miRNA-mRNA correlation network.

<p>Circuits in red, blue, yellow and green ellipse are indicating CT4, CT8, FT4 and FT8 samples, respectively. The triangles and circles in the network are indicating miRNAs and target mRNAs, respectively. Down-regulated mRNAs and miRNAs are shown as green and up-regulated mRNAs and miRNAs are shown as red.</p

Overview of DE mRNAs, DE miRNAs and length distribution of the small RNA among libraries.

<p>The histograms showing the number of DE mRNAs (A) and miRNAs (D) among libraries. The Venn diagrams showing the overlaps among four comparisons of DE mRNAs (B) and miRNAs (E). (C) refers to the length distribution of the small RNA in different libraries.</p

qRT-PCR validation for DE miRNAs and mRNAs.

<p>Twelve DE mRNA and six DE miRNA were selected for the quantitative RT-PCR analysis, including AHK4 (A), DREB1B (B), DREB1C (C), NAC100 (D), ARF6 (E), BPR (F), GI (G), GST3 (H), PP2A13 (I), HEXO1 (J), HT1 (K), ATH1 (L), csn-miR156.17(M), csn-miR398.5(N), csn-miR164.4(O), csn-miR167.6(P), csn-miR164.1(Q) and csn-miR171.2(R). The GADPH gene and 5.8S rRNA were chosen as the endogenous control for mRNA and miRNA qRT-PCR, respectively.</p

Summary for the annotation of unigenes.

<p>Summary for the annotation of unigenes.</p

Differential expression of carbohydrate metabolism and plant hormone signal transduction related genes.

<p>The histograms showing the number of up- or down-regulated carbohydrate metabolism (A) and plant hormone signal transduction (B) related genes in CT4, CT8, FT4 and FT8 samples, respectively.</p

Summary for DGE datasets.

<p>Summary for DGE datasets.</p

Biological process network of GO term enrichment for differentially expressed (DE) mRNAs.

<p>Over-represented GO terms for DE mRNAs in CT4 (A), CT8 (B), FT4 (C) and FT8 (D) samples, respectively. The node size represents the number of genes associated to a given GO term and node filled color reflects the adjusted <i>P</i>-value. End nodes were indicated by blue label and green border.</p

KEGG pathway analysis of differentially expressed (DE) mRNAs.

<p>A total of 10, 17, 10 and 6 significantly enriched KEGG pathways were identified in CT4, CT8, FT4 and FT8 samples, respectively. Line color of edge represents the <i>P</i>-value of pathway.</p

Distribution of differentially expressed transcription factors.

<p>The histograms showing the number of up- or down-regulated transcription factors in CT4 (A), CT8 (B), FT4 (C) and FT8 (D) samples, respectively.</p

Quality of sequencing.

<p>R1: Reads sequencing from the left; R2: Reads sequencing from the right.</p><p>Quality of sequencing.</p