Genetic diversity of begomoviruses infecting soybean, bean and associated weeds in Northwestern Argentina

Abstract

The subtropical Northwestern region of Argentina (provinces of Tucumán, Salta, Jujuy, Santiago del Estero and Catamarca) suffers from a high incidence of the whitefly Bemisia tabaci, and the detection of begomoviruses is also common. The Northwest is the main bean-growing region of the country, and approximately 10% of Argentina's soybean crop is grown in this area. We have used a PCR-based assay to establish the identity and genetic diversity of begomoviruses associated with bean and soybean crops in Northwestern Argentina. Universal begomovirus primers were used to direct the amplification of a fragment encompassing the 5' portion of the capsid protein gene. Amplified fragments were cloned, sequenced and subjected to phylogenetic analysis to determine the sequence identity to known begomoviruses. The data indicated the presence of four distinct begomoviruses, all related to other New World begomoviruses. The prevalent virus, which was present in 94% of bean and soybean samples and also in two weed species, is closely related to Sida mottle virus (SiMoV). A virus with high sequence identity with Bean golden mosaic virus (BGMV) was found in beans. The two remaining viruses displayed less than 89% identity with other known begomoviruses, indicating that they may constitute novel species. One of these putative novel viruses was detected in bean, soybean and tomato samples.Additional keywords: Sida mottle virus, Bean golden mosaic virus, geminivirus. RESUMO Diversidade genética de begomovírus associados às culturas da soja e feijoeiro na região Noroeste da Argentina.A região Noroeste da Argentina (províncias de Tucumán, Salta, Jujuy, Santiago del Estero e Catamarca), de clima subtropical, apresenta uma alta incidência da mosca-branca Bemisia tabaci e a detecção de begomovírus também é freqüente. O Noroeste é a principal região produtora de feijão do país e produz aproximadamente 10% da soja da Argentina. A identidade e diversidade genética de begomovírus associados à soja e ao feijoeiro no Noroeste da Argentina foram estudadas com base na amplificação de fragmentos do genoma viral via PCR, utilizando oligonucleotídeos universais para o gênero Begomovirus que amplificam um fragmento correspondente à região 5' do gene da proteína capsidial. Os fragmentos amplificados foram clonados e seqüenciados, e as seqüências foram submetidas à análise filogenética. Os resultados indicam a presença de quatro espécies de begomovírus, todas relacionadas às espécies do Novo Mundo. O vírus prevalente, detectado em 94% das amostras de feijoeiro e soja e em duas amostras de plantas daninhas, apresentou alta identidade de sequência e relacionamento filogenético com o Sida mottle virus (SiMoV). Um vírus com alta identidade de seqüência com o Bean golden mosaic virus (BGMV) foi detectado em feijoeiro. As duas outras espécies apresentaram menos de 89% de identidade com os demais begomovírus, sugerindo-se tratar de novas espécies. Uma dessas possíveis novas espécies foi detectada em plantas de feijoeiro, soja e tomateiro.Palavras-ch...

Biological and molecular characterization of bean bushy stunt virus, a novel bipartite begomovirus infecting common bean in northwestern Argentina

“…Detection tests for BGMV, ToYSV, SbBMV, ToMoWrV, ToYVSV, and SiGMBRV, based on DNA hybridization probes have demonstrated the constant presence of these viruses in the NW region [20,22,31]. In Salta province, as presented in this work, the high proportion of positive samples (100%) and the large diversity of begomoviruses, as well as the high frequency of coinfections, are likely to favor emergence of new viruses through processes such as recombination or pseudo-recombination [5,23].…”

Population Dynamics of Whiteflies and Associated Viruses in South America: Research Progress and Perspectives

“…In Argentina, BGMV and the soybean blistering mosaic virus (SbBMV) are begomoviruses found infecting bean and soybean plants [166,168]. The tomato yellow spot virus (TYSV-AR), previously known as sida mottle virus (SiMoV), isolated from Argentina, can also infect beans and soybean plants [169]. Begomoviruses are more common on beans compared to soybean in Argentina, being mainly found in soybean in the Northeast region [169].…”

“…The tomato yellow spot virus (TYSV-AR), previously known as sida mottle virus (SiMoV), isolated from Argentina, can also infect beans and soybean plants [169]. Begomoviruses are more common on beans compared to soybean in Argentina, being mainly found in soybean in the Northeast region [169]. Among these begomoviruses in Argentina, the BGMV is the most frequently found infecting bean plants [168].…”

Detection and identification of Begomovirus infecting Cucurbitaceae and Solanaceae in Yogyakarta, Indonesia

“…When complete genome or component of bipartite virus sequences are unavailable, full-length CP gene sequences can be used for rapid detection followed by prediction of Begomovirus species identification (Brown et al 2001;Mayo and Pringler 1997;Palmieri et al 2003). CP was used to analyze genetic diversity of begomoviruses infecting native and cultivated plants from Mexico (Hernandez-zepeda et al 2007), soybean and bean in Argentina (Rodriguez-Pardina et al 2006), and cotton in India (Sharma et al 2005). However, based on the International Committee of Virus Taxonomy (ICTV) guideline, the complete DNA-A sequence or monopartite genome sequence are needed for definite identification of Begomovirus species (Hernandez-Zepeda et al 2007).…”