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

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

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

Promising regions identified for developing phylogenetic markers in Asteraceae family.

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

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

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

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