Abstract
Plant viruses that are members of the Geminiviridae family have circular single-stranded DNA (ssDNA) genome and are responsible for major crop diseases worldwide. We have identified and characterized a novel monopartite geminivirus infecting tomato in Argentina. The full-length genome was cloned and sequenced. The genome-wide pairwise identity calculation that resulted in a maximum of 63% identity with all of other known geminiviruses indicated that it is a new geminivirus species. Biolistic infected plants presented interveinal yellowing, apical leaf curling and extreme root hypotrophy. Thus, the name proposed for this species is tomato apical leaf curl virus (ToALCV). The phylogenetic inferences suggested different evolutionary relationships for the replication-associated protein (Rep) and the coat protein (CP). Besides, the sequence similarity network (SSN) protein analyses showed that the complementary-sense gene products (RepA, Rep and C3) are similar to capulavirus while the viron-sense gene products (CP, MP and V3) are similar to topocuvirus, curtovirus and becurtovirus. Based on the data presented, ToALCV genome appears to have “modular organization” supported by its recombination origin. Analyses of the specificity-determining positions (SDPs) of the CP of geminiviruses defined nine subgroups that include geminiviruses that share the same type of insect vector. Our sequences were clustered with the sequences of topocuvirus, whose vector is the treehopper, Micrutalis malleifera. Also, a set of the highest scored amino acid residues was predicted for the CP, which could determine differences in virus transmission specificity. We predict that a treehopper could be the vector of ToALCV, but transmission assays need to be performed to confirm this. Given everything we demonstrate in this paper, ToALCV can be considered a type member of a new putative genus of the Geminiviridae family.
Highlights
Argentina is South America’s third largest producer of fresh tomato after Brazil and Chile (Food and Agriculture Organization [FAO], 2014)
We obtained a linear DNA fragment of about 2.8 kb generated from the digestion with PstI of rolling circle amplification (RCA) product amplified from three symptomatic plants
tomato apical leaf curl virus (ToALCV) shaped a monophyletic group with the topocuvirus Tomato pseudo-curly top virus (ToPCTV) in the coat protein (CP)- phylogenetic tree (Figure 4B), while it grouped with the sequences of the capulavirus in the replication-associated protein (Rep)-tree (Supplementary Figure S2), which corresponds with the results showed in the full-genome tree (Figure 4A)
Summary
Argentina is South America’s third largest producer of fresh tomato after Brazil and Chile (Food and Agriculture Organization [FAO], 2014). Plant viruses that are members of the Geminiviridae family are responsible for major crop diseases worldwide (Varma and Malathi, 2003; Scholthof et al, 2011; Rybicki, 2015) Their circular ssDNA genome varies between 2.5 and 5.2 kb in length and is packed into twinned icosahedral particles (Zhang et al, 2001). There are other characterized divergent geminiviruses which are not yet assigned to a genus, like the citrus chlorotic dwarf-associated virus (CCDaV), the mulberry mosaic dwarf-associated virus (MMDaV), the apple geminivirus (AGV) and the grapevine geminivirus A (Loconsole et al, 2012; Liang et al, 2015; Ma et al, 2015; Al Rwahnih et al, 2017) All these viruses are putative members of the Geminiviridae family since they have a ssDNA genome, shared conserved protein domains and common replication motifs in their intergenic regions, like the hairpin-loop, with the characteristic geminivirus nonanucleotide (TAATATTAC)
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