CR, Marino-Buslje C, López Lambertini PM. Tomato Apical Leaf Curl Virus: A Novel, Monopartite Geminivirus Detected in Tomatoes in Argentina. Front Microbiol 2018; 8:2665. [PMID: 29375528 PMCID: PMC5770407 DOI: 10.3389/fmicb.2017.02665] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/21/2017] [Indexed: 01/27/2023] Open
Abstract
Plant viruses that are members of the Geminiviridae family have circular single-stranded DNA (ssDNA) genome and are responsible for major crop diseases worldwide. We have identified and characterized a novel monopartite geminivirus infecting tomato in Argentina. The full-length genome was cloned and sequenced. The genome-wide pairwise identity calculation that resulted in a maximum of 63% identity with all of other known geminiviruses indicated that it is a new geminivirus species. Biolistic infected plants presented interveinal yellowing, apical leaf curling and extreme root hypotrophy. Thus, the name proposed for this species is tomato apical leaf curl virus (ToALCV). The phylogenetic inferences suggested different evolutionary relationships for the replication-associated protein (Rep) and the coat protein (CP). Besides, the sequence similarity network (SSN) protein analyses showed that the complementary-sense gene products (RepA, Rep and C3) are similar to capulavirus while the viron-sense gene products (CP, MP and V3) are similar to topocuvirus, curtovirus and becurtovirus. Based on the data presented, ToALCV genome appears to have “modular organization” supported by its recombination origin. Analyses of the specificity-determining positions (SDPs) of the CP of geminiviruses defined nine subgroups that include geminiviruses that share the same type of insect vector. Our sequences were clustered with the sequences of topocuvirus, whose vector is the treehopper, Micrutalis malleifera. Also, a set of the highest scored amino acid residues was predicted for the CP, which could determine differences in virus transmission specificity. We predict that a treehopper could be the vector of ToALCV, but transmission assays need to be performed to confirm this. Given everything we demonstrate in this paper, ToALCV can be considered a type member of a new putative genus of the Geminiviridae family.
Collapse
Affiliation(s)
- Carlos G Vaghi Medina
- Area de Interacción Planta-Patógeno-Vector, Instituto de Patología Vegetal, Centro de Investigaciónes Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
| | - Elin Teppa
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Fundación Instituto Leloir, Buenos Aires, Argentina
| | - Verónica A Bornancini
- Area de Interacción Planta-Patógeno-Vector, Instituto de Patología Vegetal, Centro de Investigaciónes Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
| | - Ceferino R Flores
- Estación Experimental Agropecuaria Yuto, Instituto Nacional de Tecnología Agropecuaria, Yuto, Argentina
| | - Cristina Marino-Buslje
- Instituto de Investigaciones Bioquímicas de Buenos Aires, Fundación Instituto Leloir, Buenos Aires, Argentina
| | - Paola M López Lambertini
- Area de Interacción Planta-Patógeno-Vector, Instituto de Patología Vegetal, Centro de Investigaciónes Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina
| |
Collapse
|
15
|
Genetic variability and population structure of the New World begomovirus Euphorbia yellow mosaic virus. J Gen Virol 2017; 98:1537-1551. [DOI: 10.1099/jgv.0.000784] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
|
16
|
Passos LS, Teixeira JWM, Teixeira KJML, Xavier CAD, Zerbini FM, Araújo ASF, Beserra JEA. Two new begomoviruses that infect non-cultivated malvaceae in Brazil. Arch Virol 2017; 162:1795-1797. [DOI: 10.1007/s00705-017-3283-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 01/23/2017] [Indexed: 11/28/2022]
|
17
|
Machado JPB, Calil IP, Santos AA, Fontes EPB. Translational control in plant antiviral immunity. Genet Mol Biol 2017; 40:292-304. [PMID: 28199446 PMCID: PMC5452134 DOI: 10.1590/1678-4685-gmb-2016-0092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/27/2016] [Indexed: 01/11/2023] Open
Abstract
Due to the limited coding capacity of viral genomes, plant viruses depend extensively on the host cell machinery to support the viral life cycle and, thereby, interact with a large number of host proteins during infection. Within this context, as plant viruses do not harbor translation-required components, they have developed several strategies to subvert the host protein synthesis machinery to produce rapidly and efficiently the viral proteins. As a countermeasure against infection, plants have evolved defense mechanisms that impair viral infections. Among them, the host-mediated translational suppression has been characterized as an efficient mean to restrict infection. To specifically suppress translation of viral mRNAs, plants can deploy susceptible recessive resistance genes, which encode translation initiation factors from the eIF4E and eIF4G family and are required for viral mRNA translation and multiplication. Additionally, recent evidence has demonstrated that, alternatively to the cleavage of viral RNA targets, host cells can suppress viral protein translation to silence viral RNA. Finally, a novel strategy of plant antiviral defense based on suppression of host global translation, which is mediated by the transmembrane immune receptor NIK1 (nuclear shuttle protein (NSP)-Interacting Kinase1), is discussed in this review.
