Supporting Information

Files in this Data Supplement:

Fig. 3. Six characteristic secondary structure features were extracted from a reference set of Arabidopsis thaliana miRNAs, which were downloaded from the RFAM database. Later on in the analysis, these values were used as cutoff scores to validate miRNA precursor candidates. The six features are as follows. (a) The miRNA should be part of one continuous helix. (b) The minimum folding energy of the precursor sequence should be at least –30 Kcal/mol (or more negative). (c) The sequence representing the mature miRNA should form at least 15 bp in the precursor sequence. (d and e) There must be no more than 5 unpaired bases in the miRNA (d) or in the complementary strand (e). (We do not discriminate between internal loops and bulge loops). (f) Finally, there should be no more than 5 G•U base pairs in the sequence representing the mature miRNA.

Fig. 4. Dendrogram showing the clustering of all miRNAs according to sequence similarity. More information is available in the main text.

Fig. 5. Eight of the miRNAs predicted by our pipeline target a number of genes of the ubiquitination pathway, with TIR1 as a typical member, which is targetted by MIR20. To validate prediction of MIR20, we found homologs with perfectly conserved miRNA sequences with a valid stem-loop precursor structure in three plant genomes, namely Medicago truncatula, Populus trichocarpa, and Lotus corniculatus.

Table 2. List of the potential protein targets for the 91 potential miRNAs, grouped by annotation family, and by biological function. This table is an extended version of Table 1 in the main text.

Data Set 1. A FASTA file of all miRNA sequences predicted by our pipeline (loaded in plain text format).

Data Set 2. A FASTA file of the miRNA precursor sequences (loaded in plain text format).