Pipeline used for M. truncatula miRNA identification. Counts for reads, unique/non-redundant (nr) sequences, genomic loci detected or pre-miRNA-like hairpins are given at each step of the pipeline (white boxes). Details about each filtering step (grey boxes) are indicated in Materials and methods. The arrows represent the direction of the pipeline. Mt, Medicago truncatula; nt, nucleotide; wgs, whole genome shotgun.