De Novo characterization of a Cephalotaxus hainanensis transcriptome and genes related to paclitaxel biosynthesis

• Published in: PloS one 2014-09, Vol.9 (9), p.e106900
• Main Authors: Qiao, Fei, Cong, Hanqing, Jiang, Xuefei, Wang, Rongxiang, Yin, Junmei, Qian, Dan, Wang, Zhunian, Nick, Peter
• Format: Article
• Language: English
• Subjects: Agriculture; Anticancer properties; Bioinformatics; Biology and Life Sciences; Biosynthesis; Biotechnology; Cancer; Cephalotaxus; Cephalotaxus - genetics; Cephalotaxus hainanensis; Crops; Endangered plants; Exploitation; Gene expression; Gene Expression Regulation, Plant - genetics; Genes; Genes, Plant - genetics; Genomics; Germplasm; High-performance liquid chromatography; Horticulture; Laboratories; Landscape architecture; Leaves; Leukemia; Liquid chromatography; Metabolic engineering; Metabolism; Metabolites; Molecular chains; Natural products; Paclitaxel; Paclitaxel - biosynthesis; Plant Leaves - genetics; Ribonucleic acid; RNA; Science; Sequence Analysis, DNA - methods; Sequences; Transcriptome - genetics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0106900

Cephalotaxus hainanensis, 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 Cephalotaxus 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 de novo. Raw reads comprising 4.3 Gbp were assembled de novo 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 Cephalotaxaceae 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 C. hainanensis 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.