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Using one of 21 samples showing virosis-associated symptoms, CIDER-Seq data revealed the presence of various NW begomovirus species, namely Begomovirus solanumaureivariati (tomato golden mottle virus: ToGMoV), Begomovirus solanumseveri (tomato severe leaf curl virus: ToSLCV), and Begomovirus solanumlapazense (tomato chino La Paz virus: ToChLPV). Additionally, the alphasatellites Whiflysatellite guatemalaense (whitefly-associated Guatemala alphasatellite 1: WfaGA1) and Clecrusatellite guatemalaense (whitefly-associated Guatemala alphasatellite 2: WfaGA2) were identified, demonstrating that begomoviruses can co-infect with alphasatellites; however, the pathogenic implications of the alphasatellite\u2013helper begomovirus association remain incompletely understood. PCR-based detection and Sanger sequencing of circular viral genomes revealed a high frequency of detection of mixed infections comprising all components of the begomovirus\u2013alphasatellite complex, confirming the reliability of the CIDER-Seq approach in producing high-fidelity sequences. Molecular and biological analysis revealed the complex adaptation to tomato, the monopartite nature of ToSLCV\/ToChLPV species, and the ability of these begomovirus species to act as helper viruses. To the best of our knowledge, this is the first report of leaf curl disease of tomato associated with a begomovirus\u2013alphasatellite complex in Mexico.<\/jats:p>","DOI":"10.3390\/v18090950","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T12:41:18Z","timestamp":1788266478000},"page":"950","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Circular DNA Enrichment Sequencing (CIDER-Seq) Facilitated the Discovery of a New World (NW) Begomovirus\u2013Alphasatellite Complex Associated with Leaf Curl Disease of Tomato in Morelos, Mexico"],"prefix":"10.3390","volume":"18","author":[{"given":"Enrique Alejandro","family":"Guevara-Rivera","sequence":"first","affiliation":[{"name":"Departamento de Biotecnolog\u00eda Agr\u00edcola, CIIDIR-Unidad Sinaloa, Instituto Polit\u00e9cnico Nacional, Guasave 81101, Sinaloa, 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Gen. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1146\/annurev-phyto-080615-100327","article-title":"World Management of Geminiviruses","volume":"56","author":"Rojas","year":"2018","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1007\/BF01309454","article-title":"A phylogenetic and evolutionary justification for three genera of Geminiviridae","volume":"139","author":"Rybicki","year":"1994","journal-title":"Arch. Virol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1111\/mpp.12032","article-title":"Geminivirus protein structure and function","volume":"14","author":"Fondong","year":"2013","journal-title":"Mol. Plant Pathol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1128\/jvi.70.1.148-158.1996","article-title":"A DNA structure is required for geminivirus replication origin function","volume":"70","author":"Orozco","year":"1996","journal-title":"J. Virol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Varma, A., and Singh, M.K. (2024). The Role of Satellites in the Evolution of Begomoviruses. Viruses, 16.","DOI":"10.3390\/v16060970"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"30204","DOI":"10.1038\/srep30204","article-title":"Infectivity, effects on helper viruses and whitefly transmission of the deltasatellites associated with sweepoviruses (genus Begomovirus, family Geminiviridae)","volume":"6","author":"Hassan","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1825","DOI":"10.1016\/j.febslet.2009.05.045","article-title":"Evolution of geminiviruses and their satellites","volume":"583","author":"Fauquet","year":"2009","journal-title":"FEBS Lett."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1007\/s00705-018-3854-2","article-title":"Alphasatellitidae: A new family with two subfamilies for the classification of geminivirus- and nanovirus-associated alphasatellites","volume":"163","author":"Briddon","year":"2018","journal-title":"Arch. Virol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"D708","DOI":"10.1093\/nar\/gkx932","article-title":"Virus taxonomy: The database of the International Committee on Taxonomy of Viruses (ICTV)","volume":"46","author":"Lefkowitz","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1099\/vir.0.025288-0","article-title":"An unusual alphasatellite associated with monopartite begomoviruses attenuates symptoms and reduces betasatellite accumulation","volume":"92","author":"Idris","year":"2011","journal-title":"J. Gen. