De novo assembly and comparative transcriptome analysis: novel insights into terpenoid biosynthesis in Chamaemelum nobile L

KEY MESSAGE: Analysis of terpenoids content, transcriptome from Chamaemelum nobile showed that the content of the terpenoids in the roots was the highest and key genes involved in the terpenoids synthesis pathway were identified. Chamaemelum nobile is a widely used herbaceous medicinal plant rich in volatile oils, mainly composed of terpenoids. It is widely used in food, cosmetics, medicine, and other fields. In this study, we analyzed the transcriptome and the content and chemical composition of the terpenoids in different organs of C. nobile. Gas chromatography–mass spectrometry analysis showed that the total content of the terpenoids among C. nobile organs was highest in the roots, followed by the flowers. Illumina HiSeq 2500 high-throughput sequencing technology was used to sequence the transcripts of roots, stems, leaves, and flowers of C. nobile. We obtained 139,757 unigenes using the Trinity software assembly. A total of 887 unigenes were annotated to secondary metabolism. In total, 55,711 differentially expressed genes were screened among different organs of C. nobile. We identified 16 candidate genes that may be involved in the terpenoid biosynthesis from C. nobile and analyzed their expression patterns using real-time PCR. Results showed that the expression pattern of these genes was tissue-specific and had significant differential expression levels in different organs of C. nobile. Among these genes, 13 were expressed in roots with the highest levels. Furthermore, the transcript levels of these 13 genes were positively correlated with the content of α-pinene, β-phellandrene, 1,8-cineole, camphor, α-terpineol, carvacrol, (E,E)-farnesol and chamazulene, suggesting that these 13 genes may be involved in the regulation of the synthesis of the volatile terpenoids. These results laid the foundation for the subsequent improvement of C. nobile quality through genetic engineering.