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

The codon–anticodon recognition pattern and codon usage for <i>A. adenophora</i> cp genome.

*<p>Numerals indicate the frequency of usage of each codon in 24894 codons in 87 potential protein-coding genes.</p

Promising regions identified for developing phylogenetic markers in Asteraceae family.

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

The MP phylogenetic tree is based on 35 protein-coding genes from 33

<p> <b>plant taxa.</b> The MP tree has a length of 41, 661 with a consistency index of 0.4644 and a retention index of 0.6821. Numbers above node are bootstrap support values. ML tree has the same topology but is not shown.</p

Repeat structure analysis in the <i>A. adenophora</i> cp genome.

<p>The cutoff value for tandem repeat is 15 bp and 30 bp for dispersed repeat. A. Frequency of repeats by length; B. Repeat type; C. Location distribution of all the repeats.</p

Distribution of different classes of sRNAs derived from barley chloroplast genome (A) and nuclear genome (B).

<p>Distribution of different classes of sRNAs derived from barley chloroplast genome (A) and nuclear genome (B).</p