A miR7122-Triggered phasiRNA Pathway with a Complex Evolutionary History in Plants

Plant 22 nt miRNAs are capable of triggering the production of phased, secondary siRNAs (phasiRNA) from either non-coding (TAS) or protein coding genes. These plant phasiRNAs regulate diverse biological processes. Recent data demonstrate that many plant genomes are rich in phasiRNA-producing loci, and may contain hundreds of these loci from a multitude of protein-coding gene families. Given that siRNAs, like miRNAs, can effectively silence their target genes, the phasiRNAs generated from a member of a gene family inevitably reinforce silencing strength as well as potentially target additional genes inside and outside the gene family, thereby provoking a robust regulatory cascade. In this study, we comprehensively characterized the phasiRNA-produced genes and their miRNA triggers in peach, apple and other species, and found that the phasiRNA generation is prevalent in a gene family coding for pentatricopeptide repeat (PPR) factors among all species analyzed. The PPRs utilize both miRNAs and TAS-derived secondary siRNA (tasiRNAs) as triggers that independently or cooperatively incite a complex process of phasiRNA biogenesis. We identified features of this process unique to each species. We also found that the miRNA triggers vary from species to species but share a high degree of sequence identity among apple, peach, soybean, grape and citrus; these miRNAs are all members of the super family of miR7122. Homology sequence search showed that miR7122 shares a conserved core sequence with two other miRNA super families, revealing an intrigue evolutionary relationship.