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1186\/s12985-021-01718-6","article-title":"Roles of two distinct alphasatellites modulating geminivirus pathogenesis","volume":"18","author":"Kumar","year":"2021","journal-title":"Virol. J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.virol.2010.05.003","article-title":"The first DNA 1-like \u03b1 satellites in association with New World begomoviruses in natural infections","volume":"404","author":"Paprotka","year":"2010","journal-title":"Virology"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1007\/s11262-014-1090-8","article-title":"Circomics of Cuban geminiviruses reveals the first alpha-satellite DNA in the Caribbean","volume":"49","author":"Jeske","year":"2014","journal-title":"Virus Genes"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1007\/s00705-010-0760-7","article-title":"Association of an atypical alphasatellite with a bipartite New World begomovirus","volume":"155","author":"Romay","year":"2010","journal-title":"Arch. Virol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1007\/s00705-025-06293-7","article-title":"Discovery of a novel alphasatellite of the genus Clecrusatellite associated with a wide array of New World tomato-infecting begomoviruses","volume":"170","author":"Boiteux","year":"2025","journal-title":"Arch. Virol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Rosario, K., Marr, C., Varsani, A., Kraberger, S., Stainton, D., Moriones, E., Polston, J., and Breitbart, M. (2016). Begomovirus-Associated Satellite DNA Diversity Captured Through Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae). Viruses, 8.","DOI":"10.3390\/v8020036"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Nogueira, A.M., Nascimento, M.B., Barbosa, T.M.C., Quadros, A.F.F., Gomes, J.P.A., Or\u00edlio, A.F., Barros, D.R., and Zerbini, F.M. (2021). The association between new world alphasatellites and bipartite begomoviruses: Effects on infection and vector transmission. Pathogens, 10.","DOI":"10.3390\/pathogens10101244"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"5553","DOI":"10.3390\/v7102895","article-title":"Vector-Enabled Metagenomic (VEM) Surveys Using Whiteflies (Aleyrodidae) Reveal Novel Begomovirus Species in the New and OldWorlds","volume":"7","author":"Rosario","year":"2015","journal-title":"Viruses"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.3390\/v6031219","article-title":"Viral Metagenomics: Analysis of Begomoviruses by Illumina High-Throughput Sequencing","volume":"6","author":"Idris","year":"2014","journal-title":"Viruses"},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Guevara-Rivera, E.A., Rodr\u00edguez-Negrete, E.A., Ar\u00e9chiga-Carvajal, E.T., Leyva-L\u00f3pez, N.E., and M\u00e9ndez-Lozano, J. (2022). From Metagenomics to Discovery of New Viral Species: Galium Leaf Distortion Virus, a Monopartite Begomovirus Endemic in Mexico. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.843035"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"e9","DOI":"10.1093\/nar\/gky914","article-title":"A new full-length circular DNA sequencing method for viral-sized genomes reveals that RNAi transgenic plants provoke a shift in geminivirus populations in the field","volume":"47","author":"Mehta","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_23","unstructured":"FAO (2009). El Estado Mundial de la Agricultura y la Alimentaci\u00f3n. La Ganader\u00eda, a Examen, FAO."},{"key":"ref_24","unstructured":"(2025, June 06). SIAP-SAGARPA Servicio De Informaci\u00f3n Agroalimentaria Y Pesquera, M\u00e9xico. Available online: https:\/\/www.gob.mx\/siap\/acciones-y-programas\/produccion-agricola-33119."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1178","DOI":"10.1094\/PDIS.1999.83.12.1178A","article-title":"First Report of Tomato Yellow Leaf Curl Geminivirus in Yucat\u00e1n, M\u00e9xico","volume":"83","year":"1999","journal-title":"Plant Dis."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1094\/PDIS.1999.83.4.396B","article-title":"First Report of Chino del Tomate and Pepper Hausteco Geminivurses in Greenhouse-Grown Tomato in Sonora, Mexico","volume":"83","author":"Idris","year":"1999","journal-title":"Plant Dis."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1094\/PDIS.2003.87.11.1397A","article-title":"First Report of a Geminivirus Associated with Leaf Curl in Baja California Peninsula Tomato Fields","volume":"87","year":"2003","journal-title":"Plant Dis."