Monoterpene indole alkaloid pathway.

<p>The key intermediate strictosidine is formed by condensation of tryptamine, which contributes the indole ring, and secologanin, which is produced from the monoterpene geraniol. In various plants, strictosidine is further metabolized to generate over 2,500 monoterpene indole alkaloids. Solid lines indicate single enzymatic steps; dashed lines indicate multiple steps.</p

Libraries and sequencing generated for <i>Camptotheca acuminata</i>.

1<p>Libraries used in the first, initial de novo assembly.</p>2<p>Libraries only sequenced for expression abundance estimates, reads were not included in de novo assembly.</p>3<p>Libraries used in the second, final de novo assembly.</p><p>M: Million.</p

Expression patterns of known genes in monoterpene indole alkaloid biosynthesis across different tissues and treatments.

<p>Expression values in log₂ FPKM (fragments per Kilobase of transcript per million fragments mapped) were calculated, negative values were set to zero and then were clustered using R <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052506#pone.0052506-R1" target="_blank">[39]</a>. A) <i>Catharanthus roseus</i>: Expression values were sorted in three major groups: Developmental tissues, Yeast extract (YE) treatment of suspension cells (SC), and Methyl jasmonate (MJ) treatment of sterile seedlings (SS) and hairy roots (HR). B) <i>Rauvolfia serpentina</i>. Expression values shown represent the different developmental tissues.</p

Functional annotation results.

<p>Proportion of <i>Camptotheca acuminata</i>, <i>Catharanthus roseus</i> and <i>Rauvolfia serpentina</i> transcripts with sequence similarity to the UniRef100 database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052506#pone.0052506-Suzek1" target="_blank">[17]</a>, <i>Arabidopsis thaliana</i> proteome (<a href="http://arabidopsis.org" target="_blank">http://arabidopsis.org</a>), and Pfam domain database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052506#pone.0052506-Punta1" target="_blank">[18]</a>.</p

Phylogenetic relationships.

<p><i>Camptotheca acuminata</i> (Nyssaceae) is in the order Cornales within the asterid superorder of core eudicots, and <i>Catharanthus roseus</i> and <i>Rauvolfia serpentina</i> (both Apocynaceae) are in Gentainales, also within the asterids. <i>Arabidopsis thaliana</i> is in the family Brassicales within the rosid superorder. Fabales and Astrales are shown for orientation. Redrawn and greatly simplified from APG III <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052506#pone.0052506-APGIII1" target="_blank">[19]</a>.</p

Cluster of orthologous and paralogous genes families in <i>Camptotheca acuminata</i>, <i>Catharanthus roseus,</i> and <i>Rauvolfia serpentina</i> species as identified by OrthoMCL.

<p>Predicted peptides from the <i>Camptotheca acuminata</i>, <i>Catharanthus roseus</i> and <i>Rauvolfia serpentina</i> transcriptomes were clustered using OrthoMCL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052506#pone.0052506-Li1" target="_blank">[23]</a>. A) Number of clusters (c) and genes (g) for each orthologous group. B) Number of genes in the different clusters for each species. The number of clusters and genes for each OrthoMCL group are shown. Group 1: Clusters (blue) and genes shared among <i>C. acuminata</i> (red), <i>C. roseus</i> (green) and <i>R. serpentina</i> (purple). Group 2: Clusters (blue) and genes shared among <i>C. acuminata</i> (red) and <i>C. roseus</i> (green). Group 3: Clusters (blue) and genes shared among <i>C. roseus</i> (green) and <i>R. serpentina</i> (purple). Group 4: Clusters (blue) and genes shared among <i>C. acuminata</i> (red) and <i>R. serpentina</i> (purple).</p

Libraries and sequencing generated for <i>Rauvolfia serpentin</i>a.

<p>M: Million.</p

Summary of statistics of the transcriptome de novo assemblies of <i>Camptotheca acuminata</i>, <i>Catharanthus roseus</i>, and <i>Rauvolfia serpentina</i>.

<p>Summary of statistics of the transcriptome de novo assemblies of <i>Camptotheca acuminata</i>, <i>Catharanthus roseus</i>, and <i>Rauvolfia serpentina</i>.</p

Hierarchical clustering of expression profiles from sampled tissues from <i>Camptotheca acuminata</i> (A), <i>Catharanthus roseus</i> (B), and <i>Rauvolfia serpentina</i> (C).

<p>Pearson product-moment correlation coefficient of log₂ FPKM (fragments per kb transcript per million mapped reads) expression values among RNA-seq libraries were calculated and clustered using R <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052506#pone.0052506-R1" target="_blank">[39]</a>; negative values were set to zero.</p

Frequency of Oases-derived isoforms in transcript assemblies of <i>Camptotheca acuminata</i>, <i>Catharanthus roseus</i> and <i>Rauvolfia serpentina.</i>

<p>The proportion of transcripts with single and multiple isoforms in each of the three species.</p