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The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis
Panax notoginseng, a perennial herb of the genus Panax in the family Araliaceae, has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects. Here, we report a high-quality reference genome of P. notoginseng, with a genome size...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7816079/ https://www.ncbi.nlm.nih.gov/pubmed/33511345 http://dx.doi.org/10.1016/j.xplc.2020.100113 |
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author | Jiang, Zhouqian Tu, Lichan Yang, Weifei Zhang, Yifeng Hu, Tianyuan Ma, Baowei Lu, Yun Cui, Xiuming Gao, Jie Wu, Xiaoyi Tong, Yuru Zhou, Jiawei Song, Yadi Liu, Yuan Liu, Nan Huang, Luqi Gao, Wei |
author_facet | Jiang, Zhouqian Tu, Lichan Yang, Weifei Zhang, Yifeng Hu, Tianyuan Ma, Baowei Lu, Yun Cui, Xiuming Gao, Jie Wu, Xiaoyi Tong, Yuru Zhou, Jiawei Song, Yadi Liu, Yuan Liu, Nan Huang, Luqi Gao, Wei |
author_sort | Jiang, Zhouqian |
collection | PubMed |
description | Panax notoginseng, a perennial herb of the genus Panax in the family Araliaceae, has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects. Here, we report a high-quality reference genome of P. notoginseng, with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb, produced with third-generation PacBio sequencing technology. This is the first chromosome-level genome assembly for the genus Panax. Through genome evolution analysis, we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis. We performed a detailed transcriptional analysis of P. notoginseng and explored gene-level mechanisms that regulate the formation of characteristic tubercles. Next, we studied the biosynthesis and regulation of saponins at temporal and spatial levels. We combined multi-omics data to identify genes that encode key enzymes in the P. notoginseng terpenoid biosynthetic pathway. Finally, we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P. notoginseng. The genetic information obtained in this study provides a resource for further exploration of the growth characteristics, cultivation, breeding, and saponin biosynthesis of P. notoginseng. |
format | Online Article Text |
id | pubmed-7816079 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-78160792021-01-27 The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis Jiang, Zhouqian Tu, Lichan Yang, Weifei Zhang, Yifeng Hu, Tianyuan Ma, Baowei Lu, Yun Cui, Xiuming Gao, Jie Wu, Xiaoyi Tong, Yuru Zhou, Jiawei Song, Yadi Liu, Yuan Liu, Nan Huang, Luqi Gao, Wei Plant Commun Research Article Panax notoginseng, a perennial herb of the genus Panax in the family Araliaceae, has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects. Here, we report a high-quality reference genome of P. notoginseng, with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb, produced with third-generation PacBio sequencing technology. This is the first chromosome-level genome assembly for the genus Panax. Through genome evolution analysis, we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis. We performed a detailed transcriptional analysis of P. notoginseng and explored gene-level mechanisms that regulate the formation of characteristic tubercles. Next, we studied the biosynthesis and regulation of saponins at temporal and spatial levels. We combined multi-omics data to identify genes that encode key enzymes in the P. notoginseng terpenoid biosynthetic pathway. Finally, we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P. notoginseng. The genetic information obtained in this study provides a resource for further exploration of the growth characteristics, cultivation, breeding, and saponin biosynthesis of P. notoginseng. Elsevier 2020-09-20 /pmc/articles/PMC7816079/ /pubmed/33511345 http://dx.doi.org/10.1016/j.xplc.2020.100113 Text en © 2020 The Authors http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Article Jiang, Zhouqian Tu, Lichan Yang, Weifei Zhang, Yifeng Hu, Tianyuan Ma, Baowei Lu, Yun Cui, Xiuming Gao, Jie Wu, Xiaoyi Tong, Yuru Zhou, Jiawei Song, Yadi Liu, Yuan Liu, Nan Huang, Luqi Gao, Wei The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis |
title | The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis |
title_full | The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis |
title_fullStr | The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis |
title_full_unstemmed | The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis |
title_short | The chromosome-level reference genome assembly for Panax notoginseng and insights into ginsenoside biosynthesis |
title_sort | chromosome-level reference genome assembly for panax notoginseng and insights into ginsenoside biosynthesis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7816079/ https://www.ncbi.nlm.nih.gov/pubmed/33511345 http://dx.doi.org/10.1016/j.xplc.2020.100113 |
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