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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.
Keywords
Gene expression, Genome assembly, Panax vietnamensis Ha et Grushv., Vietnamese ginseng, Whole-genome sequencing, CANCER, MAJONOSIDE-R2, EXPRESSION, PATHWAY, CLONING, TOOL

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MLA
Tien, Nguyen Quang Duc, et al. “De Novo Whole-Genome Assembly and Discovery of Genes Involved in Triterpenoid Saponin Biosynthesis of Vietnamese Ginseng (Panax Vietnamensis Ha et Grushv.).” PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS, vol. 27, no. 10, 2021, pp. 2215–29, doi:10.1007/s12298-021-01076-1.
APA
Tien, N. Q. D., Ma, X., Man, L. Q., Chi, D. T. K., Huy, N. X., Nhut, D.-T., … Loc, N. H. (2021). De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng (Panax vietnamensis Ha et Grushv.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS, 27(10), 2215–2229. https://doi.org/10.1007/s12298-021-01076-1
Chicago author-date
Tien, Nguyen Quang Duc, Xiao Ma, Le Quang Man, Duong Thi Kim Chi, Nguyen Xuan Huy, Duong-Tan Nhut, Stephane Rombauts, Tran Ut, and Nguyen Hoang Loc. 2021. “De Novo Whole-Genome Assembly and Discovery of Genes Involved in Triterpenoid Saponin Biosynthesis of Vietnamese Ginseng (Panax Vietnamensis Ha et Grushv.).” PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS 27 (10): 2215–29. https://doi.org/10.1007/s12298-021-01076-1.
Chicago author-date (all authors)
Tien, Nguyen Quang Duc, Xiao Ma, Le Quang Man, Duong Thi Kim Chi, Nguyen Xuan Huy, Duong-Tan Nhut, Stephane Rombauts, Tran Ut, and Nguyen Hoang Loc. 2021. “De Novo Whole-Genome Assembly and Discovery of Genes Involved in Triterpenoid Saponin Biosynthesis of Vietnamese Ginseng (Panax Vietnamensis Ha et Grushv.).” PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS 27 (10): 2215–2229. doi:10.1007/s12298-021-01076-1.
Vancouver
1.
Tien NQD, Ma X, Man LQ, Chi DTK, Huy NX, Nhut D-T, et al. De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng (Panax vietnamensis Ha et Grushv.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS. 2021;27(10):2215–29.
IEEE
[1]
N. Q. D. Tien et al., “De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng (Panax vietnamensis Ha et Grushv.),” PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS, vol. 27, no. 10, pp. 2215–2229, 2021.
@article{8733960,
  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.}},
  author       = {{Tien, Nguyen Quang Duc and Ma, Xiao and Man, Le Quang and Chi, Duong Thi Kim and Huy, Nguyen Xuan and Nhut, Duong-Tan and Rombauts, Stephane and Ut, Tran and Loc, Nguyen Hoang}},
  issn         = {{0971-5894}},
  journal      = {{PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS}},
  keywords     = {{Gene expression,Genome assembly,Panax vietnamensis Ha et Grushv.,Vietnamese ginseng,Whole-genome sequencing,CANCER,MAJONOSIDE-R2,EXPRESSION,PATHWAY,CLONING,TOOL}},
  language     = {{eng}},
  number       = {{10}},
  pages        = {{2215--2229}},
  title        = {{De novo whole-genome assembly and discovery of genes involved in triterpenoid saponin biosynthesis of Vietnamese ginseng (Panax vietnamensis Ha et Grushv.)}},
  url          = {{http://dx.doi.org/10.1007/s12298-021-01076-1}},
  volume       = {{27}},
  year         = {{2021}},
}

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