Collapse
Affiliation(s)
- João Paulo B Machado
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Iara P Calil
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Anésia A Santos
- Department of General Biology, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| |
Collapse
|
18
|
Melo AM, Silva SJC, Ramos-Sobrinho R, Ferro MMM, Assunção IP, Lima GSA. Cnidoscolus mosaic leaf deformation virus: a novel begomovirus infecting euphorbiaceous plants in Brazil. Arch Virol 2016; 161:2605-8. [PMID: 27278930 DOI: 10.1007/s00705-016-2919-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Begomoviruses have been detected infecting the weed Cnidoscolus urens (family Euphorbiaceae) since 2004, but the viral species to which these viruses belonged was not known. Here, we report for the first time the complete genome sequence of a bipartite begomovirus obtained from C. urens collected in the state of Alagoas, Brazil. This isolate met the criteria to be classified as a member of a new begomovirus species, and the tentative name cnidoscolus mosaic leaf deformation virus (CnMLDV) is proposed. Pairwise sequence comparisons and phylogenetic analysis showed that the DNA-A genomic component of CnMLDV is most closely related to that of passionfruit severe leaf distortion virus, with 86.3 % nucleotide sequence identity.
Collapse
Affiliation(s)
- Aline M Melo
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Sarah J C Silva
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Roberto Ramos-Sobrinho
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Mayra M M Ferro
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Iraildes P Assunção
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil
| | - Gaus S A Lima
- Setor de Fitossanidade/CECA, Universidade Federal de Alagoas, Rio Largo, AL, 57100-000, Brazil.
| |
Collapse
|
19
|
The importance of primary inoculum and area-wide disease management to crop health and food security. Food Secur 2016. [DOI: 10.1007/s12571-015-0544-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
20
|
Brustolini OJ, Machado JPB, Condori-Apfata JA, Coco D, Deguchi M, Loriato VA, Pereira WA, Alfenas-Zerbini P, Zerbini FM, Inoue-Nagata AK, Santos AA, Chory J, Silva FF, Fontes EP. Sustained NIK-mediated antiviral signalling confers broad-spectrum tolerance to begomoviruses in cultivated plants. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:1300-1311. [PMID: 25688422 PMCID: PMC4857726 DOI: 10.1111/pbi.12349] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 12/30/2014] [Accepted: 01/06/2015] [Indexed: 05/20/2023]
Abstract
Begomovirus-associated epidemics currently threaten tomato production worldwide due to the emergence of highly pathogenic virus species and the proliferation of a whitefly B biotype vector that is adapted to tomato. To generate an efficient defence against begomovirus, we modulated the activity of the immune defence receptor nuclear shuttle protein (NSP)-interacting kinase (NIK) in tomato plants; NIK is a virulence target of the begomovirus NSP during infection. Mutation of T474 within the kinase activation loop promoted the constitutive activation of NIK-mediated defences, resulting in the down-regulation of translation-related genes and the suppression of global translation. Consistent with these findings, transgenic lines harbouring an activating mutation (T474D) were tolerant to the tomato-infecting begomoviruses ToYSV and ToSRV. This phenotype was associated with reduced loading of coat protein viral mRNA in actively translating polysomes, lower infection efficiency and reduced accumulation of viral DNA in systemic leaves. Our results also add some relevant insights into the mechanism underlying the NIK-mediated defence. We observed that the mock-inoculated T474D-overexpressing lines showed a constitutively infected wild-type transcriptome, indicating that the activation of the NIK-mediated signalling pathway triggers a typical response to begomovirus infection. In addition, the gain-of-function mutant T474D could sustain an activated NIK-mediated antiviral response in the absence of the virus, further confirming that phosphorylation of Thr-474 is the crucial event that leads to the activation of the kinase.
