A Begomovirus Isolated from Chlorotic and Stunted Soybean Plants in Mexico is a New Strain of Rhynchosia golden mosaic virus

Abstract

Soybean (Glycine max Merr.) is an alternative crop during the summer in Sinaloa, a northern state of Mexico. During the last 4 years, symptoms of yellowing, curled leaves, and stunting have been observed on soybean plantings, and a scrutiny of field samples collected in 2003 identified a begomovirus related to Pepper golden mosaic virus in symptomatic plants (4). A new survey was conducted during the summer of 2004 when the soybean disease was prevalent in the region. Affected plants appeared as patches displaying symptoms ranging from mild to severe yellow mosaic with leaf deformation and stunted growth in several parcels of commercial fields of northern Sinaloa. More than 100 samples from symptomatic soybean plants and weeds growing within the same fields were collected and analyzed for the presence of begomoviruses using DNA hybridization with the coat protein gene of Pepper huasteco yellow vein virus as a probe. Thirty-eight soybean, 12 Rhynchosia sp., and 14 sunflower hybridization-positive samples were subsequently used for polymerase chain reaction (PCR) amplification with the degenerate primers pRep-DGR and pCP70-Mot (1). PCR products were cloned into pGEM-T Easy vector (Promega, Madison, WI) and sequenced. The amplified viral DNA (915 nt) from two soybean plants, Sb1 and Sb2 (GenBank Accession Nos. AY955101 and AY957561, respectively), one isolate from Rhynchosia minima (GenBank Accession No. AY955102), and one from Heliantus annum (GenBank Accession No. AY957560) were sequenced and compared with DNA sequences available at NCBI database using BLAST. The highest sequence similarity was obtained with the two known isolates of Rhynchosia golden mosaic virus, RhGMV [Honduras] (GenBank Accession No. AF239671), and RhGMV [Chiapas] (GenBank Accession No. AF408199), displaying a nucleotide identity of approximately 89% with the Sinaloa isolates. Sequence comparisons of the latter isolates showed that viruses in the weeds were 97% identical to one of the soybean isolates, RhGMV-Sb1, but differed significantly (88% of nucleotide identity) from the second soybean isolate, RhGMV-Sb2. The complete genome A sequence of RhGMV-Sb1 was determined using PCR amplification of viral DNA with four degenerate primers recently described (2), cloning of overlapping PCR products into pGEM-T Easy vector (Promega) and sequencing. The 2,604-bp DNA-A of RhGMV-Sb1 (GenBank Accession No. DQ347950) was compared with the homologous genome of RhGMV [Chiapas] and RhGMV [Honduras] using the CLUSTAL alignment method (MegAlign, DNASTAR software, London) and an overall nucleotide identity of 89.2 and 88.6%, respectively, was determined. Current taxonomic criteria for begomoviruses establish that a DNA-A sequence identity lower than 93% with other isolates of a virus is indicative of a separate strain (3). Therefore, the virus identified in this study is a new strain of RhGMV that is provisionally named Rhynchosia golden mosaic virus-Soybean [Mexico:Sinaloa:2004]. This is the first soybean-infecting begomovirus from the American continent whose genome A has been completely characterized as of today. References: (1) J. T. Ascencio-Ibañez et al. Plant Dis. 86:692, 2002. (2) R. De La Torre-Almaraz et al. Plant Dis. 90:378, 2006. (3) C. Fauquet et al. Arch. Virol. 150:2151, 2005. (4) J. Mendez-Lozano et al. Plant Dis. 90:109, 2006.

Molecular characterization of a new begomovirus infecting a leguminous weed Rhynchosia minima in India

“…However, our attempts failed to detect the association of DNAb satellite, suggesting that the virus isolate causing YMD is a typical bipartite legumovirus lacking beta satellites. The potential threat that RhYMIV may pose to grain legume cultivation may be assessed from the record of Rhynchosia as the reservoir for MYMIV [10] and also affecting soybean [22], tobacco [13], and pigeonpea [23]. RhGMYuV was also detected in Desmodium (Fabaceae) that were collected near RhGMYuV infected plants indicating how the Rhynchosia infecting viruses infect other leguminous weeds [24].…”

Molecular characterization of a distinct begomovirus species from Vernonia cinerea and its associated DNA-β using the bacteriophage Φ29 DNA polymerase

“…5) Weeds may serve as reservoirs of viruses during the non-cropping season. Weed-infecting begomoviruses have been found to infect crops [30][31][32]. Tan and Wong [33], Raj et al [34], Hallan et al [35], and Zhou et al [36] have also demonstrated that weeds act either as alternative or as reservoir hosts of viruses.…”

Una nueva cepa del Virus del Chino del Tomate aislado de plantas de soya (Glycine max L.) en México

“…Las amplificaciones de ADN viral se realizaron utilizando los iniciadores universales para begomovirus: pRep-DGR (Méndez et al, 2006), prCP70-Mot, prRepQGR-rev (De la Torre et al, 2006) y prC889 (Brown et al, 2001). Los productos de PCR comprenden la totalidad del componente A.…”