Expression pattern-based comparison between the mature microRNAs (miRNAs) and the miRNA precursors.

<p>(<b>A</b>) Expression patterns of the mature miRNAs, ath-miR780.1 and ath-miR780.2, and the corresponding pre-miRNA (precursor microRNA)/pri-miRNA (primary microRNA). For the mature miRNAs listed in the table, their detectable expression levels (in RPM; reads per million) in flowers, leaves and seedlings were highlighted in gray background based on the small RNA (sRNA) high-throughput sequencing (HTS) data. Accordingly, the mirEX-derived expression levels of the pre-miRNA/pri-miRNA detected by real-time quantitative PCR [<i>PP2A</i> (<i>phosphatase 2A</i>; <i>AT1G13320</i>) as the reference gene] in the similar organs were highlighted in pink background. (<b>B</b>) Expression patterns of the mature miRNA ath-miR163 and its precursors. For the mature miRNA listed in the first table, the detectable expression levels in flowers, leaves, roots and seedlings, based on the sRNA HTS data, were highlighted in different background colors. For the pri-miRNA in the second table, the expression levels of the identified poly(A) signals based on the MPSS (massively parallel signature sequencing) data were highlighted by the same background colors as the above table according to the organ-specific origination of the MPSS libraries. “Match site” means the location of the 5′ end of the “Sequence” within the downstream region of the pre-miRNA. Two sequences indicating the potential poly(A) signal of the <i>miR163</i> gene were identified from two independent MPSS data sets. The expression levels of the pre-miRNA/pri-miRNA detected by real-time quantitative PCR (<i>PP2A</i> as the reference gene) in different organs were highlighted similar background colors as the tables. (<b>C</b>) Expression patterns of the mature miRNA ath-miR166a and its precursors. The meanings of the expression data have been introduced in (<b>B</b>). (<b>D</b>) Expression patterns of the mature miRNAs, ath-miR850, ath-miR863-3p, ath-miR863-5p and ath-miR5026. The three miRNA genes form a cluster on <i>Arabidopsis</i> chromosome 4 (see the first table for detailed genomic positions of the corresponding pre-miRNAs). For the mature miRNAs in the second table, their expression levels in flowers, leaves, roots and seedlings, based on the sRNA HTS data, were highlighted in different background colors. The expression levels of the pre-miRNAs/pri-miRNAs detected by real-time quantitative PCR (<i>PP2A</i> as the reference gene) in different organs were highlighted in similar background colors as the second table. For (<b>A</b>) to (<b>D</b>), the sRNA HTS data sets were retrieved from GEO (Gene Expression Omnibus) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0050870#pone.0050870-Barrett1" target="_blank">[68]</a>: WT_Flower (indicated by yellow background), GSM707678; WT_Leaf (green), GSM707679; WT_Root (gray), GSM707680; WT_Seedling (red), GSM707681. For (<b>B</b>) and (<b>C</b>), the MPSS data sets (“17bp_summary.txt.gz” and “20bp_summary.txt.gz”) were retrieved from <i>Arabidopsis</i> MPSS Plus Database.¹⁸ In both data sets, the libraries INF, INS, AP1, AP3, AGM and SAP were prepared from flowers (yellow). S04, S52, LES and LEF were prepared from leaves (green). ROS and ROF were prepared from roots (gray), and GSE from young seedlings (red). The pre-miRNA/pri-miRNA expression data were retrieved from mirEX.¹⁷ Note: for all the panels, the <i>y</i> axes are in log scale.