Evolutionary Dynamics of Begomoviruses and Its Satellites Infecting Papaya in India.

The genus Begomovirus represents a group of multipartite viruses that significantly damage many agricultural crops, including papaya, and influence overall production. Papaya leaf curl disease (PaLCD) caused by the complex begomovirus species has several important implications and substantial losses in papaya production in many developing countries, including India. The increase in the number of begomovirus species poses a continuous threat to the overall production of papaya. Here, we attempted to map the genomic variation, mutation, evolution rate, and recombination to know the disease complexity and successful adaptation of PaLCD in India. For this, we retrieved 44 DNA-A and 26 betasatellite sequences from GenBank reported from India. An uneven distribution of evolutionary divergence has been observed using the maximum-likelihood algorithm across the branch length. Although there were phylogenetic differences, we found high rates of nucleotide substitution mutation in both viral and sub-viral genome datasets. We demonstrated frequent recombination of begomovirus species, with a maximum in intra-species recombinants. Furthermore, our results showed a high degree of genetic variability, demographic selection, and mean substitution rate acting on the population, supporting the emergence of a diverse and purifying selection of viruses and associated betasatellites. Moreover, variation in the genetic composition of all begomovirus datasets revealed a predominance of nucleotide diversity principally driven by mutation, which might further accelerate the advent of new strains and species and their adaption to various hosts with unique pathogenicity. Therefore, the finding of genetic variation and selection emphases on factors that contribute to the universal spread and evolution of Begomovirus and this unanticipated diversity may also provide guidelines toward future evolutionary trend analyses and the development of wide-ranging disease control strategies for begomoviruses associated with PaLCD.

Interaction between ßC1 of satellite and coat protein of Chili leaf curl virus plays a crucial role in suppression of host RNA silencing.

The monopartite Chili leaf curl virus (ChiLCV) and its ß-satellite (ChiLCB) have been found to co-exist in infected plants. The ability of ßC1 protein to suppress RNA silencing was investigated using an in-house developed in-planta reversal of silencing assay, using Nicotiana tabacum lines harboring green fluorescent protein (GFP) silenced by short hairpin GFP (ShGFP). Transient expression of recombinant ßC1 complemented and increased the suppressor activity of ChiLCV coat protein (CP), and this was confirmed by molecular analysis. In silico analysis followed by a yeast two-hybrid screen-identified ChiLCV-CP as the interacting partner of the ChiLCB-ßC1 protein. Subcellular localization through confocal analysis revealed that when ßC1 and ChiLCV-CP were co-present, the fluorescence was localized in the cytoplasm indicating that nuclear localization of both proteins was obstructed. The cytoplasmic compartmentalization of the two viral suppressors of RNA silencing may be responsible for the enhanced suppression of the host gene silencing. This study presents evidence on the interaction of ChiLCV-CP and ßC1 proteins and indicates that ChiLCB may support the ChiLCV in overcoming host gene silencing to cause Chili leaf curl disease. KEY POINTS: • CP of ChiLCV and ßC1 of ChiLCB contain RNA silencing suppression activity • The RNA silencing suppression activity of ChiLCB-ßC1 complements that of ChiLCV-CP • There is a direct interaction between ChiLCB-ßC1 and ChiLCV-CP.

Complete genome sequence of a new bipartite begomovirus associated with leaf curl disease of Capsicum annum.

The complete bipartite genome, consisting of DNA-A and DNA-B, of a novel begomovirus isolate associated with apical leaf curling and crinkled leaf disease of Chili (Capsicum annum) from New Delhi, India was cloned and sequenced. The sequence of DNA-A (2737 nt) and DNA-B (2692 nt) of the virus was submitted to NCBI, USA under the accessions MK069591 & MG597211, respectively. Sequence identity of the common region (CR) and presence of identical iterons (GAGTG) between the DNA-A and DNA-B clones indicate that they constitute a related pair. The virus corresponds to a novel species of tomato leaf curl virus and sequence analysis has ruled out the involvement of recombination events in its evolution. Therefore, we report the complete nucleotide sequence of a new bipartite begomovirus infecting Capsicum annum, a vegetable crop communally cultivated throughout India.

RNAi mediated gene silencing against betasatellite associated with Croton yellow vein mosaic begomovirus.

Plant viruses encode suppressors of posttranscriptional gene silencing, an adaptive antiviral defense responses that confines virus infection. Previously, we identified single-stranded DNA satellite (also known as DNA-ß) of ~1,350 nucleotides in length associated with Croton yellow vein mosaic begomovirus (CYVMV) in croton plants. The expression of genes from DNA-ß requires the begomovirus for packaged, replication, insect transmission and movement in plants. The present study demonstrates the effect of the ßC1 gene on the silencing pathway as analysed by using both transgenic systems and transient Agrobacterium tumefaciens based delivery. Plants that carry an intron-hairpin construct covering the ßC1 gene accumulated cognate small-interfering RNAs and remained symptom-free after exposure to CYVMV and its satellite. These results suggest that ßC1 interferes with silencing mechanism.

Complete nucleotide sequence of a begomovirus associated with satellites molecules infecting a new host Tagetes patula in India.

In the year 2012 leaf curl disease was observed on Marigold (Tagetes patula) in Lakshmangrh, Sikar province of India. Affected plants were severely stunted with apical leaf curl and crinkled leaves, symptoms typical of begomovirus infection. This is the first report of complete nucleotide sequence of a begomovirus associated with satellites molecules infecting a new host Tagetes patula in India.