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Transcriptome analysis of Dioscorea zingiberensis identifies genes involved in diosgenin biosynthesis

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Abstract

Dioscorea zingiberensis is the main plant source of diosgenin, a precursor for the production of steroid hormones used in the pharmaceutical industry. The extraction process of diosgenin from D. zingiberensis can generate high-acid and high-strength wastewater on a large scale and can threaten the environment. Bioengineering microorganisms to produce diosgenin is an effective way to avoid pollution. However, little is known about the genes that are involved in the biosynthesis of diosgenin. We obtained 85,010 unigenes (average length of 1142 bases) from the D. zingiberensis transcriptome through RNA-seq. A large number of unigenes (59,368; 69.83%) were annotated, and 2488 unigenes were assigned to 27 secondary-metabolite pathways. In our database, 66 unigenes encoding up to 40 key enzymes were found to be present in diosgenin biosynthesis pathways. In addition, we found 203 unigenes encoding CYP450 proteins and 47 unigenes encoding UGT proteins that may be involved in modifications of a downstream pathway. The expression patterns of key diosgenin biosynthesis genes were studied to identify the most important members of the enzyme family. These results add to the available genetic data of D. zingiberensis and lay the foundation for the further production of diosgenin using genetic engineering.

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Abbreviations

AS:

Amyrin synthase

CAS:

Cycloartenol synthase

IPP:

Isopentenyl pyrophosphate

EC:

Enzyme commission

FPS:

Farnesyl pyrophasphate synthase

GO:

Gene ontology

HMGR:

3-hydroxy-3-methylglutaryl CoA reductase

IDI:

Isopentenyl diphosphate isomerase

LS:

Lanosterol synthase

SQS:

Squalene synthase

OSC:

Oxidosqualene cyclase

TF:

Transcription factor

UGT:

Uridine diphosphate (UDP)-dependent glycosyltransferase

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Acknowledgements

This work benefited from financial support from the National Natural Science Foundation of China (Grant No. 31270338, 31300256), The Science and Technology Cooperation Project between Shaanxi Province and Qinghai Province (2014SJ-07), the Natural Science Foundation of Shaanxi Province, China (Grant No. 2015NY041), the National College Students Innovation and Entrepreneurship Training program (201514390767) and the Fundamental Research Funds for the Central Universities (GK201304004).

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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, Weiwei Kong, XiaoYan Cao, Chen Chen, Xiangmin Li & Zhezhi Wang

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

      Wenping Hua & Qian Liu

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    1. Wenping Hua
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    2. Weiwei Kong
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    Correspondence to Xiangmin Li or Zhezhi Wang.

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    Wenping Hua declares that he has no conflict of interest. Weiwei Kong declares that she has no conflict of interest. XiaoYan Cao declares that she has no conflict of interest. Chen chen declares that she has no conflict of interest. Qian Liu declares that she has no conflict of interest. Xiangmin Li declares that he has no conflict of interest.Zhezhi Wang declares that he has no conflict of interest.

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    Hua Wenping and Kong Weiwei have contributed equally to this study.

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    Hua, W., Kong, W., Cao, X. et al. Transcriptome analysis of Dioscorea zingiberensis identifies genes involved in diosgenin biosynthesis. Genes Genom 39, 509–520 (2017). https://doi.org/10.1007/s13258-017-0516-9

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