Revision of Begomovirus taxonomy based on pairwise sequence comparisons

dc.creatorJUDITH K. BROWN
dc.creatorJESUS NAVAS CASTILLO
dc.creatorENRIQUE MORIONES
dc.creatorROBERTO RAMOS SOBRINHO
dc.creatorJOSE C. F. SILVA
dc.creatorELVIRA FIALLO OLIVE
dc.creatorROB W. BRIDDON
dc.creatorCECILIA HERNANDEZ ZEPEDA
dc.creatorAli Idris
dc.creatorV. G. MALATHI
dc.creatorRAFAEL FRANCISCO RIVERA BUSTAMANTE
dc.creatorSHIGENORI UEDA
dc.creatorArvind Varsani
dc.date2015
dc.date.accessioned2023-07-21T19:17:45Z
dc.date.available2023-07-21T19:17:45Z
dc.identifierhttp://cicy.repositorioinstitucional.mx/jspui/handle/1003/1073
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/7736643
dc.descriptionViruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.
dc.formatapplication/pdf
dc.languageeng
dc.relationinfo:eu-repo/semantics/datasetDOI/DOI: 10.1007/s00705-015-2398-y
dc.relationcitation:Brown, J. K., Zerbini, F. M., Navas-Castillo, J., Moriones, E., Ramos-Sobrinho, R., Silva, J. C., ... & Malathi, V. G. (2015). Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Archives of Virology, 160(6), 1593-1619.
dc.rightsinfo:eu-repo/semantics/openAccess
dc.rightshttp://creativecommons.org/licenses/by-nc-nd/4.0
dc.sourceArchives of Virology, 160(6), 1593-1619, 2015
dc.subjectinfo:eu-repo/classification/Autores/BEGOMOVIRUS
dc.subjectinfo:eu-repo/classification/Autores/GENOME, VIRAL
dc.subjectinfo:eu-repo/classification/Autores/PHYLOGENY
dc.subjectinfo:eu-repo/classification/Autores/PLANT DISEASES
dc.subjectinfo:eu-repo/classification/Autores/PLANTS
dc.subjectinfo:eu-repo/classification/Autores/SEQUENCE ALIGNMENT
dc.subjectinfo:eu-repo/classification/cti/2
dc.subjectinfo:eu-repo/classification/cti/2
dc.titleRevision of Begomovirus taxonomy based on pairwise sequence comparisons
dc.typeinfo:eu-repo/semantics/article
dc.typeinfo:eu-repo/semantics/publishedVersion


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