The role of microRNAs in defense against viral phytopathogens.
MicroRNAs have been considered as an endogenous post-transcriptional gene silencing mechanism for transcription regulation. Additionally, reports are indicative of their involvement in plant viral defense. It seems that horizontal miRNA transfer from pathogenic viral and viroid genomes into plants has evolved into the counter-defense mechanism(s) against their invasions. miRNAs of a green alga and 16 other higher plant species, with/without endogenous function, were searched for their energetically favorable target sites in the complete genomes of plant-specific invading viruses and viroid. Interestingly, 6524 and 250 putative target sites were found in 759 viral and 16 viroid genomes, respectively. Also, in 5589 viral sequence or viral encoding genes, we found 7583 putative target sites from 638 plant invading viruses to be targeted by 1019 miRNAs (belonging to 636 MIRNA families). The evidence of viral/viroid miRNAs targeting plant transcriptome was lacking. The data were indicative that in only 33-40% of the cases of plant miRNAs-viral/viroid targets translation arrest occurs. Some of the MIRNA families including MIR171, MIR156, and MIR159 had a wide target range in viral genomes suggesting possible plant-virus coevolution and at the same time a degree of conservation within different viruses. This putative coevolution could suggest of immune response mechanism against these sub-genomic organisms and further suggests adaptive plant-pathogen interactions, something that is known as host specificity. Herein, we have also speculated that some MIRNA families such as; MIR915, MIR899, and MIR895 with unknown or non-validated targets in plant genomes are being involved in suppression of invading viruses/viroid.