Deep sequencing of microRNAs from hickory reveals an extensive degradation and 3′ end modification

The degradation and 3′ end modification of plant microRNAs (miRNAs) may play crucial roles in regulating miRNA function and stability. However, the mechanism as to how the degradation and the modification are processed are still poorly characterized. Here, we report a survey of miRNA degradation and 3′ modification from two hickory floral differentiation stages through deep sequencing. We constructed two small RNA (sRNA) libraries from two hickory floral differentiation stages and obtained a large number of truncated miRNAs and miRNAs with 3′ end modifications. The presence of so many truncated miRNAs suggests a mechanism degrading through both ends simultaneously. Further analysis reveals that the truncation from the 3′ end has higher probability than from the 5′ end. Single- or double-nucleotide additions to the 3′ end have been observed in many families. We found that the addition of adenine base to the 3′ end is the most common event, accounting for more than 50 % of all miRNA 3′ end modification in the two sRNA libraries. Uridine addition is the second popular modification. These observations suggest that the 3′ end modification of miRNAs preferentially selects adenine and uridine in the hickory plant. Furthermore, we observed that expression of either truncated miRNA or isomiR associates with mature miRNAs. Altogether, our study provides more information regarding the degradation and 3′ end modification of miRNAs in plants.