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1. New World Cactaceae Plants Harbor Diverse Geminiviruses

Author

Gerardo R. Argüello-Astorga, Arvind Varsani, Michael C. Lund, Simona Kraberger, Pierre Lefeuvre, Joshua Schreck, Denis Filloux, Anthony Khalifeh, Simone G. Ribeiro, Raul Puente-Martinez, Jesús Aarón Avalos-Calleros, Andrew M. Salywon, Safaa G. Kumari, Philippe Roumagnac, Kehinde A. Oyeniran, Kara Schmidlin, Rafaela S. Fontenele, Lucas C. Majure, Amulya Bhaskara, Wendy C. Hodgson, Martin F. Wojciechowski, Matias Köhler, Darren P. Martin, Kendal Smith, Koenraad Van Doorslaer, Christian Vernière, Ilaria N. Cobb, Arizona State University [Tempe] (ASU), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Desert Botanical Garden, Florida Museum of Natural History [Gainesville], University of Florida [Gainesville] (UF), University of British Columbia [Vancouver], University of Texas at Dallas [Richardson] (UT Dallas), School of Behavioral and Brain Sciences, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Laboratório de Estudos em Vegetação Campestre (LEVCamp), Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil, School of Animal and Comparative Biomedical Sciences, University of Arizona, Arizona Cancer Center, International Center for Agricultural Research in the Dry Areas (ICARDA), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), University of Cape Town, Institute of Infectious Diseases and Moleculare MedicineComputational Biolohy Group, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Embrapa Recursos Genéticos e Biotecnologia [Brasília], Structural Biology Research Unit, Department of Clinical Laboratory Sciences, The molecular work was supported by a start-up grant awarded to A.V. from Arizona State University, USA., RAFAELA S. FONTENELE, ARIZONA STATE UNIVERSITY, USA, ANDREW M. SALYWON, DESERT BOTANICAL GARDEN, USA, LUCAS C. MAJURE, UNIVERSITY OF FLORIDA, USA, ILARIA N. COBB, ARIZONA STATE UNIVERSITY, USA, AMULYA BHASKARA, ARIZONA STATE UNIVERSITY, USA, JESÚS A. AVALOS-CALLEROS, INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA, MEXICO, GERARDO R. ARGÜELLO-ASTORGA, INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA, MEXICO, KARA SCHMIDLIN, ARIZONA STATE UNIVERSITY, USA, ANTHONY KHALIFEH, ARIZONA STATE UNIVERSITY, USA, KENDAL SMITH, ARIZONA STATE UNIVERSITY, USA, JOSHUA SCHRECK, ARIZONA STATE UNIVERSITY, USA, MICHAEL C. LUND, ARIZONA STATE UNIVERSITY, USA, MATIAS KÖHLER, UFRGS, MARTIN F. WOJCIECHOWSKI, ARIZONA STATE UNIVERSITY, USA, WENDY C. HODGSON, DESERT BOTANICAL GARDEN, USA, RAUL PUENTE-MARTINEZ, DESERT BOTANICAL GARDEN, USA, KOENRAAD VAN DOORSLAER, UNIVERSITY OF ARIZONA, USA, SAFAA KUMARI, INTERNATIONAL CENTER FOR AGRICULTURAL RESEARCH IN THE DRY AREAS (ICARDA), LEBANON, KEHINDE A. OYENIRAN, UNIVERSITY OF CAPE TOWN, SOUTH AFRICA, CHRISTIAN VERNIÈRE, CIRAD, FRANCE, DENIS FILLOUX, CIRAD, FRANCE, PHILIPPE ROUMAGNAC, CIRAD, FRANCE, PIERRE LEFEUVRE, CIRAD, FRANCE, SIMONE DA GRACA RIBEIRO, Cenargen, SIMONA P. KRABERGER, ARIZONA STATE UNIVERSITY, USA, DARREN P. MARTIN, UNIVERSITY OF CAPE TOWN, SOUTH AFRICA, ARVIND VARSANI, ARIZONA STATE UNIVERSITY, USA., University of Britsh Columbia [Vancouver], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Human Biology, and Faculty of Health Sciences

