Conservation and divergence of small RNA pathways in vascular plants revealed by small RNA analyses in lycophytes and ferns

Pathways underlying miRNA biogenesis, degradation, and activity were established early in land plant evolution, but the 24-nt siRNA pathway that guides DNA methylation was incomplete in early land plants, especially lycophytes. We show that the functional diversification of key gene families such as DICER-LIKE and ARGONAUTE (AGO) as observed in angiosperms occurred early in land plants followed by parallel expansion of the AGO family in ferns and angiosperms. We uncovered an unexpected AGO family specific to lycophytes and ferns. Our phylogenetic analyses of miRNAs in lycophytes, bryophytes, ferns, and angiosperms refined the temporal origination of conserved miRNA families in land plants. Overall design: Examine the 19-26 nt small RNA in 25 samples from 4 lycophytes and 21 ferns, and the degradome of S. moellendorffii fronds.