Collapse
Affiliation(s)
- Otávio J.B. Brustolini
- Departamento de Bioquímica e Biologia Molecular, Bioagro, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Joao Paulo B. Machado
- Departamento de Bioquímica e Biologia Molecular, Bioagro, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Jorge A. Condori-Apfata
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Daniela Coco
- Departamento de Bioquímica e Biologia Molecular, Bioagro, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Michihito Deguchi
- Departamento de Bioquímica e Biologia Molecular, Bioagro, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Virgílio A.P. Loriato
- Departamento de Bioquímica e Biologia Molecular, Bioagro, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Welison A. Pereira
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Poliane Alfenas-Zerbini
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Francisco M. Zerbini
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Alice K. Inoue-Nagata
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
- Embrapa Vegetables, Brasília, DF, Brazil
| | - Anesia A. Santos
- Departamento de Bioquímica e Biologia Molecular, Bioagro, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
| | - Joanne Chory
- Howard Hughes Medical Institute and Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Fabyano F. Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Elizabeth P.B. Fontes
- Departamento de Bioquímica e Biologia Molecular, Bioagro, Viçosa, MG, Brazil
- National Institute of Science and Technology in Plant–Pest Interactions, Bioagro, Viçosa, MG, Brazil
- Correspondence (Tel +55 31 3899 2948; fax +55-31-38992864; )
| |
Collapse
|
21
|
Machado JPB, Brustolini OJB, Mendes GC, Santos AA, Fontes EPB. NIK1, a host factor specialized in antiviral defense or a novel general regulator of plant immunity? Bioessays 2015; 37:1236-42. [PMID: 26335701 DOI: 10.1002/bies.201500066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
NIK1 is a receptor-like kinase involved in plant antiviral immunity. Although NIK1 is structurally similar to the plant immune factor BAK1, which is a key regulator in plant immunity to bacterial pathogens, the NIK1-mediated defenses do not resemble BAK1 signaling cascades. The underlying mechanism for NIK1 antiviral immunity has recently been uncovered. NIK1 activation mediates the translocation of RPL10 to the nucleus, where it interacts with LIMYB to fully down-regulate translational machinery genes, resulting in translation inhibition of host and viral mRNAs and enhanced tolerance to begomovirus. Therefore, the NIK1 antiviral immunity response culminates in global translation suppression, which represents a new paradigm for plant antiviral defenses. Interestingly, transcriptomic analyses in nik1 mutant suggest that NIK1 may suppress antibacterial immune responses, indicating a possible opposite effect of NIK1 in bacterial and viral infections.
Collapse
Affiliation(s)
- Joao P B Machado
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Otavio J B Brustolini
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Giselle C Mendes
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Anésia A Santos
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elizabeth P B Fontes
- Departamento de Bioquímica e Biologia Molecular, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, Viçosa, Brazil
| |
Collapse
|
22
|
Lett JM, De Bruyn A, Hoareau M, Ouattara A, Claverie S, Dalmon A, Laplace D, Lefeuvre P, Hostachy B. Tomato chlorotic mottle Guyane virus: a novel tomato-infecting bipartite begomovirus from French Guiana. Arch Virol 2015; 160:2887-90. [PMID: 26255054 DOI: 10.1007/s00705-015-2558-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/27/2015] [Indexed: 12/01/2022]
Abstract
This is the first description of the complete genome sequence of a new bipartite begomovirus isolated from tomato (Solanum lycopersicum) in French Guiana, for which we propose the tentative name "tomato chlorotic mottle Guyane virus" (ToCMoGFV). DNA-A and -B nucleotide sequences of ToCMoGFV are only distantly related to known New World begomoviruses. They share the highest nucleotide sequence identity of 80% with the Brazilian isolates of macroptilium yellow spot virus (MacYSV) and 73% with soybean chlorotic spot virus (SBCSV). Phylogenetic analysis demonstrated that this novel virus belongs to a new lineage of New World bipartite begomoviruses. The discovery of this new virus confirms the high genetic diversity of begomoviruses in Latin America.