Subjects
0106 biological sciences, 0301 basic medicine, Cactaceae, Phylogénie, [SDV]Life Sciences [q-bio], 01 natural sciences, Genome, Curtovirus, 2. Zero hunger, Diversity, biology, Phylogenetic tree, Opuntia, QR1-502, Infectious Diseases, Geminiviridae, Curly top, Cactus, Becurtovirus, food.ingredient, Pathologie végétale, Genome, Viral, Microbiology, Article, diversity, Hemiptera, 03 medical and health sciences, food, Virology, Animals, Virus classification, Géminivirus, Plant Diseases, H20 - Maladies des plantes, Virus des végétaux, biology.organism_classification, Recombination, recombination, Recombinaison, 030104 developmental biology, Evolutionary biology, 010606 plant biology & botany
Abstract

International audience; The family Cactaceae comprises a diverse group of typically succulent plants that are native to the American continent but have been introduced to nearly all other continents, predominantly for ornamental purposes. Despite their economic, cultural, and ecological importance, very little research has been conducted on the viral community that infects them. We previously identified a highly divergent geminivirus that is the first known to infect cacti. Recent research efforts in non-cultivated and asymptomatic plants have shown that the diversity of this viral family has been under-sampled. As a consequence, little is known about the effects and interactions of geminiviruses in many plants, such as cacti. With the objective to expand knowledge on the diversity of geminiviruses infecting cacti, we used previously acquired high-throughput sequencing results to search for viral sequences using BLASTx against a viral RefSeq protein database. We identified two additional sequences with similarity to geminiviruses, for which we designed abutting primers and recovered full-length genomes. From 42 cacti and five scale insects, we derived 42 complete genome sequences of a novel geminivirus species that we have tentatively named Opuntia virus 2 (OpV2) and 32 genomes of an Opuntia-infecting becurtovirus (which is a new strain of the spinach curly top Arizona virus species). Interspecies recombination analysis of the OpV2 group revealed several recombinant regions, in some cases spanning half of the genome. Phylogenetic analysis demonstrated that OpV2 is a novel geminivirus more closely related to viruses of the genus Curtovirus, which was further supported by the detection of three recombination events between curtoviruses and OpV2. Both OpV2 and Opuntia becurtoviruses were identified in mixed infections, which also included the previously characterized Opuntia virus 1. Viral quantification of the co-infected cactus plants compared with single infections did not show any clear trend in viral dynamics that might be associated with the mixed infections. Using experimental Rhizobium-mediated inoculations, we found that the initial accumulation of OpV2 is facilitated by co-infection with OpV1. This study shows that the diversity of geminiviruses that infect cacti is under-sampled and that cacti harbor diverse geminiviruses. The detection of the Opuntia becurtoviruses suggests spill-over events between viruses of cultivated species and native vegetation. The threat this poses to cacti needs to be further investigated.

Published
2021

2. Identification of the Begomoviruses Squash Leaf Curl Virus and Watermelon Chlorotic Stunt Virus in Various Plant Samples in North America

