The symptom-modulating, single-stranded DNA satellites (known as DNA-β) associated with begomoviruses (family Geminiviridae) have proven to be widespread and important components of a large number of plant diseases across the Old World. Since they were first identified in 2000, over 260 full-length sequences (∼1,360 nucleotides) have been deposited with databases, and this number increases daily. This has highlighted the need for a standardised, concise and unambiguous nomenclature for these components, as well as a meaningful and robust classification system. Pairwise comparisons of all available full-length DNA-β sequences indicate that the minimum numbers of pairs occur at a sequence identity of 78%, which we propose as the species demarcation threshold for a distinct DNA-β. This threshold value divides the presently known DNA-β sequences into 51 distinct satellite species. In addition, we propose a naming convention for the satellites that is based upon the system already in use for geminiviruses. This maintains, whenever possible, the association with the helper begomovirus, the disease symptoms and the host plant and provides a logical and consistent system for referring to already recognised and newly identified satellites. © 2008 Springer-Verlag.
Muhire, B., D.P. Martin, J.K. Brown, J. Navas-Castillo, E. Moriones, F.M. Zerbini, R. Rivera-Bustamante,
V. G. Malathi, R. W. Briddon, and A. Varsani. 2013. A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus, Mastrevirus (family, Geminiviridae). Arch Virol. 158:1411-1424.
Geminivrus diseases of cotton are on the rise, worldwide, yet few have been studied in adequate detail to permit the implementation of rational approaches to disease control. The rising costs of managing the whitefly vector, coupled to substantial losses caused by geminivirus-incited diseases now hinder cotton production by requiring inputs that are beyond economic feasibility. The requirement for geminivirus disease resistance in numerous cotton cultivars and multiple, diverse geographic cotton production areas of the world presents a new and unique challenge. To meet this need, baseline information concerning the identity, the distribution, and the relevant characteristics of cotton-infecting geminiviruses and virus strains, thereof, are now required. This study addresses this problem by attaining and applying molecular sequence analysis to key regions of the genomes of cotton-infecting geminivirus collected from cotton growing regions of the world. Specifically, we are examining the sequence similarities of the conserved the coat protein or AV1 gene, and the similarities and particular features associated with diagnostic nucleotides found in the LIR/CR that are involved in regulating essential aspects of the disease cycle. This effort represents the first cataloging and mapping of geminivirus identity and distribution, and the first investigation of the breadth of germiniviral relationships, or the 'diversity' of geminiviruses of cotton, worldwide. It seeks to understand relationships between cotton-infecting geminiviruses and of these viruses and other well-characterized or 'reference' geminiviruses from diverse crop and weed species. This data base of molecular and biotic information will serve as the cornerstone for the rational selection of virus species and strains toward developing cotton cultivars with resistance customized to protect against disease caused by geminiviruses relevant to the production area. This approach will also permit the first precise evaluation of the breadth of disease resistance in a cultivar by permitting challenge-inoculation with narrowly and broadly divergent virus genotypes, thereby providing both a predictive capacity for sustainability of disease resistance and a safeguard to achieve long term protection against indigenous and introduced, exotic geminiviruses of cotton.
Euphorbia mosaic virus (EuMV), a tentative species within the genus Begomovirus, was isolated from Euphorbia heterophylla plants growing in the Yucatan Peninsula, Mexico. The complete bipartite genome was cloned from total DNA extracts and the nucleotide (nt) sequence was determined. The DNA-A sequence of the EuMV-Yucatan Peninsula (EuMV-YP) isolate shared 95% nt identity with the partially characterized type EuMV isolate from Puerto Rico. The EuMV-YP genome organization was like that of other New World, bipartite begomoviruses. The DNA-A component was 2613 nt in size, while the DNA-B component was 2602 nt long. The 165-nt common region (CR) sequence for the DNA-A and DNA-B components shared a lower than expected nt identity of 86%. The organization and iterons of the putative AC1 binding site of EuMV-YP were similar to those of begomoviruses in the Squash leaf curl virus (SLCV) clade. Characteristic disease symptoms were reproduced in E. heterophylla plants inoculated at the seedling stage using the cloned viral DNA-A and DNA-B components, confirming disease aetiology. Results of an experimental host-range study for EuMV-YP indicated that it infected at least five species in three plant families, including the Euphorbiaceae (E. heterophylla), Solanaceae (Datura stramonium, pepper, tomato) and Fabaceae (bean). Phylogenetic analysis of the DNA-A and DNA-B components indicated that EuMV-YP is a New World begomovirus and that it is a new member of the SLCV clade. © 2007 The Authors.