In silico analysis reveals that several tomato microRNA/microRNA∗ sequences exhibit propensity to bind to tomato leaf curl virus (ToLCV) associated genomes and most of their encoded open reading frames (ORFs)

Tomato leaf curl virus (ToLCV) is a member of family geminiviridae that constitute rapidly emerging group of phytopathogens posing threat to a large number of vegetable crops worldwide. Three different genomes are found to be associated with ToLCV viz., DNA-A, DNA-B and beta satellite DNA. MicroRNAs (miRs) are known to govern several fundamental processes in eukaryotes, including basal defense mechanisms. In animals, it has been demonstrated that certain host miRs prevent viral establishment by directly interfering with pathogen replication or by binding to viral transcripts. However, in spite of the existence of huge families of phytopathgenic viruses, no such mechanism has been observed in plants. In the present study, we performed in silico analysis to investigate whether tomato encoded miR/miR∗ sequences possess any potential to bind to viral genome and/or encoded ORFs. We observed that different sequences can bind to ToLCNDV DNA-A, ToLCNDV DNA-B and ToLCNDV associated DNA beta genomes and most of the encoded ORFs. Interestingly, our analysis revealed that several miR∗ species could similarly target genome and ORFs of ToLCNDV suggesting novel role of miR∗ in host defense response. This observation holds much importance as miR∗ molecules are presently thought to follow degradation pathway and are not assigned with any function. Moreover, we could predict targets for these miR∗ sequences that are generally involved in plant metabolism. Overall, these results shed light on new paradigm of intricate host–pathogen interactions via miRNA pathway.