RNA-Seq for excavation of genes involved in the biosynthesis of primary active components and identification of new EST-SSR markers in medicinal chrysanthemum



Chrysanthemum morifolium cv. ‘Huaihuang’, medicinal chrysanthemum, RNA-Seq, functionally related genes, EST-SSR markers


Paper description:

  • Chrysanthemum morifolium cv. ‘Huaihuang’ is a medicinal plant of China with a huge medicinal and commercial value.
  • Limited genomic and transcriptional information restricts further research on the biosynthesis of active components, its genetic background and evolutionary origin.
  • We performed RNA-Seq, excavated abundant unigenes involved in the biosynthesis of primary active components and developed new EST-SSR markers.
  • This work will contribute to the further clarification of the biosynthetic process of primary active components, it will enrich molecular marker resources and contribute to research of population structure, evolutionary adaptation and genetic breeding in ‘Huaihuang’ and other chrysanthemum species.

Abstract: Chrysanthemum morifolium cv. ‘Huaihuang’ has great medicinal and commercial value. However, limited genomic and transcriptional information restricts the further research of ‘Huaihuang’. In this study, using ‘Huaihuang’ leaf as the sample, we performed RNA-Seq and obtained numerous unigene sequences for functional characterization, and developed new EST-SSR markers. The results show that 176 unigenes were assigned to the ‘antioxidant activity’ in GO annotations, 998 unigenes were assigned to ‘Secondary metabolite biosynthesis, transport and catabolism’ in the KOG database, 381 unigenes were assigned to ‘Biosynthesis of other secondary metabolites’, and 377 unigenes were assigned to ‘Metabolism of terpenoids and polyketides’ in the KEGG database. A number of genes involved in the biosynthesis of flavones and terpenes, such as CHS, CHI, FLS, HMGR and MVD, were found in the transcription data of ‘Huaihuang’. Also, 36 new polymorphic EST-SSR markers were developed and validated. Using them, the genetic diversity was analyzed and a dendrogram of six clades was constructed among 15 medicinal chrysanthemum varieties. The excavated unigenes and identified new EST-SSR markers will provide useful resources for the study of biosynthesis of active components, genetic diversity analysis, population structure identification and in molecular breeding research of ‘Huaihuang’ and related species.


Received: December 26, 2018; Revised: April 19, 2019; Accepted: May 17, 2019; Published online: May 29, 2019

How to cite this article: Zhao X, Song L, Ma M, Liu K, Lv M, Zhu Y, Jiang L. RNA-Seq for excavation of genes involved in the biosynthesis of primary active components and identification of new EST-SSR markers in medicinal chrysanthemum. Arch Biol Sci. 2019;71(3):489-500.


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How to Cite

Zhao X, Song L, Ma M, Liu K, Lv M, Zhu Y, Jiang L. RNA-Seq for excavation of genes involved in the biosynthesis of primary active components and identification of new EST-SSR markers in medicinal chrysanthemum. Arch Biol Sci [Internet]. 2019Oct.23 [cited 2021Jul.24];71(3):489-500. Available from: http://www.serbiosoc.org.rs/arch/index.php/abs/article/view/3767