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Information on the distribution and prevalence of the economically destructive Begomovirus species and recombinant forms infecting fresh-market and processing tomato crops in Brazil is crucial in guiding breeding programs and also to understand the evolutionary mechanisms associated with the upsurge of so many species and quasi-species comprising this unique disease complex. An extensive survey was carried out over 3 years (between 2002 and 2004) aiming to study the diversity of begomoviruses in tomato plants, predominantly collected in central Brazil. Polymerase chain reaction (PCR) with degenerated primers was used to detect the begomoviruses in tomato leaf samples showing virus-like symptoms in commercial fields. Seven hundred and seventeen out of 2,295 samples were found to be PCR positive for a begomovirus infection. High quality sequences were obtained from a fragment encompassing the 5' region of the coat protein (CP) gene and a segment of the intergenic region for 295 isolates from distinct geographic regions. Comparison analyses with those available in public databases enabled preliminary classification of the isolates into four previously described and/or proposed species: Tomato severe rugose virus (61%), Tomato golden vein virus (29.8%), Tomato mottle leaf curl virus (7.1%), Tomato yellow vein streak virus (0.7%), and two putative new species (1.4% of isolates). Within the prevailing species, we noted a relatively low degree of diversity, possibly indicating the existence of recent population founder effects and/or recent selective sweeps.

BackgroundMonopartite begomoviruses (genus Begomovirus, family Geminiviridae) that infect sweet potato (Ipomoea batatas) around the world are known as sweepoviruses. Because sweet potato plants are vegetatively propagated, the accumulation of viruses can become a major constraint for root production. Mixed infections of sweepovirus species and strains can lead to recombination, which may contribute to the generation of new recombinant sweepoviruses.ResultsThis study reports the full genome sequence of 34 sweepoviruses sampled from a sweet potato germplasm bank and commercial fields in Brazil. These sequences were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic diversity and patterns of genetic exchange in sweepoviruses isolated from Brazil, as well as to review the classification and nomenclature of sweepoviruses in accordance with the current guidelines proposed by the Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV). Co-infections and extensive recombination events were identified in Brazilian sweepoviruses. Analysis of the recombination breakpoints detected within the sweepovirus dataset revealed that most recombination events occurred in the intergenic region (IR) and in the middle of the C1 open reading frame (ORF).ConclusionsThe genetic diversity of sweepoviruses was considerably greater than previously described in Brazil. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of sweepovirus species and strains and provided valuable new information for understanding the diversity and evolution of sweepoviruses.

Tomato cultivation in Brazil is threatened by a number of tomato-infecting viruses belonging to the genus Begomovirus of the family Geminiviridae. Here, we report the full DNA-A sequences of three Brazilian begomoviruses: a potentially new tomato-infecting viruses, tomato interveinal chlorosis virus (ToICV), and two previously proposed begomoviruses for which only partial DNA-A sequences are available in the databases: tomato mottle leaf curl virus (TMoLCV) and tomato golden vein virus (TGVV). The complete sequences of the DNA-B components of TMoLCV and TGVV and the DNA-A components of a number of tomato severe rugose virus variants are also presented. Collectively, all of the analyzed sequences were phylogenetically clustered within the two major groups of Brazilian tomato-infecting begomoviruses.