Novel cucumber miRNAs identified by high-throughput sequencing.

<p>LM: length of the mature miRNA; LP: length of the miRNA precursor sequence; MFE: Minimal folding free energy; MFEI: Minimal folding free energy index</p><p>Frequency in leaves and roots: normalized sequencing frequencies in leaves and roots libraries, respectively.</p

Target plots (t-plots) of miRNA targets in different categories confirmed by degradome sequencing.

<p>(A) T-plot (top) and miRNA: mRNA alignments (bottom) for two category I targets, Csa020279 and Csa009014 transcripts. The arrow indicates signatures consistent with miRNA-directed cleavage. The solid lines and dot in miRNA: mRNA alignments indicate matched RNA base pairs and GU mismatch, respectively, and the red letter indicates the cleavage site. (B) As in (A) for Csa18310 and Csa008131, a category II target for csa-miR172 and csa-miR858. (C) As in (A) for Csa014411, a category III target for csa-miR169.</p

GO analyses show that miRNAs potentially target tissue forming-related biological processes.

<p>GO analyses show that miRNAs potentially target tissue forming-related biological processes.</p

Expression levels of cucumber miRNA families assessed using Solexa sequencing.

<p>The expression level of cucumber miRNA families in each tissue was assessed by counting the number of all the reads mapping to each family, normalized by the total number of mappable sRNA in the respective libraries.</p

Predicted secondary structures of novel cucumber miRNAs.

<p>The mature miRNA and miRNA^* sequences are written with red and blue capital letters, respectively.</p

Expression analysis of miRNAs in cucumber leaves and roots by qRT-PCR.

<p>The amount of expression was normalized by the level of U6 in qRT-PCR. All reactions of qRT-PCR were repeated three times for each sample. Left indicates the miRNA relative expression generated from the high-throughput sequencing; Right indicates the miRNA relative expression tested by qRT-PCR.</p

The size distribution of the small RNAs in leaves and roots libraries of cucumber.

<p>The size distribution of the small RNAs in leaves and roots libraries of cucumber.</p

Demographics of the 4 samples.

<p>Demographics of the 4 samples.</p

the factor-loadings of EFA and CFA

<p>a: boldface means significant at 5% level in EFA</p><p>b: all the factor loadings presented were significant at 5% level in CFA</p><p>c: CrI = Credibility Interval estimated by Bayesian estimator</p><p>the factor-loadings of EFA and CFA</p

The results of the validity test

<p>*: p < 0.05,</p><p>**p < 0.01</p><p>a: because of the missing data, the samples in this table are different from the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115948#pone.0115948.t001" target="_blank">Table 1</a></p><p>The results of the validity test</p