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1094\/Phyto-83-514","article-title":"Inoculation of Peppers with infectious Clones of a new Geminivirus by a Biolistic Procedure","volume":"83","year":"1993","journal-title":"Phytopathology"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1094\/PDIS.1998.82.5.592B","article-title":"First Report of Tomato Mottle Geminivirus Infecting Tomatoes in Yucatan, Mexico","volume":"82","author":"Gilbertson","year":"1998","journal-title":"Plant Dis."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1094\/PD-90-0973B","article-title":"A New Strain of Tomato chino La Paz virus Associated with a Leaf Curl Disease of Tomato in Baja California Sur, Mexico","volume":"90","author":"Brown","year":"2006","journal-title":"Plant Dis."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1094\/PD-90-1116A","article-title":"First Report of Tomato severe leaf curl virus in M\u00e9xico","volume":"90","year":"2006","journal-title":"Plant Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1094\/PDIS-91-11-1513B","article-title":"First Report of Tomato golden mottle virus on Lycopersicon esculentum and Solanum rostratum in Mexico","volume":"91","year":"2007","journal-title":"Plant Dis."},{"key":"ref_33","first-page":"11","article-title":"A rapid DNA isolation procedure for small quantities of fresh leaf tissue","volume":"19","author":"Doyle","year":"1987","journal-title":"Phytochem. Bull."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1186\/1743-422X-7-275","article-title":"Analysis of a new strain of Euphorbia mosaic virus with distinct replication specificity unveils a lineage of begomoviruses with short Rep sequences in the DNA-B intergenic region","volume":"7","year":"2010","journal-title":"Virol. J."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1016\/j.jviromet.2003.11.015","article-title":"A simple method for cloning the complete begomovirus genome using the bacteriophage 29 DNA polymerase","volume":"116","author":"Albuquerque","year":"2004","journal-title":"J. Virol. Methods"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1023\/A:1006496308160","article-title":"pGreen: A versatile and flexible binary Ti vector for Agrobacterium-mediated plant transformation","volume":"42","author":"Hellens","year":"2000","journal-title":"Plant Mol. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"310","DOI":"10.5423\/PPJ.NT.03.2014.0025","article-title":"A Rapid and Efficient Method for Construction of an Infectious Clone of Tomato yellow leaf curl virus","volume":"30","author":"Bang","year":"2014","journal-title":"Plant Pathol. J."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"1673","DOI":"10.1038\/s41596-020-0301-0","article-title":"Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq","volume":"15","author":"Mehta","year":"2020","journal-title":"Nat. Protoc."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise alignment for nucleotide sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"Gigascience"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"2678","DOI":"10.1093\/bioinformatics\/bts503","article-title":"Qualimap: Evaluating next-generation sequencing alignment data","volume":"28","author":"Okonechnikov","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and applications. BMC Bioinform., 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: Multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1006\/viro.1994.1458","article-title":"Geminivirus Replication Origins Have a Group-Specific Organization of Iterative Elements: A Model for Replication","volume":"203","year":"1994","journal-title":"Virology"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1007\/s007050170072","article-title":"An iteron-related domain is associated to Motif 1 in the replication proteins of geminiviruses: Identification of potential interacting amino acid-base pairs by a comparative approach","volume":"146","year":"2001","journal-title":"Arch. Virol."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"2283","DOI":"10.1007\/s00705-014-2073-8","article-title":"A novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages","volume":"159","year":"2014","journal-title":"Arch. Virol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1111\/ppa.12270","article-title":"Arabidopsisthaliana, an experimental host for tomato yellow leaf curl disease-associated begomoviruses by agroinoculation and whitefly transmission","volume":"64","author":"Hogenhout","year":"2015","journal-title":"Plant Pathol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.jviromet.2018.03.002","article-title":"Lanai: A small, fast growing tomato variety is an excellent model system for studying geminiviruses","volume":"256","author":"Rajabu","year":"2018","journal-title":"J. Virol. Methods"},{"key":"ref_50","unstructured":"Mehta, D., Hirsch-Hoffmann, M., Patrignani, A., Gruissem, W., and Vanderschuren, H. (2017). CIDER-Seq: Unbiased virus enrichment and single-read, full length genome sequencing. bioRxiv, 168724."