MOESM2 of Integrated analyses of miRNAome and transcriptome reveal zinc deficiency responses in rice seedlings

Additional file 2: Figure S1. Pearson’s correlation (R-value) of three biological replicates of shoot and root samples for RNA sequencing under control, Zn deficiency, and Zn resupply conditions. Zn plus shoot, ZPS; Zn minus shoot, ZMS; Zn plus root, ZPR; Zn minus root, ZMR; Zn resupply shoot, ZRS; Zn resupply root, ZRR. Figure S2. Length distribution of the small RNAs from the small RNA sequencing data in the six samples. Each bar indicates the mean ± SD of three biological replicates. Figure S3. Pearson’s correlation (R-value) of three biological replicates of shoot and root samples for small RNA high-throughput sequencing under control, Zn deficiency, and Zn resupply conditions. Figure S4. Venn diagram representing the overlap of the Zn-deficiency- and Zn-resupply- responsive miRNAs (a, known and novel miRNAs; b, novel miRNAs) in roots and shoots. Figure S5. Predicted secondary structures of 38 Zn-responsive novel miRNAs identified in this study. The red lines indicate the mature miRNA sequences that were found to be differentially expressed under Zn deficiency and/or Zn resupply. The blue lines indicate the miRNA* sequences that were detected by the small RNA sequencing. If no blue line was indicated, it means that no miRNA* sequences were detected by the small RNA sequencing. Figure S6. Gene ontology (GO) representation of the overrepresented GO terms of biological processes in the potential target genes of the differentially expressed miRNAs under Zn deficiency and/or Zn resupply. The GO representation was generated using single enrichment analysis (SEA) tool on AgriGO (http://bioinfo.cau.edu.cn/agriGO/) (Fisher’s test, P < 0.05, FDR < 0.05). The number in parenthesis represents the FDR value. Figure S7. Gene ontology (GO) representation of the overrepresented GO terms of cellular component in the potential target genes of the differentially expressed miRNAs under Zn deficiency and/or Zn resupply. The GO representation was generated using single enrichment analysis (SEA) tool on AgriGO (http://bioinfo.cau.edu.cn/agriGO/) (Fisher’s test, P < 0.05, FDR < 0.05). The number in parenthesis represents the FDR value. Figure S8. Gene ontology (GO) representation of the overrepresented GO terms of biological process in the DEGs recovered by Zn resupply in roots and shoots. The GO representation was generated using single enrichment analysis (SEA) tool on AgriGO (http://bioinfo.cau.edu.cn/agriGO/) (Fisher’s test, P < 0.05, FDR < 0.05). The number in parenthesis represents the FDR value.