-Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants. The aim of this study was to further characterize the diversity of begomoviruses infecting weeds (mostly Sida spp.) in Brazil. Total DNA was extracted from weed samples collected in Viçosa (Minas Gerais state) and in some municipalities of Alagoas state in 2009 and 2010. Viral genomes were amplified by RCA, cloned and sequenced. A total of 26 DNA-A clones were obtained. Sequence analysis indicated the presence of 10 begomoviruses. All viral isolates from Blainvillea rhomboidea belonged to the same species, Blainvillea yellow spot virus (BlYSV ), thereby suggesting that BlYSV may be the only begomovirus present in this weed species. Four isolates represent new species, for which the following names are proposed: Sida yellow blotch virus (SiYBV), Sida yellow net virus (SiYNV), Sida mottle Alagoas virus (SiMoAV) and Sida yellow mosaic Alagoas virus (SiYMAV). Recombination events were detected among the SiYBV isolates and in the SiYNV isolate. These results constitute further evidence of the high species diversity of begomoviruses in Sida spp. However, the role of this weed species as a source of begomoviruses infecting crop plants remains to be determined.Keywords: geminivirus, recombination, Blainvillea rhomboidea, Sida micrantha, Sida urens, Sida santaremnensis RESUMO -Begomovírus são vírus de DNA circular fita simples transmitidos por mosca branca, os quais são frequentemente associados com plantas daninhas. O objetivo deste trabalho foi caracterizar a diversidade de begomovírus infectando plantas daninhas (principalmente Sida spp.) no Brasil. DNA total foi extraído a partir de plantas daninhas coletadas em Viçosa (Minas Gerais) e em alguns municípios do estado de Alagoas em 2009 e 2010. Os genomas virais foram amplificados por RCA, clonados e sequenciados. Um total de 26 clones de DNA-A foram obtidos. A análise das sequências indicou a presença de dez diferentes begomovírus. Todos os isolados originários de Blainvillea rhomboidea pertencem a uma única espécie viral, Blainvillea yellow spot virus (BlYSV), sugerindo que o BlYSV pode ser o único begomovírus presente nesta espécie de planta invasora. Quatro isolados representam espécies novas, para as quais os seguintes nomes são propostos: Sida yellow blotch virus (SiYBV), Sida yellow net virus (SiYNV), Sida mottle Alagoas virus (SiMoAV) e Sida yellow mosaic Alagoas virus (SiYMAV). Eventos de recombinação foram detectados entre isolados de SiYBV e no isolado de SiYNV. Estes resultados constituem uma evidência adicional da alta diversidade de espécies de begomovírus em Sida spp. Contudo, o possível papel dessas plantas daninhas como fonte de begomovírus para plantas cultivadas ainda permanece indeterminado.

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Begomoviruses are whitefly-transmitted single-stranded DNA viruses of great economic importance in the tropics and subtropics. Several begomovirus species have been reported in tomatoes in Brazil, but only a few predominate in the field, for unknown reasons. In this study begomovirus-infected tomato samples were collected in Viçosa, State of Minas Gerais, in Nov/2009 and Dec/2010. Viral genomes were amplified, cloned and sequenced. A total of 36 DNA-A components were obtained. Sequence comparisons indicated the presence of a single begomovirus, Tomato severe rugose virus (ToSRV), with pairwise identities between isolates ranging from 97.3 to 100%. Subdivision tests indicated the existence of a single population. The analysis of variability descriptors indicated that the ToSRV population has a genetic variability similar to other begomovirus populations described in Brazil infecting tomato. Neutrality tests suggested the occurrence of purifying selection acting upon the population. Recombination analysis identified recombination events with begomoviruses from the weed species Sida micrantha. The wide distribution of ToSRV in the field and the detection of recombination indicate that continuous monitoring of viral populations in the field will be required to enable an efficient resistance-based control strategy for begomoviruses

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