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"777","DOI":"10.1038\/nrmicro3117","article-title":"Geminiviruses: Masters at redirecting and reprogramming plant processes","volume":"11","author":"Bejarano","year":"2013","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1835","DOI":"10.1007\/s00705-012-1358-z","article-title":"A new strain of tomato severe leaf curl virus and a unique variant of tomato yellow leaf curl virus from Mexico","volume":"157","year":"2012","journal-title":"Arch. Virol."},{"key":"ref_53","first-page":"1","article-title":"A new full-length virus genome sequencing method reveals that antiviral RNAi changes geminivirus populations in field-grown cassava","volume":"47","author":"Mehta","year":"2018","journal-title":"bioRxiv"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1007\/s00705-010-0674-4","article-title":"DNA-binding specificity determinants of replication proteins encoded by eukaryotic ssDNA viruses are adjacent to widely separated RCR conserved motifs","volume":"155","year":"2010","journal-title":"Arch. Virol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.1128\/JVI.01474-08","article-title":"RNA silencing against geminivirus: Complementary action of posttranscriptional gene silencing and transcriptional gene silencing in host recovery","volume":"83","year":"2009","journal-title":"J. Virol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"5397","DOI":"10.1128\/JVI.00234-13","article-title":"Characterization of a New World Monopartite Begomovirus Causing Leaf Curl Disease of Tomato in Ecuador and Peru Reveals a New Direction in Geminivirus Evolution","volume":"87","author":"Melgarejo","year":"2013","journal-title":"J. Virol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2263","DOI":"10.1007\/s00705-011-1093-x","article-title":"Tomato chlorotic leaf distortion virus, a new bipartite begomovirus infecting Solanum lycopersicum and Capsicum chinense in Venezuela","volume":"156","author":"Zambrano","year":"2011","journal-title":"Arch. Virol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1146\/annurev-virology-092818-015536","article-title":"Life on the Edge: Geminiviruses at the Interface Between Crops and Wild Plant Hosts","volume":"6","author":"Zerbini","year":"2019","journal-title":"Annu. Rev. Virol."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1111\/j.1364-3703.2011.00734.x","article-title":"Facilitative and antagonistic interactions between plant viruses in mixed infections","volume":"13","author":"Syller","year":"2012","journal-title":"Mol. Plant Pathol."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1094\/PHYTO.2003.93.3.270","article-title":"Interactions Between Geminiviruses in a Naturally Occurring Mixture: Pepper huasteco virus and Pepper golden mosaic virus","volume":"93","author":"Fauquet","year":"2003","journal-title":"Phytopathology"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1186\/1743-422X-8-104","article-title":"Geminivirus mixed infection on pepper plants: Synergistic interaction between PHYVV and PepGMV","volume":"8","year":"2011","journal-title":"Virol. J."},{"key":"ref_62","first-page":"155","article-title":"Detection of Mixed Infections Caused by Begomovirus and Curtovirus in Chili pepper for drying plants in San Luis Potosi, Mexico Detecci\u00f3n de Infecciones Mixtas Causadas por Begomovirus y Curtovirus en Plantas de Chile para Secado en San Luis Potos\u00ed, M\u00e9xic","volume":"30","author":"Torres","year":"2012","journal-title":"Rev. Mex. Fitopatol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"2132","DOI":"10.1105\/tpc.20.00099","article-title":"The EccDNA replicon: A heritable, extranuclear vehicle that enables gene amplification and glyphosate resistance in amaranthus palmeri","volume":"32","author":"Molin","year":"2020","journal-title":"Plant Cell"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1094\/PD-89-0341A","article-title":"A New Begomovirus Causes Tomato Leaf Curl Disease in Baja California Sur, Mexico","volume":"89","year":"2005","journal-title":"Plant Dis."