Collapse
Affiliation(s)
- Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France.
| | - Alexandre De Bruyn
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France.,Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Alassane Ouattara
- Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Sohini Claverie
- Université de La Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Anne Dalmon
- INRA, UR Abeilles et Environnement, Domaine Saint-Paul, 228 route de l'Aérodrome, CS40509, 84914, Avignon Cedex 9, France
| | - Damien Laplace
- DAAF de Guyane, Service de l'alimentation, BP 5002, 97305, Cayenne Cedex, France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, Ile de La Réunion, France
| | - Bruno Hostachy
- ANSES-LSV Réunion, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410, Saint-Pierre, La Réunion, France
| |
Collapse
|
23
|
Tomato mottle wrinkle virus, a recombinant begomovirus infecting tomato in Argentina. Arch Virol 2014; 160:581-5. [PMID: 25252814 DOI: 10.1007/s00705-014-2216-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 08/26/2014] [Indexed: 10/24/2022]
Abstract
Begomoviruses seriously threaten tomato production in South America. Here, we present the molecular characterization of a novel tomato-infecting begomovirus isolated in Argentina and demonstrate its infectivity. After cloning and sequencing the complete genome of this new virus, pairwise genetic distance and phylogenetic analyses revealed that it is a novel virus that is closely related to other begomoviruses found in Argentina, Brazil and Bolivia. We have proposed naming the virus tomato mottle wrinkle virus (ToMoWrV), based on symptoms produced upon its biolistic inoculation into tomato plants. Recombination analysis revealed that ToMoWrV is a recombinant, with parental sequences likely belonging to the South American begomoviruses soybean blistering mosaic virus (SoBlMV) and tomato yellow vein streak virus (ToYVSV).
Collapse
|
24
|
Silva FN, Lima ATM, Rocha CS, Castillo-Urquiza GP, Alves-Júnior M, Zerbini FM. Recombination and pseudorecombination driving the evolution of the begomoviruses Tomato severe rugose virus (ToSRV) and Tomato rugose mosaic virus (ToRMV): two recombinant DNA-A components sharing the same DNA-B. Virol J 2014; 11:66. [PMID: 24708727 PMCID: PMC4113279 DOI: 10.1186/1743-422x-11-66] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 03/27/2014] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Begomoviruses are dicot-infecting, whitefly-transmitted viruses with a genome comprised of one or two molecules of circular, single-stranded DNA. In Brazil, tomato-infecting begomoviruses have emerged as serious pathogens since the introduction of a new biotype of the insect vector in the mid-1990's. Tomato rugose mosaic virus (ToRMV) and Tomato severe rugose virus (ToSRV) are often found in tomato fields. The complete sequence of the DNA-B components of ToSRV and ToRMV show an identity of 98.2%. Additionally, the high nucleotide identity (96.2%) between their common regions indicates that these two viruses may share the same DNA-B. METHODS Tomato seedlings were biolistically inoculated with ToSRV (DNA-A and DNA-B) and ToRMV (DNA-A and DNA-B) infectious clones in every possible combination of single or mixed infection. Symptom expression was evaluated for up to 35 days post-inoculation (dpi). DNA was extracted at 28 dpi and the presence of each viral genomic component was examined by rolling circle amplification (RCA) followed by digestion, as well as by quantitative, real-time PCR. Sequence comparisons, recombination and phylogenetic analyzes were performed using EMBOSS needle, RDP program and maximum likelihood inference, respectively. RESULTS Symptoms in tomato plants inoculated with the different combinations of ToRMV and ToSRV DNA-A and DNA-B components consisted of a typical mosaic in all combinations. Pseudorecombinants were formed in all possible combinations. When two DNA-A or two DNA-B components were inoculated simultaneously, the ToRMV components were detected preferentially in relation to the ToSRV components. The combination of minor changes in both the Rep protein and the CR may be involved in the preferential replication of ToRMV components. Recombination and phylogenetic analyzes support the exchange of genetic material between ToRMV and ToSRV. CONCLUSIONS ToRMV and ToSRV form viable pseudorecombinants in their natural host (Solanum lycopersicum) and share the same DNA-B. ToRMV DNA components are preferentially replicated over ToSRV components. These results indicate that the emergence of ToRMV involved both recombination and pseudorecombination, further highlighting the importance of these mechanisms in the emergence and adaptation of begomoviruses.
