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Revision of Begomovirus taxonomy based on pairwise sequence comparisons
Judith K Brown1, F Murilo Zerbini, Jesús Navas-Castillo
1School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA, jbrown@ag.arizona.edu.
Archives of Virology
|April 21, 2015
Summary
Revised guidelines for classifying begomoviruses (family Geminiviridae) are proposed. New thresholds for species and strain demarcation, based on genome-wide pairwise identities, improve begomovirus taxonomy and nomenclature.
Area of Science:
- Plant virology
- Molecular biology
- Bioinformatics
Background:
- Begomoviruses (family Geminiviridae) are significant crop pathogens globally.
- Increased availability of begomovirus genome sequences necessitates updated taxonomic criteria.
- Existing species demarcation methods have proven inadequate for accurate classification.
Purpose of the Study:
- To propose revised guidelines for begomovirus classification and nomenclature.
- To establish operationally useful species demarcation criteria.
- To address shortcomings in current virus classification mechanisms.
Main Methods:
- Analysis of 3,123 full-length begomovirus genome sequences (as of December 2012).
- Utilized the Sequence Demarcation Tool for pairwise sequence alignments and identity calculations.
- Considered genus-level biological characteristics alongside sequence data.
Main Results:
- Proposed genome-wide pairwise identity thresholds: 91% for species and 94% for strains.
- The new guidelines align with recent recommendations for related genera (Mastrevirus, Curtovirus).
- Outlined procedures for resolving classification conflicts near demarcation thresholds.
Conclusions:
- Revised guidelines enhance the accuracy and consistency of begomovirus classification.
- The proposed thresholds provide a standardized approach to defining begomovirus species and strains.
- Improved taxonomy facilitates better understanding and management of begomovirus diseases.
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