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Moreno-F\u00e9lix, M.L., Rodr\u00edguez-Negrete, E.A., Camacho-Beltr\u00e1n, E., Leyva-L\u00f3pez, N.E., Mel\u00e9ndrez-Boj\u00f3rquez, N., and M\u00e9ndez-Lozano, J. (2018). A new isolate of Pepper huasteco yellow vein virus (PHYVV) breaks geminivirus tolerance in tomato (Solanum lycopersicum) commercial lines. Acta Hortic., 35\u201344.","DOI":"10.17660\/ActaHortic.2018.1207.4"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1111\/aab.12329","article-title":"The ever increasing diversity of begomoviruses infecting non-cultivated hosts: New species from Sida spp. and Leonurus sibiricus, plus two New World alphasatellites","volume":"170","author":"Ferro","year":"2017","journal-title":"Ann. Appl. Biol."},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Cant\u00fa-Iris, M., Pastor-Palacios, G., Mauricio-Castillo, J.A., Ba\u00f1uelos-Hern\u00e1ndez, B., Avalos-Calleros, J.A., Ju\u00e1rez-Reyes, A., Rivera-Bustamante, R., and Arg\u00fcello-Astorga, G.R. (2019). Analysis of a new begomovirus unveils a composite element conserved in the CP gene promoters of several Geminiviridae genera: Clues to comprehend the complex regulation of late genes. PLoS ONE, 14.","DOI":"10.1371\/journal.pone.0210485"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"99","DOI":"10.1038\/nrmicro2491","article-title":"The good viruses: Viral mutualistic symbioses","volume":"9","author":"Roossinck","year":"2011","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1146\/annurev-virology-110615-042323","article-title":"Symbiosis: Viruses as Intimate Partners","volume":"4","author":"Roossinck","year":"2017","journal-title":"Annu. Rev. Virol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1094\/PHYTO-97-0051","article-title":"Symptom Remission and Specific Resistance of Pepper Plants After Infection by Pepper golden mosaic virus","volume":"97","year":"2007","journal-title":"Phytopatology"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1094\/MPMI-06-10-0126","article-title":"Characterization of Geminivirus resistance in an accession of Capsicum chinense Jacq","volume":"24","year":"2011","journal-title":"Mol. Plant Microbe. Interact."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"737","DOI":"10.1007\/s00705-017-3662-0","article-title":"Characterization of tomato leaf curl purple vein virus, a new monopartite New World begomovirus infecting tomato in Northeast Brazil","volume":"163","author":"Macedo","year":"2018","journal-title":"Arch. Virol."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Romay, G., Geraud-Pouey, F., Chirinos, D., Mahillon, M., Gillis, A., Mahillon, J., and Bragard, C. (2019). Tomato Twisted Leaf Virus: A Novel Indigenous New World Monopartite Begomovirus Infecting Tomato in Venezuela. Viruses, 11.","DOI":"10.3390\/v11040327"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1007\/s007050170067","article-title":"Complementation of bipartite begomovirus movement functions by topocuviruses and curtoviruses Brief Report","volume":"146","author":"Briddon","year":"2001","journal-title":"Arch. Virol."},{"key":"ref_75","doi-asserted-by":"crossref","unstructured":"Zhao, L., Che, X., Wang, Z., Zhou, X., and Xie, Y. (2022). Functional Characterization of Replication-Associated Proteins Encoded by Alphasatellites Identified in Yunnan Province, China. Viruses, 14.","DOI":"10.3390\/v14020222"},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1094\/PDIS.2004.88.2.221A","article-title":"Pepper golden mosaic virus Affecting Tomato Crops in the Baja California Peninsula, Mexico","volume":"88","year":"2004","journal-title":"Plant Dis."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1146\/annurev.phyto.43.040204.135939","article-title":"Exploiting Chinks in the Plant\u2019s Armor: Evolution and Emergence of Geminiviruses","volume":"43","author":"Rojas","year":"2005","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1266","DOI":"10.1094\/PDIS-06-10-0444","article-title":"First Report of Tomato yellow leaf curl virus Co-infecting Pepper with Tomato chino La Paz virus in Baja California Sur, Mexico","volume":"94","author":"Poghosyan","year":"2010","journal-title":"Plant Dis."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.jviromet.2006.07.017","article-title":"Methods for effective real-time RT-PCR analysis of virus-induced gene silencing","volume":"138","author":"Rotenberg","year":"2006","journal-title":"J. Virol. 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