Author

Pierre Lefeuvre, Gerardo R. Argüello-Astorga, Arvind Varsani, Simone G. Ribeiro, Simona Kraberger, Lucas C. Majure, Philippe Roumagnac, Jesús Aarón Avalos-Calleros, Ilaria N. Cobb, Kara Schmidlin, Amulya Bhaskara, Andrew M. Salywon, Rafaela S. Fontenele, Darren P. Martin, Arizona State University [Tempe] (ASU), The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life sciences, University of Texas at Dallas [Richardson] (UT Dallas), School of Behavioral and Brain Sciences, University of Northern British Columbia [Prince George] (UNBC), Florida Museum of Natural History [Gainesville], University of Florida [Gainesville] (UF), Desert Botanical Garden, Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Embrapa Recursos Genéticos e Biotecnologia [Brasília], University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Structural Biology Research Unit [Cape Town], Department of Integrative Biomedical Sciences [Cape Town], University of Cape Town-University of Cape Town, The molecular work was supported by a start-up grant awarded to AV from Arizona State University, USA., RAFAELA S. FONTENELE, Arizona State University, USA, AMULYA BHASKARA, Arizona State University, USA, ILARIA N. COBB, Arizona State University, USA, LUCAS C. MAJURE, University of Florida, Gainesville, USA, ANDREW M. SALYWON, Desert Botanical Garden, USA, JESÚS A. AVALOS-CALLEROS, Instituto Potosino de Investigación Científica y Tecnológica, Mexico, GERARDO R. ARGÜELLO-ASTORGA, Instituto Potosino de Investigación Científica y Tecnológica, Mexico, KARA SCHMIDLIN, Arizona State University, USA, PHILIPPE ROUMAGNAC, CIRAD, UMR PHIM, France, SIMONE DA GRACA RIBEIRO, Cenargen, SIMONA KRABERGER, Arizona State University, USA, DARREN P. MARTIN, University of Cape Town, South Africa, PIERRE LEFEUVRE, CIRAD, UMR PVBMT, France, ARVIND VARSANI, Arizona State University, USA., Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], pseudo-recombination, Bemisia tabaci, 01 natural sciences, Plant Viruses, 2. Zero hunger, Recombination, Genetic, biology, Phylogenetic tree, food and beverages, Genomics, Plants, QR1-502, 3. Good health, Infectious Diseases, Phenotype, Geminiviridae, Begomovirus, Cucurbitaceae, Solanaceae, Whitefly, Genome, Viral, Microbiology, Virus, Article, 03 medical and health sciences, Pseudo-recombination, begomovirus, Virology, Botany, H20 - Maladies des plantes, Génome, Computational Biology, Virus des végétaux, Sequence Analysis, DNA, biology.organism_classification, Recombination, recombination, Recombinaison, 030104 developmental biology, Oleaceae, North America, 010606 plant biology & botany
Abstract

Geminiviruses are a group of plant-infecting viruses with single-stranded DNA genomes. Within this family, viruses in the genus Begomovirus are known to have a worldwide distribution causing a range of severe diseases in a multitude of dicotyledonous plant species. Begomoviruses are transmitted by the whitefly Bemisia tabaci, and their ssDNA genomes can be either monopartite or bipartite. As part of a viral survey, various plants including those in the families Alliaceae, Amaranthaceae, Apiaceae, Asteraceae, Brassicaceae, Cactaceae, Cucurbitaceae, Lamiaceae, Lauraceae, Malvaceae, Oleaceae and Solanaceae were sampled and screened for begomoviruses using both a high-throughput sequencing and a begomovirus-specific primer pair approach. Based on the sequences derived using these approaches, the full-length genome of various begomoviruses were amplified from plants using abutting primers. Squash leaf curl virus (SLCV) and watermelon chlorotic stunt virus (WCSV) were identified in Cactaceae (n = 25), Solanaceae (n = 7), Cucurbitaceae (n = 2) and Lamiaceae (n = 1) samples. WCSV is an Old World bipartite begomovirus that has only recently been discovered infecting watermelons in the Americas. Our discovery of WCSV in the USA is the first indication that it has reached this country and indicates that this virus might be widespread throughout North America. Phylogenetic analysis suggests WCSV was introduced to the New World twice. The detection of begomoviruses in cactus plants suggests possible spillover events from agricultural areas into native vegetation. Since WCSV and SLCV have previously been found in mixed infections, pseudo-recombination infection experiments were conducted. We demonstrate that WCSV DNA-B is successfully trans-replicated by SLCV DNA-A despite very low degree of similarity between the replication-associated iterative sequences present in their common region, an essential feature for binding of the replication associated protein. This study highlights the importance of viral surveys for the detection of spillover events into native vegetation, but also suggests the need for more surveillance of WCSV in the USA, as this virus is a serious threat to watermelon cultivation in the Middle East.

