title: Molecular characterization and prevalence of two capulaviruses: Alfalfa leaf curl virus from France and Euphorbia caput-medusae latent virus from South Africa.
abstract: Little is known about the prevalence, diversity, evolutionary processes, genomic structures and population dynamics of viruses in the divergent geminivirus lineage known as the capulaviruses. We determined and analyzed full genome sequences of 13 Euphorbia caput-medusae latent virus (EcmLV) and 26 Alfalfa leaf curl virus (ALCV) isolates, and partial genome sequences of 23 EcmLV and 37 ALCV isolates. While EcmLV was asymptomatic in uncultivated southern African Euphorbia caput-medusae, severe alfalfa disease symptoms were associated with ALCV in southern France. The prevalence of both viruses exceeded 10% in their respective hosts. Besides using patterns of detectable negative selection to identify ORFs that are probably functionally expressed, we show that ALCV and EcmLV both display evidence of inter-species recombination and biologically functional genomic secondary structures. Finally, we show that whereas the EcmLV populations likely experience restricted geographical dispersion, ALCV is probably freely moving across the French Mediterranean region.
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
authors.forename: Pauline
authors.initials: P
authors.lastname: Bernardo
authors.affiliation: Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa.
authors.forename: Brejnev
authors.initials: B
authors.lastname: Muhire
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France; INRA, UMR 1333, DGIMI, Montpellier, France; CNRS-IRD-UM1-UM2, UMR 5290, MIVEGEC, Avenue Agropolis, Montpellier, France.
authors.forename: Sarah
authors.initials: S
authors.lastname: François
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
authors.forename: Maëlle
authors.initials: M
authors.lastname: Deshoux
authors.affiliation: Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa.
authors.forename: Penelope
authors.initials: P
authors.lastname: Hartnady
authors.affiliation: School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
authors.forename: Kata
authors.initials: K
authors.lastname: Farkas
authors.affiliation: School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.
authors.forename: Simona
authors.initials: S
authors.lastname: Kraberger
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
authors.forename: Denis
authors.initials: D
authors.lastname: Filloux
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Fernandez
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
authors.forename: Serge
authors.initials: S
authors.lastname: Galzi
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Ferdinand
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France.
authors.forename: Martine
authors.initials: M
authors.lastname: Granier
authors.affiliation: INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France; Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France.
authors.forename: Armelle
authors.initials: A
authors.lastname: Marais
authors.affiliation: Unidad de Sanidad Vegetal, Centro de Investigacion y Tecnologıa Agroalimentaria de Aragon (CITA), Av. Montañana 930, 50059 Zaragoza, Spain.
authors.forename: Pablo
authors.initials: P
authors.lastname: Monge Blasco
authors.affiliation: INRA, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France; Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon Cedex, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Candresse
authors.affiliation: Unidad de Sanidad Vegetal, Centro de Investigacion y Tecnologıa Agroalimentaria de Aragon (CITA), Av. Montañana 930, 50059 Zaragoza, Spain; Unidad de Sanidad Vegetal, Instituto Agroalimentario de Aragón IA2 (CITA - Universidad de Zaragoza), Av. Montañana 930, 50059 Zaragoza, Spain.
authors.forename: Fernando
authors.initials: F
authors.lastname: Escriu
authors.affiliation: School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, USA; Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, South Africa.
authors.forename: Arvind
authors.initials: A
authors.lastname: Varsani
authors.affiliation: South African National Bioinformatics Institute, MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Cape Town, South Africa.
authors.forename: Gordon W
authors.initials: GW
authors.lastname: Harkins
authors.affiliation: Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa.
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.affiliation: CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, Montpellier Cedex-5, France. Electronic address: philippe.roumagnac@cirad.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Roumagnac
mesh_terms: D004279:DNA, Viral; D017753:Ecosystem; D028481:Euphorbia / Q000821:virology*; D005602:France; D017791:Geminiviridae / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000502:physiology; D016679:Genome, Viral; D000455:Medicago sativa / Q000821:virology*; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D013019:South Africa; D017735:Virus Latency
chemical_list: D004279:DNA, Viral
keywords: Alfalfa leaf curl virus; Euphorbia caput-medusae latent virus; France; Geminiviridae; Genome organization; Prevalence; Recombination; Secondary structure; South Africa; Spain