SUMMARY
Post-transcriptional gene silencing (PTGS) in plants results from independent activities of microRNAs (miRNAs) and small interfering RNAs (siRNAs). Phased siRNAs (phasiRNAs) require miRNA triggers to initiate their production. Hundreds of loci generating 21- and 24-nt phasiRNAs (PHAS loci) have been identified in rice and maize; triggered by miR2118 and miR2275 respectively, originate from non-coding RNAs, and accumulate to very high levels in anthers. In this work, we sequenced small RNA (sRNAs) from rice panicles and anther across different developmental stages, and applied bioinformatics techniques to decipher the activities of phasiRNAs. Using new rice data plus published maize data we demonstrate that 21-nt phasiRNAs can function in cis to target their own precursors. We also show that the first cycle of processed phasiRNAs from each precursor accumulates weakly, presumably due to combination of reasons including its length and sequence biased making it less preferred to be loaded into Argonaute proteins. Additionally, comparing phasiRNAs from both strands of the precursors, we observed in both rice and maize a strong bias towards phasiRNAs produced from Pol II derived strand (top-strand) as opposed to RDR6 derived strand (bottom-strand). Finally, our results suggest that, even though phasiRNAs are processed in “phases”, they demonstrate differential accumulation relative to their originating transcript.