Sequencing reads, assembly and annotation.

<p>Size distribution of 454 high-quality reads (a) and assembled contigs (b). Black and white bars represents reads and contigs from <i>pap1</i> and BR086 transcriptome data respectively. Annotation of unigenes of <i>pap1</i> (c) and BR086 (d) was carried out against TAIR, NR and CDD databases. Out of all annotated unigenes, 25,343 and 19,225 unigenes from <i>pap1</i> and BR086, respectively, had common BLAST hits to annotated proteins by different databases.</p

Differential expression of methyltransferases (a) and dehydrogenases (b) with their differential expression in <b><i>pap1</i></b> and BR086.

<p>Two columns in each represent <i>pap1</i> and BR086, while each row represents contigs encoding members of these families (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065622#pone.0065622.s014" target="_blank">Table S10</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0065622#pone.0065622.s015" target="_blank">S11</a>). Clustering was carried out with log tpm value of each contig in <i>pap1</i> and BR086 transcriptome to visualize differential expression.</p

Phenotype of fresh latex and specific alkaloid content in <b><i>pap1</i></b><b> and BR086.</b>

<p>Fresh latex of BR086 is brown or red whereas <i>pap1</i> exuded white latex (a). Content of specific alkaloids in latex was measured in <i>pap1</i> and BR086 (b) using High Pressure Liquid Chromatography. *** indicate values that differ significantly from BR086.</p

Histogram of gene ontology classification.

<p>The results are summarized in three main categories: Biological Process, Cellular Component and Molecular Function. Bars represent the assign percent of unigenes in <i>pap1</i> (white bars) and BR086 (black bars) with BLAST matches in the TAIR9 database to each GO term.</p

Combined assembly and annotation.

<p>Size distribution of combined assembled contig length and frequency (a) using high–quality reads from <i>pap1</i> and BR086. Annotation statistics (b) of unigenes of combined assembly queried against TAIR, NR and CDD databases.</p

Summary of 454 sequencing and assembly for <i>pap1</i> mutant and BR086 line of <i>Papaver somnifera.</i>

<p>Summary of 454 sequencing and assembly for <i>pap1</i> mutant and BR086 line of <i>Papaver somnifera.</i></p

The unigenes related to secondary metabolites.

<p>The unigenes related to secondary metabolites.</p