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
Reads0
Chats0
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
Citations
More filters
Posted ContentDOI
Tobacco leaf curl Puer virus: a novel monopartite begomovirus infecting Nicotiana tabacum in China.
TL;DR: According to the current International Committee on Taxonomy of Viruses (ICTV )taxonomic criteria, this is a new species of begomovirus for which the name “Tobacco leaf curl Puer virus” is proposed.
Journal ArticleDOI
Begomovirus diversity in tomato crops in Costa Rica
E. Hernandez,N. Barboza +1 more
TL;DR: In Costa Rica, various species of bipartite begomoviruses have been reported, which are Pepper golden mosaic virus (PepGMV), ToYMoV, Tomato leaf curl Sinaloa virus (ToLCSiV), and the monopartite herbivirus Tomato yellow leaf curl virus (TYLCV) as mentioned in this paper .
Journal ArticleDOI
Efficacy of Three Antiviral Agents and Resistant Cultivars on Tomato Yellow Leaf Curl Virus in Tomato
TL;DR: In this paper , Salicylic acid (SA), chitosan (CH), or eugenol (EG) were evaluated in tomato yellow leaf curl virus (TYLCV) infection of greenhouse-grown tomato plants.
Journal ArticleDOI
High molecular diversity and divergent subpopulations of the begomovirus cnidoscolus mosaic leaf deformation virus associated with Cnidoscolus urens.
Adso L. S. F. Mendes,Aline M. Melo,Roberto Ramos-Sobrinho,Sarah Jacqueline Cavalcanti da Silva,Camila G. Ferro,Camila G. Ferro,Mayra Machado de Medeiros Ferro,F. Murilo Zerbini,Gaus Silvestre de Andrade Lima,Iraildes Pereira Assunção +9 more
TL;DR: In this article, the bipartite begomovirus cnidoscolus mosaic leaf deformation virus (CnMLDV) was identified based on nucleotide sequence comparisons.
Journal ArticleDOI
Molecular and biological characterization of a new Tomato mild yellow leaf curl Aragua virus strain producing severe symptoms in tomato
Gustavo Romay,Dorys T. Chirinos,Francis Geraud-Pouey,Annika Gillis,Jacques Mahillon,Cécile Desbiez,Claude Bragard +6 more
TL;DR: Interestingly, tomato plants inoculated with ToMYLCV Zulia-219 displayed severe symptoms, including severe chlorotic leaf curling, in contrast to mild symptoms associated with the type strain of this begomovirus, indicating potential risks associated with this new TomyLCV strain for tomato production in Venezuela.
References
More filters
Journal ArticleDOI
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Journal ArticleDOI
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
TL;DR: MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs, and a new option, MUSCLE-fast, designed for high-throughput applications.
Book ChapterDOI
The International Committee on Taxonomy of Viruses
Frederick A. Murphy,Claude M. Fauquet,David H. L. Bishop,Said A. Ghabrial,Audrey W. Jarvis,Giovanni P. Martelli,Michael Mayo,Max D. Summers +7 more
Journal ArticleDOI
Bemisia tabaci: A Statement of Species Status
TL;DR: There is now sufficient evidence to state that B. tabaci is not made up of biotypes and that the use of biotype in this context is erroneous and misleading.