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An insight into the genes involved in secoiridoid biosynthesis in Gentiana macrophylla by RNA-seq

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Abstract

The dried root of Gentiana macrophylla is a well-known traditional Chinese herbal medicine for treating jaundice, hepatitis, and stomachic and choleretic ailments. However, natural sources are now in short supply. A lack of information about its genetic background has been a great hindrance to producing its active constituents via genetic engineering. We performed RNA-seq to obtain 42,918 unigenes (average length = 667 bp) in its transcriptome. Of these, 32,141 (74.89 %) were annotated and 2,339 unigenes were assigned to secondary-metabolite pathways. In all, 114 putative unigenes involved in secoiridoid biosynthesis were identified in our transcriptome library. A Blast X search against the Arabidopsis gene regulatory information server showed that 4,413 unigenes are homologous to transcription factor genes from Arabidopsis. Organ-specific genes and candidate gene expression profiles were also investigated with digital gene expression technology. Quantitative PCR was used to verify the expression patterns of several novel transcripts involved in secoiridoid biosynthesis. Our results not only enrich the gene resource but will also benefit research into the molecular genetics and functional genomics of this species.

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Acknowledgments

This work benefited from financial support from the National Natural Science Foundation of China (Grant No. 31270338, 31300256), the postdoctoral fund of Shaanxi Province, the Natural Science Foundation of Shaanxi Province, China (Grant No. 2012JQ4013), the Science and Technology Project of Xi’an (Grant No. NC1206-5) and the Fundamental Research Funds for the Central Universities (GK201302043).

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Authors and Affiliations

  1. Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, 710062, People’s Republic of China

    Wenping Hua, Peng Zheng, Yihan He, Langjun Cui, Weiwei Kong & Zhezhi Wang

  2. Department of Life Sciences, Shaanxi XueQian Normal University, Xi’an, 710100, Shaanxi, People’s Republic of China

    Wenping Hua

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  1. Wenping Hua
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  2. Peng Zheng
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  3. Yihan He
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  4. Langjun Cui
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  5. Weiwei Kong
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  6. Zhezhi Wang
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Corresponding author

Correspondence to Zhezhi Wang.

Additional information

Wenping Hua and Peng Zheng have contributed equally to this study.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplemental File 1. Size distribution of Gentiana macrophylla unigenes. (TIFF 1057 kb)

11033_2014_3352_MOESM2_ESM.doc

Supplemental File 2. Twenty most-represented pathways in the Gentiana macrophylla transcriptome. Supplemental File 3. Output statistics from DGE sequencing of different organs from Gentiana macrophylla. (DOC 71 kb)

Supplemental File 4. Top 50 unigenes expressed in different organs of Gentiana macrophylla. (XLS 74 kb)

11033_2014_3352_MOESM4_ESM.xls

Supplemental File 5. Expression patterns for unigenes derived from four organ libraries for Gentiana macrophylla. (XLS 5718 kb)

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Hua, W., Zheng, P., He, Y. et al. An insight into the genes involved in secoiridoid biosynthesis in Gentiana macrophylla by RNA-seq. Mol Biol Rep 41, 4817–4825 (2014). https://doi.org/10.1007/s11033-014-3352-x

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  • DOI: https://doi.org/10.1007/s11033-014-3352-x

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