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

  • Weiwei Zhang
  • Tingting Tao
  • Xiaomeng Liu
  • Feng Xu
  • Jie Chang
  • Yongling Liao
Original Article


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.


Matricaria chamomilla Sesquiterpenoid biosynthesis Transcriptome Differentially expressed genes MVA pathway MEP pathway 



This study was supported by the National Natural Science Foundation of China (31400603).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11738_2018_2706_MOESM1_ESM.rar (1.3 mb)
Table S1 Primers sequences used in qRT-PCR. qRT-PCR primers of fourteen candidate unigenes involved in sesquiterpene biosynthesis were designed using the Primer premier 5.0. Table S2 List of Unigenes with KEGG Pathway ID and their categorization into various functional classes. Table S3 DEGs between flower and stem. Table S4 DEGs between flower and root. Table S5 DEGs between flower and leaf. Table S6 DEGs between stem and root. Table S7 DEGs between stem and leaf. Table S8 DEGs between root and leaf. Table S9 The frequency of SSR structure and the number of repeat units. Six types of SSRs were identified from the M. chamomilla unigenes using the MISA. The gene ID, length, SSR type, SSR, SSR start, SSR end, and sequence were listed in this table (RAR 1372 KB)


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Copyright information

© Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2018

Authors and Affiliations

  1. 1.College of Horticulture and GardeningYangtze UniversityJingzhouChina
  2. 2.Hubei Collaborative Innovation Center of Targeted Antitumor DrugJingchu University of TechnologyJingmenChina

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