Tête à Tête of Tomato Yellow Leaf Curl Virus and Tomato Yellow Leaf Curl Sardinia Virus in Single Nuclei

Viral diseases occur wherever sweet potato (Ipomoea batatas) is cultivated and because this crop is vegetatively propagated, accumulation and perpetuation of viruses can become a major constraint for production. Up to 90 % reductions in yield have been reported in association with viral infections. About 20 officially accepted or tentative virus species have been found in sweet potato and other Ipomoea species. They include three species of begomoviruses (genus Begomovirus, family Geminiviridae) whose genomes have been fully sequenced. In this investigation, we conducted a search for begomoviruses infecting sweet potato and Ipomoea indica in Spain and characterized the complete genome of 15 isolates. In addition to sweet potato leaf curl virus (SPLCV) and Ipomoea yellowing vein virus, we identified three new begomovirus species and a novel strain of SPLCV. Our analysis also demonstrated that extensive recombination events have shaped the populations of Ipomoea-infecting begomoviruses in Spain. The increased complexity of the unique Ipomoea-infecting begomovirus group, highlighted by our results, open new horizons to understand the phylogeny and evolution of the family Geminiviridae. INTRODUCTIONSweet potato (Ipomoea batatas, family Convolvulaceae) is ranked as the seventh most important food crop in global production. This crop originated in South America (O'Brien, 1972) but today it is grown in most tropical, subtropical and temperate regions of the world. Numerous ornamental Ipomoea species are grown worldwide. Ipomoea indica is widely grown ornamentally in the Mediterranean basin, where it is frequently naturalized. The putative role of I. indica and other species in the genus as a reservoir for sweet potato pathogens has not been explored.Because sweet potato is vegetatively propagated, accumulation of viruses can become a major constraint for production. About 20 accepted or tentative virus species have been described in sweet potato . Three begomovirus species have been described as infecting Ipomoea species and their genomes have been fully sequenced. These are: sweet potato leaf curl virus (SPLCV) (Lotrakul et al., 1998;Lotrakul & Valverde., 1999), Ipomoea yellow vein virus (IYVV) (Banks et al., 1999) and sweet potato leaf curl Georgia virus (SPLCGV) (Lotrakul et al., 2003). SPLCV or related begomoviruses have been isolated from sweet potato in the Americas (Lotrakul et al., 2003;Fuentes & Salazar, 2003), Asia (Onuki & Hanada, 1998;Luan et al., 2006) and Africa (Miano et al., 2006) and from I. indica in Europe . Begomoviruses are likely to be present in many regions where sweet potato is grown but their prevalence and distribution is still unknown. Difficulties in detecting and isolating begomoviruses directly from sweet potato plants could have impeded additional reports (Kokkinos & Clark., 2006b).Information about the variability among isolates of the described sweet potato begomoviruses is limited. Comparisons and phylogenetic analyses of partial sequences of the AC1 gene of several isolates collect...

Section: G Lozano and Others 2556mentioning

confidence: 99%

Novel begomovirus species of recombinant nature in sweet potato (Ipomoea batatas) and Ipomoea indica: taxonomic and phylogenetic implications

Lozano

Trenado

Valverde

et al. 2009

“…It appears to heavily contribute to begomovirus genetic diversity, increasing the evolutionary potential and local adaptation of strains (Berrie et al, 2001;Graham et al, 2010;Harrison & Robinson, 1999;Monci et al, 2002;Padidam et al, 1999). There is ample opportunity for recombination because multiple begomovirus species are often found co-infecting the same plant (Davino et al, 2009;García-Andrés et al, 2006;Harrison et al, 1997;Pita et al, 2001;Ribeiro et al, 2003;Sanz et al, 2000;Torres-Pacheco et al, 1996), and more than one virus can simultaneously replicate in the same nucleus (Morilla et al, 2004). Additionally, the high recombination frequency observed for begomoviruses may be explained by a theoretical recombination-dependent replication mechanism (RDR) (Jeske et al, 2001), in addition to the welldocumented rolling circle replication (RCR) (Saunders et al, 2001).…”

Section: Introductionmentioning

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

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.

“…Therefore, it is conceivable that geminiviruses have evolved the capacity for RDR to solve this problem efficiently. A natural consequence of RDR is that, if two related geminivirus genomes enter the same nucleus (Morilla et al, 2004), it is very probable that RDR will produce a wide variety of chimaeric genomes.…”

mentioning

confidence: 99%

Replicative intermediates of maize streak virus found during leaf development

Erdmann

Shepherd

Martin

et al. 2009

Geminiviruses of the genera Begomovirus and Curtovirus utilize three replication modes: complementary-strand replication (CSR), rolling-circle replication (RCR) and recombinationdependent replication (RDR). Using two-dimensional gel electrophoresis, we now show for the first time that maize streak virus (MSV), the type member of the most divergent geminivirus genus, Mastrevirus, does the same. Although mastreviruses have fewer regulatory genes than other geminiviruses and uniquely express their replication-associated protein (Rep) from a spliced transcript, the replicative intermediates of CSR, RCR and RDR could be detected unequivocally within infected maize tissues. All replicative intermediates accumulated early and, to varying degrees, were already present in the shoot apex and leaves at different maturation stages. Relative to other replicative intermediates, those associated with RCR increased in prevalence during leaf maturation. Interestingly, in addition to RCR-associated DNA forms seen in other geminiviruses, MSV also apparently uses dimeric open circular DNA as a template for RCR.