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A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants

The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ 85287, USA
School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
Desert Botanical Garden, Phoenix, AZ 85008, USA
Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
Center for Research in Engineering, Science and Technology, Paradise Valley High School, 3950 E Bell Rd, Phoenix, AZ 85032, USA
División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., Camino a la Presa de San José 2055, Lomas 4ta Secc, San Luis Potosi 78216, S.L.P., Mexico
Departamento de BotânicaPrograma de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91501970, Brazil
School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and UA Cancer Center, University of Arizona, Tucson, AZ 85721, USA
International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol Station, Beqa’a, Zahle, Lebanon
CIRAD, BGPI, 34398 Montpellier, France
BGPI, INRAE, CIRAD, SupAgro, Univ Montpellier, 34398 Montpellier, France
CIRAD, UMR PVBMT, F-97410 St. Pierre, La Réunion, France
Embrapa Recursos Genéticos e Biotecnologia, Brasília, CEP 70770-917, Brazil
Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7925, South Africa
Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA
Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town 7925, South Africa
Author to whom correspondence should be addressed.
Viruses 2020, 12(4), 398;
Received: 15 January 2020 / Revised: 29 March 2020 / Accepted: 31 March 2020 / Published: 3 April 2020
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
Cactaceae comprise a diverse and iconic group of flowering plants which are almost exclusively indigenous to the New World. The wide variety of growth forms found amongst the cacti have led to the trafficking of many species throughout the world as ornamentals. Despite the evolution and physiological properties of these plants having been extensively studied, little research has focused on cactus-associated viral communities. While only single-stranded RNA viruses had ever been reported in cacti, here we report the discovery of cactus-infecting single-stranded DNA viruses. These viruses all apparently belong to a single divergent species of the family Geminiviridae and have been tentatively named Opuntia virus 1 (OpV1). A total of 79 apparently complete OpV1 genomes were recovered from 31 different cactus plants (belonging to 20 different cactus species from both the Cactoideae and Opuntioideae clades) and from nine cactus-feeding cochineal insects (Dactylopius sp.) sampled in the USA and Mexico. These 79 OpV1 genomes all share > 78.4% nucleotide identity with one another and < 64.9% identity with previously characterized geminiviruses. Collectively, the OpV1 genomes display evidence of frequent recombination, with some genomes displaying up to five recombinant regions. In one case, recombinant regions span ~40% of the genome. We demonstrate that an infectious clone of an OpV1 genome can replicate in Nicotiana benthamiana and Opuntia microdasys. In addition to expanding the inventory of viruses that are known to infect cacti, the OpV1 group is so distantly related to other known geminiviruses that it likely represents a new geminivirus genus. It remains to be determined whether, like its cactus hosts, its geographical distribution spans the globe. View Full-Text
Keywords: geminivirus; Cactoideae; Opuntioideae; ssDNA virus; cochineal insects geminivirus; Cactoideae; Opuntioideae; ssDNA virus; cochineal insects
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Fontenele, R.S.; Salywon, A.M.; Majure, L.C.; Cobb, I.N.; Bhaskara, A.; Avalos-Calleros, J.A.; Argüello-Astorga, G.R.; Schmidlin, K.; Khalifeh, A.; Smith, K.; Schreck, J.; Lund, M.C.; Köhler, M.; Wojciechowski, M.F.; Hodgson, W.C.; Puente-Martinez, R.; Van Doorslaer, K.; Kumari, S.; Vernière, C.; Filloux, D.; Roumagnac, P.; Lefeuvre, P.; Ribeiro, S.G.; Kraberger, S.; Martin, D.P.; Varsani, A. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants. Viruses 2020, 12, 398.

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