Additional file 4: Figure S3. of Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

Expression level of 32 PmWRKY genes in different tissues. Actin was an internal reference gene. (DOC 797 kb

Additional file 3: Table S1. of Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

The identified PmWRKY proteins in Broomcorn millet and their putative orthologous gene in rice. (DOC 47 kb

Additional file 2: Figure S2. of Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

Sequence logos of PmWRKY domain. The PmWRKY proteins domain submitted to MEME server. The total height of stack was used to shows ‘information content’ of that position in the motif. Height of letters in stack suggests probability of each amino acids at that position. (DOC 558 kb

Additional file 1: Figure S1. of Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.)

Multiple-sequence alignment of the WRKY protein domain from PmWRKYs and OsWRKYs. Conserved amino acids were indicated by blank background, conserved WRKY domains and zinc-finger motifs were indicated by red box. (DOC 1365 kb

Percent identity plot for comparison of six Asteraceae chloroplast genomes using mVISTA program.

<p>Top line shows genes in order (transcriptional direction indicated with arrow). Sequence similarity of aligned regions between <i>A. adenophora</i> and other five species is shown as horizontal bars indicating average percent identity between 50–100% (shown on y-axis of graph). The x-axis represents the coordinate in the chloroplast genome. Genome regions are color coded as protein-coding (exon), rRNA, tRNA and conserved non-coding sequences (CNS).</p

Maximum parsimony (MP) trees of all the selected 24 chloroplast regions of six Asteraceae species

<p>. The phylogram of “combined regions” was constructed from the MP analysis using all the 24 regions together.</p

The genes having intron in the <i>A. adenophora</i> cp genome and the length of the exons and introns.

*<p>rps12 is trans-spliced gene with 5′ end exon located in the LSC region and the duplicated 3′ end exon located in IR regions.</p

Genes present in the <i>A. adenophora</i> cp genome.

a<p>Gene containing two introns.</p>b<p>Gene containing a single intron.</p>c<p>Two gene copies in the IRs.</p>d<p>Gene divided into two independent transcription units.</p>e<p>Pseudogene.</p

Global Identification of MicroRNAs and Their Targets in Barley under Salinity Stress

<div><p>Salinity is a major limiting factor for agricultural production worldwide. A better understanding of the mechanisms of salinity stress response will aid efforts to improve plant salt tolerance. In this study, a combination of small RNA and mRNA degradome sequencing was used to identify salinity responsive-miRNAs and their targets in barley. A total of 152 miRNAs belonging to 126 families were identified, of which 44 were found to be salinity responsive with 30 up-regulated and 25 down-regulated respectively. The majority of the salinity-responsive miRNAs were up-regulated at the 8h time point, while down-regulated at the 3h and 27h time points. The targets of these miRNAs were further detected by degradome sequencing coupled with bioinformatics prediction. Finally, qRT-PCR was used to validate the identified miRNA and their targets. Our study systematically investigated the expression profile of miRNA and their targets in barley during salinity stress phase, which can contribute to understanding how miRNAs respond to salinity stress in barley and other cereal crops.</p></div

Promising regions identified for developing phylogenetic markers in Asteraceae family.

*<p>commonly used phylogenetic markers included for comparison.</p