Revision of Begomovirus taxonomy based on pairwise sequence comparisons

Judith K Brown, F. Murilo Zerbini, Jesús Navas-Castillo, Enrique Moriones, Roberto Ramos-Sobrinho, José C F Silva, Elvira Fiallo-Olivé, Rob W. Briddon, Cecilia Hernández-Zepeda, Ali Idris, V. G. Malathi, Darren P. Martin, Rafael Rivera-Bustamante, Shigenori Ueda, Arvind Varsani

Research output: Contribution to journalArticle

292 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1593-1619
Number of pages27
JournalArchives of Virology
Volume160
Issue number6
DOIs
StatePublished - Jun 1 2015

    Fingerprint

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Brown, J. K., Zerbini, F. M., Navas-Castillo, J., Moriones, E., Ramos-Sobrinho, R., Silva, J. C. F., Fiallo-Olivé, E., Briddon, R. W., Hernández-Zepeda, C., Idris, A., Malathi, V. G., Martin, D. P., Rivera-Bustamante, R., Ueda, S., & Varsani, A. (2015). Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Archives of Virology, 160(6), 1593-1619. https://doi.org/10.1007/s00705-015-2398-y