The results of conservation analysis for miRNA duplicated blocks in the four test plant species.

<p>ath: <i>A. thaliana</i>; ptc: <i>P. trichocarpa</i>; osa: <i>O. sativa</i>; sbi: <i>S. bicolor</i>.</p

Characterization and variation between RrmiRNAs and NRrmiRNAs.

<p>(A) The distribution of miRNA hairpin precursor sequence lengths in RrmiRNAs and NRrmiRNAs. (B) The G-C content in miRNA hairpin precursor sequences in RrmiRNAs and NRrmiRNAs (C) The MFEs for miRNA hairpin precursors in RrmiRNAs and NRrmiRNAs.</p

The overall percentage and copy number data for tandemly duplicated miRNAs in the four test plant species.

<p>(A) The percentage of miRNA families and miRNAs arising by tandem duplication with respect to the total number of miRNA families containing at least one miRNA, and the number of members of the corresponding miRNA family, respectively, for each species tested. (B) The average miRNA copy number in tandemly duplicated regions. (C) The percentage distribution of tandemly duplicated miRNAs on the same or opposite strands. (D) The percentage of conserved or species-specific tandemly duplicated miRNAs with respect to the total number of observed tandemly duplicated miRNAs for each species tested.</p

The distribution and conservation of repeat-related miRNAs in the four test plant species.

<p>(A) The percentage of RrmiRNAs and NRrmiRNAs in the <i>A. thaliana</i>, <i>P. trichocarpa</i>, <i>O. sativa</i> and <i>S. bicolor</i> genomes. (B) The percentage of repetitive element-related miRNAs located in intragenic regions compared to all known miRNAs in the corresponding genome. (C) The percentage of repeat-related miRNAs with differing degrees of conservation.</p

The number of segmental duplications and flanking conserved protein-coding genes within each block.

a<p>The number of observed duplicated blocks, containing miRNAs within the same family or within the different family, that have at least two flanking protein-coding gene surrounding miRNAs.</p>b<p>The percentage of observed duplicated blocks in each test species with respect to the total number of duplicated blocks.</p><p>ath: <i>A. thaliana</i>; ptc: <i>P. trichocarpa</i>; osa: <i>O. sativa</i>; sbi: <i>S. Bicolor.</i></p

The overview for origins and expansion of miRNAs derived from duplicated events in the four test plant species.

<p>ath: <i>A. thaliana</i>; ptc: <i>P. trichocarpa</i>; osa: <i>O. sativa</i>; sbi: <i>S. bicolor</i>.</p

Construction, Model-Based Analysis, and Characterization of a Promoter Library for Fine-Tuned Gene Expression in <i>Bacillus subtilis</i>

Promoters are among the most-important and most-basic tools for the control of metabolic pathways. However, previous research mainly focused on the screening and characterization of some native promoters in <i>Bacillus subtilis</i>. To develop a broadly applicable promoter system for this important platform organism, we created a <i>de novo</i> synthetic promoter library (SPL) based on consensus sequences by analyzing the microarray transcriptome data of <i>B. subtilis</i> 168. A total of 214 potential promoters spanning a gradient of strengths was isolated and characterized by a green fluorescence assay. Among these, a detailed intensity analysis was conducted on nine promoters with different strengths by reverse-transcription polymerase chain reaction (RT-PCR) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Furthermore, reconstructed promoters and promoter cassettes (tandem promoter cluster) were designed via statistical model-based analysis and tandem dual promoters, which showed strength that was increased 1.2- and 2.77-fold compared to that of promoter P43, respectively. Finally, the SPL was employed in the production of inosine and acetoin by repressing and over-expressing the relevant metabolic pathways, yielding a 700% and 44% increase relative to the respective control strains. This is the first report of a <i>de novo</i> synthetic promoter library for <i>B. subtilis</i>, which is independent of any native promoter. The strategy of improving and fine-tuning promoter strengths will contribute to future metabolic engineering and synthetic biology projects in <i>B. subtilis</i>