Multiple infection, recombination and genome relationships among begomovirus isolates found in cotton and other plants in Pakistan

Sanz, Ana I.; Fraile, Aurora; García‐Arenal, Fernando; Zhou, Xueping; Robinson, David J.; Khalid, Shahida; Butt, T. B.; Harrison, B. D.

doi:10.1099/0022-1317-81-7-1839

Cited by 120 publications

(84 citation statements)

References 25 publications

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“…Geminiviruses are characterized by twin icosahedral capsids and small, single-stranded DNA (ssDNA) genomes (56) that display high levels of genetic variability (62). Several studies have indicated that recombination contributes to geminivirus diversity (48,60,71). However, unlike doublestranded DNA (dsDNA) viruses, there is also mounting evidence that ssDNA viruses are subject to high nucleotide mutation rates similar to the levels reported previously for RNA viruses (34,35,53).…”

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confidence: 89%

High-Frequency Reversion of Geminivirus Replication Protein Mutants during Infection

Argüello‐Astorga

Ascencio-Ibáñez

Dallas

et al. 2007

J Virol

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The geminivirus replication protein AL1 interacts with retinoblastoma-related protein (RBR), a key regulator of the plant division cell cycle, to induce conditions permissive for viral DNA replication. Previous studies of tomato golden mosaic virus (TGMV) AL1 showed that amino acid L148 in the conserved helix 4 motif is critical for RBR binding. In this work, we examined the effect of an L148V mutation on TGMV replication in tobacco cells and during infection of Nicotiana benthamiana plants. The L148V mutant replicated 100 times less efficiently than wild-type TGMV in protoplasts but produced severe symptoms that were delayed compared to those of wild-type infection in plants. Analysis of progeny viruses revealed that the L148V mutation reverted at 100% frequency in planta to methionine, leucine, isoleucine, or a second-site mutation depending on the valine codon in the initial DNA sequence. Similar results were seen with another geminivirus, cabbage leaf curl virus (CaLCuV), carrying an L145A mutation in the equivalent residue. Valine was the predominant amino acid recovered from N. benthamiana plants inoculated with the CaLCuV L145A mutant, while threonine was the major residue in Arabidopsis thaliana plants. Together, these data demonstrated that there is strong selection for reversion of the TGMV L148V and CaLCuV L145A mutations but that the nature of the selected revertants is influenced by both the viral background and host components. These data also suggested that high mutation rates contribute to the rapid evolution of geminivirus genomes in plants.

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confidence: 89%

High-Frequency Reversion of Geminivirus Replication Protein Mutants during Infection

Argüello‐Astorga

Ascencio-Ibáñez

Dallas

et al. 2007

J Virol

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“…Numerous examples of recombination in geminiviruses have been reported, between members both belonging to the same genus (Hou & Gilbertson, 1996;Zhou et al, 1997;Navas-Castillo et al, 2000;Sanz et al, 2000;Martin et al, 2001;Monci et al, 2002, Ndunguru et al, 2005Bull et al, 2006;García-Andrés et al, 2006;Owor et al, 2007) and of different genera (Briddon et al, 1996;Klute et al, 1996). Recombination can result in significant changes in the biological properties of viruses, such as the ability to increase the relative fitness (Fernández-Cuartero et al, 1994).…”

Section: Introductionmentioning

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

Journal of General Virology

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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...

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“…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

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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Multiple infection, recombination and genome relationships among begomovirus isolates found in cotton and other plants in Pakistan

Cited by 120 publications

References 25 publications

High-Frequency Reversion of Geminivirus Replication Protein Mutants during Infection

High-Frequency Reversion of Geminivirus Replication Protein Mutants during Infection

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

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

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