Fig. 3

T-plots of the predicted targets cleaved by miRNAs confirmed by degradome sequencing. The alignment along with the detected cleavage frequencies (absolute numbers) were shown beside the black arrow and it showed the miRNA with a portion of its target sequence (top). The two dots indicated matched RNA base pairs, and one dot showed a GU mismatch whereas none dot represent other types of mismatch. Category 0 indicated that the position had a depth > 1, an abundance equal to the maximum of the transcript abundance, and the transcript had only one maximum value; Category 1 indicated that the position had a depth > 1 and an abundance equal to the maximum value of the transcript abundance, and the transcript had two or more maxima [45, 47]. The T-plots showed the distribution of 3′ end of the degradome tags within the full-length of the predicted target mRNA sequence (bottom). The red line represented the cleaved target tags and was shown in red arrow. a–c T-plots of Sugarcane_Unigene_BMK.74449 cleaved simultaneously by miR165a, miR166a, and miR166g-3p at position 4321. d and e T-plots of Sugarcane_Unigene_BMK.61043 cleaved by nov-mir-84 and nov-mir-41 at positions 324 and 785, respectively. f T-plot of Sugarcane_Unigene_BMK.72615 cleaved by miR165a at position 761