Collapse
Affiliation(s)
- Fábio N Silva
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Alison TM Lima
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Carolina S Rocha
- Current address: FuturaGene Brasil, Avenida José Lembo 1010, Itapeteninga, SP 18210-780, Brazil
| | | | - Miguel Alves-Júnior
- Current address: Faculdade de Ciências Agrárias, Universidade Federal do Pará, Altamira, PA 68372-040, Brazil
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| |
Collapse
|
25
|
Carmo LST, Resende RO, Silva LP, Ribeiro SG, Mehta A. Identification of host proteins modulated by the virulence factor AC2 of Tomato chlorotic mottle virus in Nicotiana benthamiana. Proteomics 2013; 13:1947-60. [PMID: 23533094 DOI: 10.1002/pmic.201200547] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/08/2013] [Accepted: 02/25/2013] [Indexed: 11/09/2022]
Abstract
Tomato, one of the most important crops cultivated worldwide, has been severely affected by begomoviruses such as the Tomato chlorotic mottle virus (ToCMoV). Virulence factor AC2 is considered crucial for a successful virus-plant interaction and is known to act as a transcriptional activator and in some begomoviruses to function as an RNA silencing suppressor factor. However, the exact functions of the AC2 protein of the begomovirus ToCMoV are not yet established. The aim of the present study was to identify differentially expressed proteins of the model plant Nicotiana benthamiana in response to the expression of the AC2 gene, isolated from ToCMoV. N. benthamiana plants were inoculated with Agrobacterium tumefaciens containing the viral vector Potato virus X (PVX) and with the PVX-AC2 construction. 2DE was performed and proteins were identified by MS. The results showed that the expression of ToCMoV AC2 alters the levels of several host proteins, which are important for normal plant development, causing an imbalance in cellular homeostasis. This study highlights the effect of AC2 in the modulation of plant defense processes by increasing the expression of several oxidative stress-related and pathogenesis-related proteins, as well as its role in modulating the proteome of the photosynthesis and energy production systems.
Collapse
|
26
|
Rocha CS, Castillo-Urquiza GP, Lima ATM, Silva FN, Xavier CAD, Hora-Júnior BT, Beserra-Júnior JEA, Malta AWO, Martin DP, Varsani A, Alfenas-Zerbini P, Mizubuti ESG, Zerbini FM. Brazilian begomovirus populations are highly recombinant, rapidly evolving, and segregated based on geographical location. J Virol 2013; 87:5784-99. [PMID: 23487451 PMCID: PMC3648162 DOI: 10.1128/jvi.00155-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 03/04/2013] [Indexed: 01/21/2023] Open
Abstract
The incidence of begomovirus infections in crop plants sharply increased in Brazil during the 1990s following the introduction of the invasive B biotype of the whitefly vector, Bemisia tabaci. It is believed that this biotype transmitted begomoviruses from noncultivated plants to crop species with greater efficiency than indigenous B. tabaci biotypes. Either through rapid host adaptation or selection pressure in genetically diverse populations of noncultivated hosts, over the past 20 years various previously unknown begomovirus species have became progressively more prevalent in cultivated species such as tomato. Here we assess the genetic structure of begomovirus populations infecting tomatoes and noncultivated hosts in southeastern Brazil. Between 2005 and 2010, we sampled and sequenced 126 DNA-A and 58 DNA-B full-length begomovirus components. We detected nine begomovirus species in tomatoes and eight in the noncultivated host samples, with four species common to both tomatoes and noncultivated hosts. Like many begomoviruses, most species are obvious interspecies recombinants. Furthermore, species identified in tomato have probable parental viruses from noncultivated hosts. While the population structures of five well-sampled viral species all displayed geographical subdivision, a noncultivated host-infecting virus was more genetically variable than the four predominantly tomato-infecting viruses.
Collapse
Affiliation(s)
- Carolina S. Rocha
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gloria P. Castillo-Urquiza
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Alison T. M. Lima
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Fábio N. Silva
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Cesar A. D. Xavier
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Braz T. Hora-Júnior
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José E. A. Beserra-Júnior
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Antonio W. O. Malta
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Arvind Varsani
- Electron Microscope Unit, University of Cape Town, Rondebosch, Cape Town, South Africa
- School of Biological Sciences, University of Canterbury, Ilam, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Ilam, Christchurch, New Zealand
| | - Poliane Alfenas-Zerbini
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Eduardo S. G. Mizubuti
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - F. Murilo Zerbini
- Dep. de Fitopatologia/BIOAGRO and National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Viçosa, MG, Brazil
| |
Collapse
|