Abstract
MicroRNAs (miRNAs) are ~21 nucleotide-long regulatory RNAs that arise from endonucleolytic processing of hairpin precursors. Many function as critical post-transcriptional regulators of target mRNAs and long non-coding RNAs. Alongside miRNAs, plants also produce large numbers of short interfering RNAs (siRNAs), which are distinguished from miRNAs primarily by their biogenesis (typically processed from long double-stranded RNA instead of single-stranded hairpins) and functions (typically via roles in transcriptional regulation instead of post-transcriptional regulation). Technical advances over the last decade in high-throughput DNA sequencing have flooded databases with newly identified plant small RNAs. This resulted in the realization that endogenous siRNAs are frequently more abundant and much more sequence-diverse than miRNAs. Conceptual and computational advances have facilitated increasingly rigorous classification of these RNAs, using our improved understanding of their biogenesis. However, the sheer number of endogenous siRNAs compared to miRNAs has been a major factor in the erroneously annotation of siRNAs as miRNAs. Historical inaccuracies in both miRNA annotations and definitions should be recognized and updated, and improved annotation systems for all classes of plant small RNAs are needed. We therefore offer updated criteria for plant miRNA annotations that are suitable for the era of ‘big data’ in biology.