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Open Access Highly Accessed Research article

Identification of phenylpropanoid biosynthetic genes and phenylpropanoid accumulation by transcriptome analysis of Lycium chinense

Shicheng Zhao1, Pham Anh Tuan1, Xiaohua Li1, Yeon Bok Kim1, HyeRan Kim2, Chun Geon Park3, Jingli Yang4, Cheng Hao Li4* and Sang Un Park1*

Author Affiliations

1 Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Korea

2 Green Bio Research Center, Cabbage Genomics Assisted Breeding Supporting Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Korea

3 National Institute of Horticultural and Herbal Science, RDA, Bisanro 92, Eumseong, Chungbuk, 369-873, Korea

4 State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China

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BMC Genomics 2013, 14:802  doi:10.1186/1471-2164-14-802

Published: 19 November 2013



Lycium chinense is well known in traditional Chinese herbal medicine for its medicinal value and composition, which have been widely studied for decades. However, further research on Lycium chinense is limited due to the lack of transcriptome and genomic information.


The transcriptome of L. chinense was constructed by using an Illumina HiSeq 2000 sequencing platform. All 56,526 unigenes with an average length of 611 nt and an N50 equaling 848 nt were generated from 58,192,350 total raw reads after filtering and assembly. Unigenes were assembled by BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology identifiers. Using these transcriptome data, the majority of genes that are associated with phenylpropanoid biosynthesis in L. chinense were identified. In addition, phenylpropanoid biosynthesis-related gene expression and compound content in different organs were analyzed. We found that most phenylpropanoid genes were highly expressed in the red fruits, leaves, and flowers. An important phenylpropanoid, chlorogenic acid, was also found to be extremely abundant in leaves.


Using Illumina sequencing technology, we have identified the function of novel homologous genes that regulate metabolic pathways in Lycium chinense.

Illumina sequencing; Lycium chinense; Phenylpropanoids; Chlorogenic acid