Published
2021

3. Unveiling Crucivirus Diversity by Mining Metagenomic Data

Author

Simona Kraberger, Alyssa A. Pratt, Jennifer M. Arnold, Anisha Dayaram, Kenneth M. Stedman, James V. Briskie, Amberlee Maluenda, François Enault, Maxime Bisseux, George W. Kasun, Simone G. Ribeiro, Peyman Zawar-Reza, Robyn White, Stephen A. Oswald, Viviane Ravet, David G. Ainley, Jon S. Harding, Ellis L. Torrance, Ignacio de la Higuera, Arvind Varsani, Helen R. Taylor, Joshua Schreck, Sharyn J. Goldstien, Jonathan Colombet, Christopher Gomez, Rafaela S. Fontenele, Daisy Stainton, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), IGNACIO DE LA HIGUERA, PORTLAND STATE UNIVERSITUY, USA, GEORGE W. KASUN, PORTLAND STATE UNIVERSITY, USA, ELLIS L. TORRANCE, PORTLAND STATE UNIVERSITY, USA, ALYSSA A. PRATT, PORTLAND STATE UNIVERSITY, USA, AMBERLEE MALUENDA, PORTLAND STATE UNIVERSITY, USA, JONATHAN COLOMBET, UNIVERSITÉ CLERMONT AUVERGNE, FRANCE, MAXIME BISSEUX, UNIVERSITÉ CLERMONT AUVERGNE, FRANCE, VIVIANE RAVET, UNIVERSITÉ CLERMONT AUVERGNE, FRANCE, ANISHA DAYARAM, CHARITÉ-UNIVERSITÄTSMEDIZIN, GERMANY, DAISY STAINTON, UNIVERSITY OF ARKANSAS SYSTEM, USA, SIMONA KRABERGER, ARIZONA STATE UNIVERSITY, USA, PEYMAN SAWAR-REZA, UNIVERSITY OF CANTERBURY, NEW ZEALAND, SHARYN GOLDSTIEN, UNIVERSITY OF CANTERBURY, NEW ZEALAND, JAMES V. BRISKIE, UNIVERSITY OF CANTERBURY, NEW ZEALAND, ROBYN WHITE, UNIVERSITY OF CANTERBURY, NEW ZEALAND, HELEN TAYLOR, UNIVERSITY OF OTAGO, NEW ZEALAND, CHRISTOPHER GOMEZ, KOBE UNIVERSITY, JAPAN, DAVID G. AINLEY, HT HARVEY AND AZZOCIATES, USA, JON S. HARDING, UNIVERSITY OF CANTERBURY, NEW ZEALAND, RAFAELA S. FONTENELE, ARIZONA STATE UNIVERSITY, USA, JOSHUA SCHRECK, ARIZONA STATE UNIVERSITY, USA, SIMONE DA GRACA RIBEIRO, Cenargen, STEPHEN A. OSWALD, PENNSYLVANIA STATE UNIVERSITY, USA, JENNIFER M. ARNOLD, PENNSYLVANIA STATE UNIVERSITY, USA, FRANÇOIS ENAULT, UNIVERSITÉ CLERMONT AUVERGNE, FRANCE, ARVIND VARSANI, ARIZONA STATE UNIVERSITY, USA, and KENNETH M. STEDMAN, PORTLAND STATE UNIVERSITY, USA.

Subjects
environmental virology, [SDV]Life Sciences [q-bio], viruses, Protein domain, Sequence assembly, Genome, Viral, Ecological and Evolutionary Science, Computational biology, Genetic recombination, Genome, Microbiology, crucivirus, 03 medical and health sciences, chemistry.chemical_compound, Tombusviridae, Virology, Data Mining, RNA Viruses, gene transfer, Gene transfer, Gene, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, virus evolution, 0303 health sciences, biology, 030306 microbiology, DNA Viruses, Crucivirus, RNA, Environmental virology, biology.organism_classification, Virus evolution, recombination, Recombination, QR1-502, CRESS-DNA viruses, chemistry, Evolutionary biology, Viral evolution, Horizontal gene transfer, Metagenome, Capsid Proteins, Metagenomics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], DNA, Research Article
Abstract

