Genomic diversity of sweet potato geminiviruses in a Brazilian germplasm bank

Abstract

Begomoviruses cause major diseases of sweet potato worldwide impairing considerably the yields of this important food staple. Since sweet potato plants are vegetatively propagated and globally transported, they are prone to accumulate and disseminate geminiviruses. Effective diagnostic tools are, therefore, desirable. We studied the genomic diversity of geminiviruses present in naturally-infected sweet potato accessions belonging to a Brazilian germplasm bank collection. Fifty-five samples from different sweet potato accessions displaying geminivirus-like symptoms were analyzed by combining rolling circle amplification (RCA) with restriction fragment length polymorphism (RFLP) and sequencing. The restriction enzyme MspI (HpaII) revealed diverse band patterns in 55 samples and digestion with BamHI, SstI or PstI resulted in full-length sweet potato geminivirus DNAs of about 3 kb in 46 samples. In addition, smaller fragments were identified as either viral "Defective DNAs" (D-DNAs) or mitochondrial plasmid DNAs. The diversity of sweet potato-associated geminiviruses was found to be very high under Brazilian conditions. Representative viral full-length DNAs have been cloned and sequenced yielding two new tentative species, three strains and several variants of previously described sweet potato geminiviruses. Sequence comparisons identified footprints of recombination in their genomes underscoring the risk of generating new geminiviruses in vegetatively propagated germplasm bank material. The sites of recombination were found in conjunction with predicted hairpin structures. We propose diagnostic routines to screen germplasm bank material for geminiviruses by the rapid and reliable RCA/RFLP as the technique of choice.

Genetic diversity and recombination analysis of sweepoviruses from Brazil

“…It is worth noting that a few sweepovirus isolates were likely misclassified according to the taxonomic criteria for geminivirus classification [36] (the proposed new names are shown in Table  1 and Additional File 2). These isolates were SPLCV-Ceara[Brazil:Fortaleza1] (SPLCV-CE[BR:For1], FJ969832), SPLCV-Rio Grande do Sul1[Brazil:Tavares1] (SPLCV-RS1[BR:Tav1], FJ969833) [12], Sweet potato golden vein-associated virus-[United States:Mississipi:1b-3:07] (SPGVaV-[US:MS:1B-3], HQ333143) [11], SPGVaV-Para[Brazil:Belem1] (SPGVaV-PA[BR:Bel1], FJ969829) [12] and Ipomoea yellow vein virus-[Spain:Malaga:IG1:2006] (IYVV-[ES:Mal:IG1:06], EU839576) [6]. The genome of isolate SPLCV-CE[BR:For1] shares <89% nucleotide identity with all other begomovirus sequences (Additional File 2), and in accordance with the cut-off point of 89% identity established for species separation within the genus Begomovirus [35], it most likely belongs to a new species, proposed here as Sweet potato leaf curl Brazil virus (SPLCBRV).…”

“…Subsequently, begomovirus infections in sweet potato have been reported from many countries, including Peru [5], Spain [6], China [7,8], Italy [9], Uganda [10], the United States [11] and Brazil [12,13], resulting in the description of ten additional novel species [6,7,10-13]. Phylogenetically, these viruses, for which the name sweepoviruses has been proposed [14], group in a monophyletic cluster that is distinct from the two main begomovirus branches, the Old and New World groups [6,15].…”

Fluorescence in situ hybridization analysis of endosymbiont genera reveals novel infection patterns in a tomato-infesting Bemisia tabaci population from Brazil

“…In fact, it is quite possible that GroEL proteins might be begomovirus-specific or even virus strain-specific. In Brazil, so far only bipartite begomovirus species have been detected in tomato and other crops (Ribeiro et al 2003;Fernandes et al 2008;Fernandes 2010), with exception for sweet-potatoes where solely monopartite species were detected (Paprotka et al 2010). In this scenario, it would be of interest to carry out additional studies aiming to demonstrate if the localization of the endosymbionts and their gene products might be correlated with the transmission ability/efficiency by the Brazilian MEAM 1 populations of the complex of more than 20 bipartite begomovirus species described infecting tomatoes so far (Ribeiro et al 2003;Fernandes et al 2008;Fernandes 2010).…”

Light-dependent segregation of begomoviruses in Asystasia gangetica leaves

“…Defective DNA molecules are a common feature of geminivirus, and particularly for begomovirus and curtovirus infections of plants (Bach and Jeske, 2014;Horn et al, 2011;Liu et al, 1998;Paprotka et al, 2010;Paximadis and Rey, 2001;Stanley et al, 1997). They may attenuate virus symptoms (Stanley et al, 1990(Stanley et al, , 1997, increase symptom severity, or have no effect (Bach and Jeske, 2014;Horn et al, 2011).…”