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De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng (Panax vietnamensis Ha et Grushv.)

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Abstract

Vietnamese ginseng (Panax vietnamensis Ha et Grushv.), also known as Ngoc Linh ginseng, is a high-value herb in Vietnam. Vietnamese ginseng has been proven to be effective in enhancing the immune system, human memory, anti-stress, anti-inflammatory, anti-cancer, and prevent aging. The present study reports the first draft whole-genome of Vietnamese ginseng and the identification of potential genes involved in the triterpenoid metabolic pathway. De novo whole-genome assembly was performed successfully from a data of approximately 139 Gbps of 394,802,120 high quality reads to generate 9815 scaffolds with an N50 value of 572,722 bp from the leaf of Vietnamese ginseng. The assembled genome of Vietnamese ginseng is 3,001,967,204 bp long containing 79,374 gene models. Among them, there are 55,012 genes (69.30%) were annotated by various public molecular biology databases. The potential genes involved in triterpenoid saponin biosynthesis in Vietnamese ginseng and their metabolic pathway were also predicted.“ Three genes encoding squalene monooxygenase isozymes in Vietnamese ginseng were cloned, sequenced and characterized. Moreover, expression levels of several key genes involved in terpenoid biosynthesis in different parts of Vietnamese ginseng were also analyzed. The SSR markers were detected by various programs from both of assembly full dataset of Vietnamese ginseng genome and predicted genes. The present work provided important data of the draft whole-genome of Vietnamese ginseng for further studies to understand the role of genes involved in ginsenoside biosynthesis and their metabolic pathway at the molecular level of this rare medicinal species.

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Acknowledgements

This research was financially supported by the National Foundation for Science and Technology Development (NAFOSTED), Vietnam (Grant number 106.02-2018.49).

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Authors and Affiliations

  1. Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000, Vietnam

    Nguyen Quang Duc Tien, Le Quang Man, Duong Thi Kim Chi & Nguyen Hoang Loc

  2. Department of Biology, Bioactive Compound Institute, University of Sciences, Hue University, Hue, 530000, Vietnam

    Nguyen Quang Duc Tien & Nguyen Hoang Loc

  3. Hue University, Hue, 530000, Vietnam

    Nguyen Xuan Huy

  4. Tay Nguyen Institute of Scientific Research, Vietnam Academy of Science and Technology, Dalat, 670000, Vietnam

    Duong-Tan Nhut

  5. VIB-UGent Center for Plant Systems Biology, Ghent University, 9000, Ghent, Belgium

    Xiao Ma & Stephane Rombauts

  6. Ngoc Linh Ginseng and Medicinal Materials Development Center, Quang Nam, Quang Ngai, 51000, Vietnam

    Tran Ut

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  1. Nguyen Quang Duc Tien
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  2. Xiao Ma
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  3. Le Quang Man
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  4. Duong Thi Kim Chi
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  5. Nguyen Xuan Huy
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  7. Stephane Rombauts
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  8. Tran Ut
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  9. Nguyen Hoang Loc
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Contributions

Loc NH, Tien NQD and Nhut DT conceived, designed, and performed the overall study. Ma X and Rombauts S performed genome assembly. Ma X, Rombauts S and Tien NQD performed genome annotation, gene ontology analysis, and prediction of genes involved in triterpenoid biosynthesis in Vietnamese ginseng. Tien NQD performed gene clusters analysis, detection of SSR markers, and prediction of metabolic pathways. Tien NQD, Man LQ, Chi DTK conducted full-length cloning of genes encoding squalene epoxidase isoenzymes and the analysis of their characteristics. Tien NQD, Nhut DT, Man LQ and Huy NX analyzed gene expression. Ut T provides samples. Tien NQD and Loc NH wrote and approved the final manuscript.

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Correspondence to Nguyen Hoang Loc.

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Tien, N.Q.D., Ma, X., Man, L.Q. et al. De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng (Panax vietnamensis Ha et Grushv.). Physiol Mol Biol Plants 27, 2215–2229 (2021). https://doi.org/10.1007/s12298-021-01076-1

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  • DOI: https://doi.org/10.1007/s12298-021-01076-1

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