<i>De Novo</i> Characterization of a <i>Cephalotaxus hainanensis</i> Transcriptome and Genes Related to Paclitaxel Biosynthesis

<div><p><i>Cephalotaxus hainanensis</i>, an endangered plant, is known to contain several metabolites with anti-cancer activity. Despite its clinical impact, the alkaloid metabolism of this species has remained largely uncharacterized. The potential of <i>Cephalotaxus</i> for metabolic engineering of medically interesting compounds has, so far, not been exploited, due to the almost complete lack of molecular information. We have therefore performed a high throughput RNA-seq analysis and assembled the transcriptome <i>de novo</i>. Raw reads comprising 4.3 Gbp were assembled <i>de novo</i> into 39,416 unique sequences (unigenes) with a mean length of 1,089.8 bp and a total assembly size of 45.8 Mbp, which equals to more than 50 times the number of <i>Cephalotaxaceae</i> sequences currently deposited in the GenBank (as of August 2013). As proof of principle for medically interesting pathways, gene fragments related to paclitaxel biosynthesis were searched and detected. To verify their functionality, the metabolic product paclitaxel, and its precursor baccatin III, were identified in the leaves of <i>C. hainanensis</i> by HPLC, and shown to be induced by MeJA. This finding demonstrates exemplarily the potential of the annotated transcriptome as information resource for the biotechnological exploitation of plant secondary metabolism.</p></div

Distribution of frequency (absolute numbers) over the length.

<p>The constructed unigenes from <i>de-novo</i> assembly of <i>Cephalotaxus hainanensis</i> short reads were generated by Illumina Hiseq 2000 sequencing. The total number of assembled unigenes is 39,416 unigene.</p

Frequency of individual di- and trinucleotide SSR motives in the ESTs constructed from <i>C. hainanensis</i>.

<p>Frequency of individual di- and trinucleotide SSR motives in the ESTs constructed from <i>C. hainanensis</i>.</p

List of selected unigenes involved in paclitaxel biosynthesis.

<p>List of selected unigenes involved in paclitaxel biosynthesis.</p

Frequency distribution ontological classifications.

<p>The results are grouped into three main categories: biological process, cellular component and molecular function. The right y-axis indicates the number of genes in a category. The left y-axis indicates the percentage of a specific category of genes in that main category. Note that this axis is logarithmic to appropriately depict the large variations in abundance.</p

Frequency of single-stranded repeats (SSR) in the ESTs constructed from <i>C. hainanensis</i>.

<p>Frequency of single-stranded repeats (SSR) in the ESTs constructed from <i>C. hainanensis</i>.</p