Viruses are the most abundant biological entities on Earth. In addition to their impact on animal and plant health, viruses have important roles in ecosystem dynamics as well as in the evolution of the biosphere. Circular Rep-encoding single-stranded (CRESS) DNA viruses are ubiquitous in nature, many are agriculturally important, and they appear to have multiple origins from prokaryotic plasmids. A subset of CRESS-DNA viruses, the cruciviruses, have homologues of capsid proteins encoded by RNA viruses. The genetic structure of cruciviruses attests to the transfer of capsid genes between disparate groups of viruses. However, the evolutionary history of cruciviruses is still unclear. By collecting and analyzing cruciviral sequence data, we provide a deeper insight into the evolutionary intricacies of cruciviruses. Our results reveal an unexpected diversity of this virus group, with frequent recombination as an important determinant of variability., The discovery of cruciviruses revealed the most explicit example of a common protein homologue between DNA and RNA viruses to date. Cruciviruses are a novel group of circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viruses that encode capsid proteins that are most closely related to those encoded by RNA viruses in the family Tombusviridae. The apparent chimeric nature of the two core proteins encoded by crucivirus genomes suggests horizontal gene transfer of capsid genes between DNA and RNA viruses. Here, we identified and characterized 451 new crucivirus genomes and 10 capsid-encoding circular genetic elements through de novo assembly and mining of metagenomic data. These genomes are highly diverse, as demonstrated by sequence comparisons and phylogenetic analysis of subsets of the protein sequences they encode. Most of the variation is reflected in the replication-associated protein (Rep) sequences, and much of the sequence diversity appears to be due to recombination. Our results suggest that recombination tends to occur more frequently among groups of cruciviruses with relatively similar capsid proteins and that the exchange of Rep protein domains between cruciviruses is rarer than intergenic recombination. Additionally, we suggest members of the stramenopiles/alveolates/Rhizaria supergroup as possible crucivirus hosts. Altogether, we provide a comprehensive and descriptive characterization of cruciviruses.

Published
2020

4. A Novel Divergent Geminivirus Identified in Asymptomatic New World Cactaceae Plants

Author

Anthony Khalifeh, Christian Vernière, Kendal Smith, Michael C. Lund, Simona Kraberger, Kara Schmidlin, Rafaela S. Fontenele, Amulya Bhaskara, Darren P. Martin, Ilaria N. Cobb, Andrew M. Salywon, Arvind Varsani, Raul Puente-Martinez, Simone G. Ribeiro, Koenraad Van Doorslaer, Gerardo R. Argüello-Astorga, Martin F. Wojciechowski, Denis Filloux, Lucas C. Majure, Safaa G. Kumari, Matias Köhler, Jesús Aarón Avalos-Calleros, Pierre Lefeuvre, Philippe Roumagnac, Joshua Schreck, Wendy C. Hodgson, Arizona State University [Tempe] (ASU), Desert Botanical Garden, University of Florida [Gainesville] (UF), University of Northern British Columbia [Prince George] (UNBC), Instituto Potosino de Investigacion Cientifica y Tecnologica (IPICYT), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), International Center for Agricultural Research in the Dry Areas [Jordanie] (ICARDA), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Embrapa Recursos Genéticos e Biotecnologia [Brasília], University of Cape Town, Arizona State University, USA, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), RAFAELA S. FONTENELE, ARIZONA STATE UNIVERSITY, USA, ANDREW M. SALYWON, DESERT BOTANICAL GARDEN, USA, LUCAS C. MAJURE, DESERT BOTANICAL GARDEN, USA, ILARIA N. COBB, ARIZONA STATE UNIVERSITY, USA, AMULYA BHASKARA, ARIZONA STATE UNIVERSITY, USA, JESÚS A. AVALOS-CALLEROS, INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA, MEXICO, GERARDO R. ARGÜLLO-ASTORGA, INSTITUTO POTOSINO DE INVESTIGACIÓN CIENTÍFICA Y TECNOLÓGICA, MEXICO, KARA SCHMIDLIN, ARIZONA STATE UNIVERSITY, USA, ANTHONY KHALIFEH, ARIZONA STATE UNIVERSITY, USA, KENDAL SMITH, ARIZONA STATE UNIVERSITY, USA, JOSHUA SCHRECK, ARIZONA STATE UNIVERSITY, USA, MICHAEL C. LUND, ARIZONA STATE UNIVERSITY, USA, MATIAS KÖHLER, UFRGS, MARTIN F. WOJCIECHOWSKI, ARIZONA STATE UNIVERSITY, USA, WENDY C. HODGSON, DESERT BOTANICAL GARDEN, USA, RAUL PUENT-MARTINEZ, DESERT BOTANICAL GARDEN, USA, KOENRAAD VAN DOORSLAER, UNIVERSITY OF ARIZONA, USA, SAFAA KUMARI, ICARDA, CHRISTIAN VERNIÈRE, CIRAD, FRANCE, DENIS FILLOUX, CIRAD, FRANCE, PHILIPPE ROUMAGNAC, CIRAD, FRANCE, PIERRE LEFEUVRE, CIRAD, FRANCE, SIMONE DA GRACA RIBEIRO, Cenargen, SIMONA KRABERGER, ARIZONA STATE UNIVERSITY, USA, DARREN P. MARTIN, UNIVERSITY OF CAPE TOWNM, SOUTH AFRICA, and ARVIND VARSANI, ARIZONA STATE UNIVERSITY, USA.

