Various Tomato microRNAs could target a Mild and a Severe Strain of Tomato Leaf Curl Virus

Geminiviruses are one of the main constraints in tomato production worldwide. Tomato leaf curl virus (ToLCV) is a geminivirus (family geminiviridae) that produces various symptoms in plants including leaf curling, yellowing and stunting. MicroRNAs are endogenous small RNAs which play a key role in both plants and animal defense and development. Certain animal viruses were found to be targeted by host miRNA which prevent their establishments. In plants, on the other hand, there is no experimental evidence for such an effect on plant viruses. However, based on in silico analysis, viral plants also could be targeted by host miRNAs. Here, we investigated if different sets of tomato miRNAs could potentially bind to a mild and severe species of ToLCV using in silico analysis. We found that tomato miRNAs including mir156 bind to both strains of ToLCV. The mild strain, ToLCV-Ir, was found to be targeted by mir157, 168, 396 and 166 while the severe strain, ToLCV-Au, was targeted by other groups of miRNAs including mir159, mir319 and mir403. The possible role of the identified miRNAs in production of mild and severe symptoms by both strains is discussed. All sequences except miR156a target the coding regions of the virus. In ToLCV-Au miRNA319c binds to the V1 gene, which encodes the precoat protein and which is involved in symptom expression and virus movement. miR159c and miR403 bind to the C1 and C3 genes, respectively, genes that are involved in virus replication. The C1 ORF of ToLCV-Ir can be targeted by both miRNAs miR157a and miR156h. The V2 gene can be targeted by three miRNAs (miR168b, miR396b and miR166i) at different sites. This suggests the potential importance of regulation of this particular ORF by miRNAs.