Fig. 4

Size distribution of small RNA reads. a Relative proportions of small RNA reads as percentages for each size category in total reads in species with NRPE1 as shown in Fig. 3. b Relative proportions of small RNA reads as percentages for each size category in total reads in four lycophytes. There are no obvious 24-nt peaks in S. moellendorffii (red) and Selaginella uncinata (blue). For a and b, the total numbers of small RNA reads for each sample are included in Additional file 1: Table S1. c Ratio of counts of 24- and 21-nt small RNAs. Ratios in species with NRPE1 and without NRPE1 are grouped and plotted, and the difference between these two groups is significant (as shown with asterisk). The P value (0.018) was determined with a Wilcoxon test. d Model for NRPD1/E1 origination. In the most recent common ancestor of land plants, an extra NRPB1 copy from a duplication event fused with a DeCL domain at the C-terminus and formed the ancestral NRPE1. In the most recent common ancestor of euphyllophytes, this copy duplicated and one copy lost some C-terminal sequences and formed NRPD1. The other copy retained the whole protein structure as NRPE1 in ancient seed plants, but lost the long C-terminal extension in the most recent common ancestors of ferns. RPB domains are represented by the magenta (NRPB1), blue (NRPE1), or purple (NRPD1) rectangles and the DeCL domain is represented by the green rectangles. Heptapeptide repeats of NRPB1 are shown as brown rectangles. NRPE1 is shown in orange for bryophytes and angiosperms and in yellow for lycophytes and ferns