Subjects
Cactaceae, 0106 biological sciences, 0301 basic medicine, Opuntia microdasys, [SDV]Life Sciences [q-bio], lcsh:QR1-502, SsDNA virus, 01 natural sciences, Genome, lcsh:Microbiology, ssDNA viruses [EN], Genus, Opuntioideae, Clade, Phylogeny, Cactoideae, Recombination, Genetic, Dactylopius, Geminiviridae, Infectious Diseases, ssDNA virus, Cactus, Geminivirus, cochineal insects, geminivirus, Genome, Viral, Biology, Article, Hemiptera, 03 medical and health sciences, Virology, Tobacco, Animals, Cochineal insects, Mexico, Géminivirus, Plant Diseases, H20 - Maladies des plantes, biology.organism_classification, United States, 030104 developmental biology, Evolutionary biology, 010606 plant biology & botany
Abstract

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 &gt, 78.4% nucleotide identity with one another and &lt, 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.

Published
2020

5. Single Stranded DNA Viruses Associated with Capybara Faeces Sampled in Brazil

Author

Kara Schmidlin, Simone G. Ribeiro, Arvind Varsani, Rafaela S. Fontenele, Natalia S. Lamas, Cristiano Lacorte, RAFAELA S. FONTENELE, ARIZONA STATE UNIVERSITY, USA, CRISTIANO CASTRO LACORTE, Cenargen, NATALIA S. LAMAS, KARA SCHMIDLIN, ARIZONA STATE UNIVERSITY, USA, ARVIND VARSANI, ARIZONA STATE UNIVERSITY, USA, and SIMONE DA GRACA RIBEIRO, Cenargen.

Subjects
Viral metagenomics, food.ingredient, Microviridae, lcsh:QR1-502, Zoology, Smacoviridae, DNA, Single-Stranded, Hydrochoerus hydrochaeris, Rodentia, Genome, Viral, Biology, Genome, lcsh:Microbiology, Article, CRESS DNA virus, chemistry.chemical_compound, Feces, food, Virology, Genomoviridae, Animals, Bacteriophages, Phylogeny, Circoviridae, Herbivore, DNA Viruses, Sequence Analysis, DNA, biology.organism_classification, Infectious Diseases, Cyclovirus, chemistry, DNA, Viral, Metagenomics, DNA, Brazil
Abstract

Capybaras (Hydrochoerus hydrochaeris), the world&rsquo, s largest rodents, are distributed throughout South America. These wild herbivores are commonly found near water bodies and are well adapted to rural and urban areas. There is limited information on the viruses circulating through capybaras. This study aimed to expand the knowledge on the viral diversity associated with capybaras by sampling their faeces. Using a viral metagenomics approach, we identified diverse single-stranded DNA viruses in the capybara faeces sampled in the Distrito Federal, Brazil. A total of 148 complete genomes of viruses in the Microviridae family were identified. In addition, 14 genomoviruses (family Genomoviridae), a novel cyclovirus (family Circoviridae), and a smacovirus (family Smacoviridae) were identified. Also, 37 diverse viruses that cannot be assigned to known families and more broadly referred to as unclassified circular replication associated protein encoding single-stranded (CRESS) DNA viruses were identified. This study provides a snapshot of the viral diversity associated with capybaras that may be infectious to these animals or associated with their microbiota or diet.

Published
2019

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