Revision of Begomovirus taxonomy based on pairwise sequence comparisons
Judith K. Brown,F. Murilo Zerbini,Jesús Navas-Castillo,Enrique Moriones,Roberto Ramos-Sobrinho,José Cleydson F. Silva,Elvira Fiallo-Olivé,Rob W. Briddon,Cecilia Hernández-Zepeda,Ali M. Idris,V. G. Malathi,Darren P. Martin,Rafael F. Rivera-Bustamante,Shigenori Ueda,Arvind Varsani +14 more
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TLDR
Revised guidelines for the classification and nomenclature of begomoviruses are proposed and genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomviruses belonging to different species and strains, respectively.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.read more
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Analysis of watermelon chlorotic stunt virus and tomato leaf curl Palampur virus mixed and pseudo-recombination infections.
Maryam Esmaeili,Jahangir Heydarnejad,Hossain Massumi,Arvind Varsani,Arvind Varsani,Arvind Varsani +5 more
TL;DR: Co-infection using agroinfectious clones of WmCSV and ToLCPMV caused severe symptoms in watermelon and zucchini in comparison to symptoms observed from individual infections, demonstrating that replication-associated protein of DNA-A of each virus is able to bind to cis elements of the DNA-B molecules of another virus.
Journal ArticleDOI
Identification of a distinct strain of Cotton leaf curl Gezira virus infecting tomato in Oman
Journal ArticleDOI
Characterization, phylogeny and recombination analysis of Pedilanthus leaf curl virus -Petunia isolate and its associated betasatellite
TL;DR: Phylogenetic analysis suggests that PeLCV originated from Pakistan and later spread to India, and is identified as an emerging broad host range Begomovirus that is resident in Pakistan and, more recently, has alsospread to India.
Journal ArticleDOI
First Association of Pedilanthus leaf curl virus, Papaya leaf curl virus, Cotton leaf curl Kokhran virus, and Papaya leaf curl betasatellite with Symptomatic Chilli Pepper in Pakistan
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Croton golden mosaic virus: a new bipartite begomovirus isolated from Croton hirtus in Colombia
TL;DR: Phylogenetic analysis revealed that CroGMV segregates into a single clade and has some relationship with viruses from Central America and the Caribbean and is the first Croton-infecting bipartite begomovirus reported in the world.
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