title: Revision of Begomovirus taxonomy based on pairwise sequence comparisons.
abstract: Viruses 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.
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA, jbrown@ag.arizona.edu.
authors.forename: Judith K
authors.initials: JK
authors.lastname: Brown
authors.forename: F Murilo
authors.initials: FM
authors.lastname: Zerbini
authors.forename: Jesús
authors.initials: J
authors.lastname: Navas-Castillo
authors.forename: Enrique
authors.initials: E
authors.lastname: Moriones
authors.forename: Roberto
authors.initials: R
authors.lastname: Ramos-Sobrinho
authors.forename: José C F
authors.initials: JC
authors.lastname: Silva
authors.forename: Elvira
authors.initials: E
authors.lastname: Fiallo-Olivé
authors.forename: Rob W
authors.initials: RW
authors.lastname: Briddon
authors.forename: Cecilia
authors.initials: C
authors.lastname: Hernández-Zepeda
authors.forename: Ali
authors.initials: A
authors.lastname: Idris
authors.forename: V G
authors.initials: VG
authors.lastname: Malathi
authors.forename: Darren P
authors.initials: DP
authors.lastname: Martin
authors.forename: Rafael
authors.initials: R
authors.lastname: Rivera-Bustamante
authors.forename: Shigenori
authors.initials: S
authors.lastname: Ueda
authors.forename: Arvind
authors.initials: A
authors.lastname: Varsani
mesh_terms: D053839:Begomovirus / Q000145:classification* / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D010944:Plants / Q000821:virology; D016415:Sequence Alignment