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.

附加文件2：图S1。对照、缺锌及锌复供条件下，地上部与根部样本的3次生物学重复RNA测序（RNA sequencing）的皮尔逊相关系数（R值）。其中，供锌地上部（Zn plus shoot, ZPS）、缺锌地上部（Zn minus shoot, ZMS）、供锌根部（Zn plus root, ZPR）、缺锌根部（Zn minus root, ZMR）、锌复供地上部（Zn resupply shoot, ZRS）及锌复供根部（Zn resupply root, ZRR）。
图S2。6个样本的小RNA测序（small RNA sequencing）数据中小RNA的长度分布。每根柱状条代表3次生物学重复的平均值±标准差（Standard Deviation, SD）。
图S3。对照、缺锌及锌复供条件下，地上部与根部样本的3次生物学重复小RNA高通量测序（small RNA high-throughput sequencing）的皮尔逊相关系数（R值）。
图S4。维恩图展示根部与地上部中受缺锌及锌复供调控的miRNA的重叠情况（a：已知miRNA与新预测miRNA；b：新预测miRNA）。
图S5。本研究中鉴定出的38个锌响应新miRNA的预测二级结构。红色线条代表在缺锌和/或锌复供条件下差异表达的成熟miRNA序列；蓝色线条代表通过小RNA测序检测到的miRNA*序列；若无蓝色线条，则表示未通过小RNA测序检测到miRNA*序列。
图S6。缺锌和/或锌复供条件下差异表达miRNA的潜在靶基因的生物学过程基因本体（Gene Ontology, GO）富集条目分析。该分析通过AgriGO平台（http://bioinfo.cau.edu.cn/agriGO/）的单富集分析（Single Enrichment Analysis, SEA）工具完成（Fisher检验，P < 0.05，错误发现率（False Discovery Rate, FDR） < 0.05），括号内数值为FDR值。
图S7。缺锌和/或锌复供条件下差异表达miRNA的潜在靶基因的细胞组分基因本体（Gene Ontology, GO）富集条目分析。该分析通过AgriGO平台（http://bioinfo.cau.edu.cn/agriGO/）的单富集分析（SEA）工具完成（Fisher检验，P < 0.05，FDR < 0.05），括号内数值为FDR值。
图S8。根部与地上部中经锌复供恢复表达的差异表达基因（Differentially Expressed Genes, DEGs）的生物学过程GO富集条目分析。该分析通过AgriGO平台（http://bioinfo.cau.edu.cn/agriGO/）的单富集分析（SEA）工具完成（Fisher检验，P < 0.05，FDR < 0.05），括号内数值为FDR值。