Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa

Abstract

Background: The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miRNAs, miR2118 and miR2275, were mainly responsible for the triggering of 21-nt and 24-nt phasiRNAs biogenesis, respectively. However, compare to other plant species, relative fewer phasiRNA biogenesis pathways have been discovered in rice, which limits the comprehensive understanding of the mechanism of phasiRNA biogenesis and the miRNA derived regulatory network. Results: In this study, we performed a systematical searching for phasiRNA biogenesis pathways in rice. As a result, five novel 21-nt phasiRNA biogenesis pathways and five novel 24-nt phasiRNA biogenesis pathways were identified. Further exploration of the regulatory function of phasiRNAs revealed eleven novel phasiRNAs with 21-nt length targeting forty-one genes, most of which involving in the growth and development of rice. In addition, five novel phasiRNAs with 24-nt length were found targeting the promoter of an OsCKI1 gene and causing higher methylation status in panicle, implying their regulatory function of the transcription of OsCKI1, and subsequently affect the development of rice. Conclusions: These results substantially extended the information of phasiRNA biogenesis pathways and their regulatory function in rice.