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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.
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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.)
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Yan Z, Wolters AMA, Navas-Castillo J, Bai Y. The Global Dimension of Tomato Yellow Leaf Curl Disease: Current Status and Breeding Perspectives. Microorganisms 2021; 9:740. [PMID: 33916319 PMCID: PMC8066563 DOI: 10.3390/microorganisms9040740] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
Tomato yellow leaf curl disease (TYLCD) caused by tomato yellow leaf curl virus (TYLCV) and a group of related begomoviruses is an important disease which in recent years has caused serious economic problems in tomato (Solanum lycopersicum) production worldwide. Spreading of the vectors, whiteflies of the Bemisia tabaci complex, has been responsible for many TYLCD outbreaks. In this review, we summarize the current knowledge of TYLCV and TYLV-like begomoviruses and the driving forces of the increasing global significance through rapid evolution of begomovirus variants, mixed infection in the field, association with betasatellites and host range expansion. Breeding for host plant resistance is considered as one of the most promising and sustainable methods in controlling TYLCD. Resistance to TYLCD was found in several wild relatives of tomato from which six TYLCV resistance genes (Ty-1 to Ty-6) have been identified. Currently, Ty-1 and Ty-3 are the primary resistance genes widely used in tomato breeding programs. Ty-2 is also exploited commercially either alone or in combination with other Ty-genes (i.e., Ty-1, Ty-3 or ty-5). Additionally, screening of a large collection of wild tomato species has resulted in the identification of novel TYLCD resistance sources. In this review, we focus on genetic resources used to date in breeding for TYLCVD resistance. For future breeding strategies, we discuss several leads in order to make full use of the naturally occurring and engineered resistance to mount a broad-spectrum and sustainable begomovirus resistance.
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Affiliation(s)
- Zhe Yan
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
| | - Anne-Marie A. Wolters
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
| | - Jesús Navas-Castillo
- Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”, Consejo Superior de Investigaciones Científicas Universidad de Málaga (IHSM-CSIC-UMA), Avenida Dr. Weinberg s/n, 29750 Algarrobo-Costa, Málaga, Spain;
| | - Yuling Bai
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands; (Z.Y.); (A.-M.A.W.)
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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.
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Yan Z, Pérez-de-Castro A, Díez MJ, Hutton SF, Visser RGF, Wolters AMA, Bai Y, Li J. Resistance to Tomato Yellow Leaf Curl Virus in Tomato Germplasm. FRONTIERS IN PLANT SCIENCE 2018; 9:1198. [PMID: 30177938 PMCID: PMC6110163 DOI: 10.3389/fpls.2018.01198] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/26/2018] [Indexed: 05/19/2023]
Abstract
Tomato yellow leaf curl virus (TYLCV) is a virus species causing epidemics in tomato (Solanum lycopersicum) worldwide. Many efforts have been focused on identification of resistance sources by screening wild tomato species. In many cases, the accession numbers were either not provided in publications or not provided in a consistent manner, which led to redundant screenings. In the current study, we summarized efforts on the screenings of wild tomato species for TYLCV resistance from various publications. In addition, we screened 708 accessions from 13 wild tomato species using different inoculation assays (i.e., whitefly natural infection and Agrobacterium-mediated inoculation) from which 138 accessions exhibited no tomato yellow leaf curl disease (TYLCD) symptoms. These symptomless accessions include 14 accessions from S. arcanum, 43 from S. chilense, 1 from S. chmielewskii, 28 from S. corneliomulleri, 5 from S. habrochaites, 4 from S. huaylasense, 2 from S. neorickii, 1 from S. pennellii, 39 from S. peruvianum, and 1 from S. pimpinellifolium. Most of the screened S. chilense accessions remained symptomless. Many symptomless accessions were also identified in S. arcanum, S. corneliomulleri, and S. peruvianum. A large number of S. pimpinellifolium accessions were screened. However, almost all of the tested accessions showed TYLCD symptoms. Further, we studied allelic variation of the Ty-1/Ty-3 gene in few S. chilense accessions by applying virus-induced gene silencing and allele mining, leading to identification of a number of allele-specific polymorphisms. Taken together, we present a comprehensive overview on TYLCV resistance and susceptibility in wild tomato germplasm, and demonstrate how to study allelic variants of the cloned Ty-genes in TYLCV-resistant accessions.
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Affiliation(s)
- Zhe Yan
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding, Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Ana Pérez-de-Castro
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Ciudad Politécnica de la Innovación, Universitat Politècnica de València, Valencia, Spain
| | - Maria J. Díez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, Ciudad Politécnica de la Innovación, Universitat Politècnica de València, Valencia, Spain
| | - Samuel F. Hutton
- Gulf Coast Research and Education Center, University of Florida, Gainesville, FL, United States
| | - Richard G. F. Visser
- Plant Breeding, Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Anne-Marie A. Wolters
- Plant Breeding, Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Yuling Bai
- Plant Breeding, Graduate School Experimental Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Junming Li
- The Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Carmo LST, Murad AM, Resende RO, Boiteux LS, Ribeiro SG, Jorrín-Novo JV, Mehta A. Plant responses to tomato chlorotic mottle virus: Proteomic view of the resistance mechanisms to a bipartite begomovirus in tomato. J Proteomics 2016; 151:284-292. [PMID: 27457268 DOI: 10.1016/j.jprot.2016.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 07/17/2016] [Accepted: 07/18/2016] [Indexed: 12/27/2022]
Abstract
Tomato chlorotic mottle virus (ToCMoV) is a widespread bipartite Begomovirus species found in tomato fields in Brazil. In this study, plant responses and putative mechanisms associated with the 'Tyking'-derived recessive resistance to ToCMoV were investigated. Changes in the protein profile in the inoculated plants of two near isogenic tomato lines resistant ('LAM 157') and susceptible ('Santa Clara') to ToCMoV were analyzed. Seedlings were biolistically inoculated with an infectious ToCMoV clone. Leaves from infected plants (confirmed by PCR) were sampled at 15days after inoculation. Proteins were extracted using phenol and analyzed by shotgun MS (2D-nanoUPLC/HDMSE). Out of the 534 identified proteins, 82 presented statistically significant differences in abundance, including 35 unique proteins displayed in the resistant tomato inoculated with ToCMoV. Proteins associated to chromatin structure, cytoskeleton structure, cuticle biosynthesis, and ubiquitin pathway were identified and their putative roles during virus infection process were discussed. The protein profile analysis allowed for the development of a hypothetical model showing how the resistant host cell responds to ToCMoV infection. The data obtained provide a better understanding of resistant mechanisms used by the host plant to contain viral infection and could be the basis for further investigation in other plant-begomovirus pathosystems. BIOLOGICAL SIGNIFICANCE In this study we propose a model of resistance to begomovirus in tomato and highlight host proteins, which could be targets for future investigations in plant-begomovirus pathosystems.
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Affiliation(s)
- Lílian S T Carmo
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil; Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brazil
| | - André M Murad
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Renato O Resende
- Departamento de Biologia Celular, Instituto de Biologia, Universidade de Brasília, Brasília, DF, Brazil
| | | | - Simone G Ribeiro
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | | | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil.
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