High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affinis in northeastern Brazil

Silva, Sarah J. C. da; Urquiza, Gloria Patricia Castillo; Júnior, B. T. Hora; Assunção, Iraíldes Pereira; Lima, Gaus Silvestre Andrade; Pio-Ribeiro, Gilvan; Mizubuti, Eduardo S. G.; Zerbini, F. Murilo

doi:10.1007/s00705-011-1119-4

Cited by 36 publications

(26 citation statements)

References 36 publications

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“…Second, PepGMV and PHYVV proteins are under purifying selection, as generally described for most begomoviruses (Sanz et al. 1999; Silva et al. 2011; González-Aguilera et al.…”

Section: Discussionmentioning

confidence: 99%

The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico

2015

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Current declines in biodiversity put at risk ecosystem services that are fundamental for human welfare. Increasing evidence indicates that one such service is the ability to reduce virus emergence. It has been proposed that the reduction of virus emergence occurs at two levels: through a reduction of virus prevalence/transmission and, as a result of these epidemiological changes, through a limitation of virus genetic diversity. Although the former mechanism has been studied in a few host-virus interactions, very little is known about the association between ecosystem biodiversity and virus genetic diversity. To address this subject, we estimated genetic diversity, synonymous and non-synonymous nucleotide substitution rates, selection pressures, and frequency of recombinants and re-assortants in populations of Pepper golden mosaic virus (PepGMV) and Pepper huasteco yellow vein virus (PHYVV) that infect chiltepin plants in Mexico. We then analyzed how these parameters varied according to the level of habitat anthropization, which is the major cause of biodiversity loss. Our results indicated that genetic diversity of PepGMV (but not of PHYVV) populations increased with the loss of biodiversity at higher levels of habitat anthropization. This was mostly the consequence of higher rates of synonymous nucleotide substitutions, rather than of adaptive selection. The frequency of recombinants and re-assortants was higher in PepGMV populations infecting wild chiltepin than in those infecting cultivated ones, suggesting that genetic exchange is not the main mechanism for generating genetic diversity in PepGMV populations. These findings provide evidence that biodiversity may modulate the genetic diversity of plant viruses, but it may differentially affect even two closely related viruses. Our analyses may contribute to understanding the factors involved in virus emergence.

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“…Second, PepGMV and PHYVV proteins are under purifying selection, as generally described for most begomoviruses (Sanz et al. 1999; Silva et al. 2011; González-Aguilera et al.…”

Section: Discussionmentioning

confidence: 99%

The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico

2015

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“…The standing genetic variabilities of four tomato-infecting begomovirus populations were much lower than that of a begomovirus population from a non-cultivated host (Blainvillea yellow spot virus) sampled in south-eastern Brazil (although these results are based on different sample sizes) (Rocha, 2011). The genetic structure was also determined for a population of Cleome leaf crumple virus infecting an annual weed (Cleome affinis, family Capparaceae) often associated with leguminous crops in Brazil (Silva et al, 2011). Several recombination events and a high molecular variability were estimated for this population.…”

Section: Discussionmentioning

confidence: 99%

Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts

Lima

Sobrinho

Aguilera

et al. 2013

Journal of General Virology

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Begomoviruses are ssDNA plant viruses that cause serious epidemics in economically important crops worldwide. Non-cultivated plants also harbour many begomoviruses, and it is believed that these hosts may act as reservoirs and as mixing vessels where recombination may occur. Begomoviruses are notoriously recombination-prone, and also display nucleotide substitution rates equivalent to those of RNA viruses. In Brazil, several indigenous begomoviruses have been described infecting tomatoes following the introduction of a novel biotype of the whitefly vector in the mid-1990s. More recently, a number of viruses from non-cultivated hosts have also been described. Previous work has suggested that viruses infecting non-cultivated hosts have a higher degree of genetic variability compared with crop-infecting viruses. We intensively sampled cultivated and non-cultivated plants in similarly sized geographical areas known to harbour either the weed-infecting Macroptilium yellow spot virus (MaYSV) or the crop-infecting Tomato severe rugose virus (ToSRV), and compared the molecular evolution and population genetics of these two distantly related begomoviruses. The results reinforce the assertion that infection of non-cultivated plant species leads to higher levels of standing genetic variability, and indicate that recombination, not adaptive selection, explains the higher begomovirus variability in non-cultivated hosts.

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“…The fact that some "Brazilian" viruses cluster with "Central American" viruses has been previously observed (Castillo-Urquiza et al, 2008;Silva et al, 2011a) and suggests a common origin for these two begomovirus lineages. The significance of this observation lies in the fact that begomoviruses in Central and South America are clearly segregated, and have never mixed.…”

Section: Discussionmentioning

confidence: 54%

Further molecular characterization of weed-associated begomoviruses in Brazil with an emphasis on Sida spp

Tavares

Ramos-Sobrinho

Aguilera³

et al. 2012

Planta daninha

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-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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High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affinis in northeastern Brazil

Cited by 36 publications

References 36 publications

The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico

The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: A study of chiltepin-infecting begomoviruses in Mexico

Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts

Further molecular characterization of weed-associated begomoviruses in Brazil with an emphasis on Sida spp

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