Revision of Begomovirus taxonomy based on pairwise sequence comparisons
AuthorsBrown, Judith K.
Zerbini, F. Murilo
Silva, José C. F.
Briddon, Rob W.
Malathi, V. G.
Martin, Darren P.
KAUST DepartmentDesert Agriculture Initiative
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AbstractViruses 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.
SponsorsThe analysis described in this manuscript was part of the taxonomic proposal 2013.015a,bP, approved by the Executive Committee of the ICTV in July 2013 and ratified in March 2014. JKB and FMZ are past and current chairs, respectively, of the Geminiviridae Study Group of the ICTV. JNC, EM, RWB, CHZ, AI, VGM, DPM, RRB, SU and AV were members of the Geminiviridae SG during 2012-2014, when the work was performed. JNC and EM are members of the Research Group AGR-214, partially funded by Consejeria de Economia, Innovacion y Ciencia, Junta de Andalucia, Spain, cofinanced by FEDER-FSE. DPM and AV are supported by the National Research Foundation of South Africa.
JournalArchives of Virology