Phytochemical and comparative transcriptome analysis reveals different regulatory mechanisms in terpenoids pathways between Matricaria recutita L. and Chamaemelum nobile L

Background Matricaria recutita (German chamomile) and Chamaemelum nobile (Roman chamomile) belong to the botanical family Asteraceae. These two herbs are not only morphologically distinguishable, but their secondary metabolites – especially the essential oils in flowers are also different, especially the terpenoids. The aim of this project was to preliminarily reveal differential regulatory mechanisms in terpenoids biosynthetic pathway between German and Roman chamomile by performing comparative transcriptomic and metabolomics analyses. Results We determined the content of essential oil in disk florets and ray florets in these two chamomiles, and found that the terpenoids content of German chamomile is greater than that of Roman chamomile. In addition, comparisons between German and Roman chamomile were studied by RNA-Seq, which showed that 54% of genes shared >75% sequence identity between the two species. In particular, more highly expressed DEGs (differentially expressed genes) and TFs (transcription factors), different regulation of CYPs (cytochrome P450 enzymes) and rapid evolution of the downstream enzymes in terpenoids biosynthetic pathways in German chamomile, and maybe the reasons result to differences in the types and levels of terpenoids compounds in these two chamomiles. In addition, the phylogenetic tree of single copay genes showed that German chamomile and Roman chamomile had a high identity to C. nankingense. Conclusion This work provided first insights into the terpenoids biosynthesis of chamomiles, and the candidate unigenes related to terpenoids biosynthesis can serve as important information for molecular breeding approaches to modulate the essential oil composition.