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De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis

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Abstract

Cornus officinalis Sieb. et Zucc. is a small tree that is recognized with notable medicinal, economic, and ecological values. It has been used as traditional Chinese medicine (TCM) for thousands of years in China. Modern pharmacological research has revealed that cornel iridoid glycosides (CIGs, e.g., loganin and morroniside) in dried pericarp of C. officinalis have significant medicinal activities for strengthening immune functions. However, little is known on the molecular processes responsible for the production of these compounds. This is partly due to the absence of genomic resources, such as sequences of key enzyme genes in the biosynthetic pathways. In the present study, the transcriptome of C. officinalis was analyzed by the RNA sequencing. A total of 54,827 unigenes were yielded by de novo assembly, of which 31,780 unigenes were successfully annotated. As potential molecular markers, 121, 118, 96, 89, and 82 transcription factors belonged to bHLH, MYB, PHD, WRKY, and AP2-ERF were obtained, respectively. Moreover, the results showing that geraniol 10-hydroxylase (G10H) and secologanin synthase (SLS) were differentially expressed in fruits and leaves during different growing stages were confirmed by qRT-PCR. Furthermore, we identified two distinct expression patterns of G10H and SLS in loganin synthesis of C. officinalis fruits. Collectively, the genomic information and gene expression results presented in this study will be helpful for future studies on gene discovery and molecular process of loganin synthesis in C. officinalis.

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Acknowledgments

We thank Drs. Yinghua Zha and Lei Zhang for their helpful revision on this manuscript. We thank Drs. Robin Buell and Dongyan Zhao for their kind assistance on genome sequences. We also thank Professor Vincent Courdavault for the technical support on the figures. This work was supported by the Innovation Team Project of Breeding and Standardized Production of New Varieties of Traditional Chinese Medicine in Fundamental Research Funds of the Central Universities [GK201801008 to CKB], the National Natural Science Foundation of China [31100241 to CKB], and the Fundamental Research Funds for the Central Universities [GK201503046 to GSL].

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Authors and Affiliations

  1. National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi’an, 710062, China

    Chengke Bai, Yongmei Wu, Jun Xu & Guishuang Li

  2. Core Research Laboratory, the Second Affiliated Hospital, School of Medicine, Xi’an Jiaotong University, Xi’an, 710004, China

    Bo Cao

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  1. Chengke Bai
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Correspondence to Chengke Bai.

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This article does not contain any studies with human participants or animals performed by any of the authors.

Data archiving statement

The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus (Edgar et al. 2002) and are accessible through GEO Series accession number GSE108216 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE108216).

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Communicated by C. Dardick

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Bai, C., Wu, Y., Cao, B. et al. De novo transcriptome assembly based on RNA-seq and dynamic expression of key enzyme genes in loganin biosynthetic pathway of Cornus officinalis. Tree Genetics & Genomes 14, 57 (2018). https://doi.org/10.1007/s11295-018-1270-0

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  • DOI: https://doi.org/10.1007/s11295-018-1270-0

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