Stem loop structures of core pre-miRNAs. (a) Stem-loop structures of miR156 in A. thaliana (AtMIR156), G. hirsutum (GhMIR156), and G. raimondii (GrMIR156) showing overall conserved structures among them and slightly different sequence composition and structure between GhMIR156 and GrMIR156. (b) The conserved miR482 is located in the 3' end of the stem in Populus trichocarpa (PtMIR482) and G. hirsutum (GhMIR482). (c) Stem-loop structures of four novel miRNAs (Gh-MIR2948, Gh-MIR2947, GhMIR2949a, and GhMIR2950) in G. hirsutum. One of the three predicted pre-GhMIR2949a EST stem-loops is shown. Gh-miR482-5p is located in the 5' end of the stem in the new miRNA Gh-MIR2948. Gh-miR2948 was predicted to possess different targets from Gh-miR482 (b). Mature miRNAs and miRNA* are shown in red and green, respectively. The numbers in (b, c) indicate total miRNA and miRNA* sequence reads, respectively, in four tissues examined.