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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gb4gv: a genome browser for geminivirus
TL;DR: The goal is to build a comprehensive Geminivirus genomics database, namely gb4gv, that not only preserves genomic characteristics of the virus, but also supplements biologically relevant annotations that help to interrogate this virus, for example, the targeted host, putative iterons, siRNA targets, etc.
Journal ArticleDOI
High genetic stability of potato yellow mosaic Panama virus infecting tomato in Panama
Salvatore Davino,Salvatore Davino,Stefano Panno,A. Caruso,Mario Davino,José Angel Herrera Vásquez +5 more
TL;DR: The relevant regions in Panama involved in commercial tomato production, including the Chiriquí, Veraguas, Herrera, Los Santos and Panama Oeste provinces, were surveyed for the distribution and genetic diversity of potato yellow mosaic Panama virus (PYMPV) in the growing seasons of 2011 and 2012.
Journal ArticleDOI
Phenotypic screening of cultivated and wild okra germplasm against yellow vein mosaic and enation leaf curl diseases of okra in India
Venkataravanappa Venkataravanappa,Satish Kumar Sanwal,C. N. Lakshminarayana Reddy,R. P. Singh,SK Nafeez Umar,M. Krishna Reddy +5 more
TL;DR: In this paper , the authors evaluated 178 cultivated/advanced lines (147 Advances okra lines + 31 popular varieties) and 146 accessions from 14 wild species originally collected from different national institutes located at different agro-climatic zones of India were evaluated for their response against OYVMD and OELCuD.
Journal ArticleDOI
Complete genome sequence of a new bipartite begomovirus associated with leaf curl disease of Capsicum annum.
TL;DR: The complete nucleotide sequence of a new bipartite begomovirus infecting Capsicum annum, a vegetable crop communally cultivated throughout India is reported, and sequence analysis has ruled out the involvement of recombination events in its evolution.
Journal ArticleDOI
A novel East African monopartite begomovirus-betasatellite complex that infects Vernonia amygdalina
Happyness G. Mollel,Joseph Ndunguru,Peter Sseruwagi,Titus Alicai,John Colvin,Jesús Navas-Castillo,Elvira Fiallo-Olivé +6 more
TL;DR: The complete genomes of a monopartite begomovirus and an associated betasatellite found infecting Vernonia amygdalina Delile in Uganda were cloned and sequenced and it is proposed that vernonia crinkle virus (VeCrV) is proposed for this novel begoovirus species.
References
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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.