De novo assembly and comparative transcriptome analysis: novel insights into sesquiterpenoid biosynthesis in Matricaria chamomilla L.

Matricaria chamomilla , originally native to the temperate zone of Eurasia, has been one of the most popular herbal plants owing to its pharmacologically active sesquiterpenoid metabolites, such as (-)-α-bisabolol and bisabolol oxide A. Although the sesquiterpenoids of M. chamomilla has been well characterized, information on genes responsible for the biosynthesis of these compounds are scarce, and further investigations on the plant have been hindered by the lack of genomic information. In this study, we performed a de novo assembly of the M. chamomilla transcriptome using Illumina HiSeq 2500 high-throughput sequencing. A single run yielded 21 Gb clean reads that were assembled into 83,741 unigenes. A total of 21,626 and 18,929 unigenes were assigned to Gene Ontology categories and the Cluster of Orthologous Groups, respectively. Differentially expressed genes (DEGs) in flowers, stems, roots, and leaves were screened, and 1115 DEG unigenes were assigned to specific secondary metabolites using the Kyoto Encyclopedia of Genes and Genomes (KEGG). We selected a set of putative genes that were most likely involved in the biosynthesis of sesquiterpenoid in M. chamomilla . The genes in the sesquiterpenoid synthesis pathway displayed significant differential expression in different organs. Out of the 83,741 unigenes, 5555 were identified as having simple sequence repeat motifs, with mono-nucleotide repeats being the most frequently found repeat type. Our data provided a comprehensive sequence resource for M. chamomilla belonging to the Asteraceae family, which contains many medicinal herbs. The present mass sequence data are expected to facilitate further study on the regulatory mechanism of the terpenoid biosynthetic pathway in M. chamomilla .