NDLI: Revision of Begomovirus taxonomy based on pairwise sequence comparisons

Content Provider	Springer Nature Link
Author	Brown, Judith K. Zerbini, F. Murilo Navas Castillo, Jesús Moriones, Enrique Ramos Sobrinho, Roberto Silva, José C. F. Fiallo Olivé, Elvira Briddon, Rob W. Hernández Zepeda, Cecilia Idris, Ali Malathi, V. G. Martin, Darren P. Rivera Bustamante, Rafael Ueda, Shigeri Varsani, Arvind
Copyright Year	2015
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.
Starting Page	1593
Ending Page	1619
Page Count	27
File Format	PDF
ISSN	03048608
Journal	Archives of Virology
Volume Number	160
Issue Number	6
e-ISSN	14328798
Language	English
Publisher	Springer Vienna
Publisher Date	2015-04-18
Publisher Place	Vienna
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Geminiviridae Nomenclature Sequence Demarcation Tool Single-stranded DNA virus Species demarcation Taxonomy Whitefly-transmitted viruses Virology Medical Microbiology Infectious Diseases
Content Type	Text
Resource Type	Article
Subject	Virology Medicine

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