The Medicinal Herb Panax notoginseng Genome Provides Insights into Ginsenoside Biosynthesis and Genome Evolution

Zhang, Dan; Li, Wei; Xia, Enhua; Zhang, Qun‐Jie; Liu, Yuan; Zhang, Yun; Tong, Yan; Zhao, Yuan; Niu, Yongchao; Xu, Jianxin; Gao, Li‐Zhi

doi:10.1016/j.molp.2017.02.011

Cited by 86 publications

(62 citation statements)

References 11 publications

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“…PgDel LTR‐RTs largely account for genome size variation among seven Panax species (Figure b,e). P. ginseng has doubled orthologous sequences compared to diploid P. notoginseng (Zhang et al ., ), and their modal K s value (0.035, Figure c,d) implies divergence 2.62 MYA, which is similar value to chloroplast analysis (Figure a). A unique high copy En/Spm ‐like CACTA transposon ( PgCACTA1 ) encoding two transposase genes and maintaining 31‐bp conserved terminal inverted repeats (TIR) has highly diverse copy number of Pg167TR (Waminal et al ., ) in the last intron of the second transposase (Figures a and S10), providing a molecular barcode for identification of individual chromosomes (Figure S11; Waminal et al ., ).…”

Section: Resultssupporting

confidence: 80%

Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

Kim

Jayakodi

Lee

et al. 2018

Plant Biotechnology Journal

153

123

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Summary Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane‐type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome‐scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics‐assisted breeding or metabolic engineering.

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Section: Resultssupporting

confidence: 80%

Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

Kim

Jayakodi

Lee

et al. 2018

Plant Biotechnology Journal

153

123

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“…Panax notoginseng (Burk) F. H. Chen is a perennial herbaceous plant, belonging to the genus Panax , Araliaceae. It is a diploid (2n = 2X = 24) with the haploid genome size of ~ 2.0 gigabases 1 – 3 , while the ginseng ( P. ginseng ) and American ginseng ( P. quinquefolium ), are tetraploids (2n = 4X = 48) with haploid genome sizes of ~ 3.2 and 4.9 gigabases, respectively 4 – 6 . P. notoginseng is mainly cultivated in Yunnan Province, China, consuming as a famous traditional Chinese herb for about 400 years 7 .…”

Section: Introductionmentioning

confidence: 99%

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng

Zhang

Chen

et al. 2020

Sci Rep

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Panax notoginseng is one of the most widely used traditional Chinese herbs with particularly valued roots. Triterpenoid saponins are mainly specialized secondary metabolites, which medically act as bioactive components. Knowledge of the ginsenoside biosynthesis in P. notoginseng, which is of great importance in the industrial biosynthesis and genetic breeding program, remains largely undetermined. Here we combined single molecular real time (SMRT) and Second-Generation Sequencing (SGS) technologies to generate a widespread transcriptome atlas of P. notoginseng. We mapped 2,383 full-length non-chimeric (FLNC) reads to adjacently annotated genes, corrected 1,925 mis-annotated genes and merged into 927 new genes. We identified 8,111 novel transcript isoforms that have improved the annotation of the current genome assembly, of which we found 2,664 novel lncRNAs. We characterized more alternative splicing (AS) events from SMRT reads (20,015 AS in 6,324 genes) than Illumina reads (18,498 AS in 9,550 genes), which contained a number of AS events associated with the ginsenoside biosynthesis. The comprehensive transcriptome landscape reveals that the ginsenoside biosynthesis predominantly occurs in flowers compared to leaves and roots, substantiated by levels of gene expression, which is supported by tissue-specific abundance of isoforms in flowers compared to roots and rhizomes. Comparative metabolic analyses further show that a total of 17 characteristic ginsenosides increasingly accumulated, and roots contained the most ginsenosides with variable contents, which are extraordinarily abundant in roots of the three-year old plants. We observed that roots were rich in protopanaxatriol- and protopanaxadiol-type saponins, whereas protopanaxadiol-type saponins predominated in aerial parts (leaves, stems and flowers). The obtained results will greatly enhance our understanding about the ginsenoside biosynthetic machinery in the genus Panax.

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“…Because P. notoginseng is an important Chinese traditional medicine, two draft genomes of P. notoginseng were published in 2017. Chen etc.’s genome assembly was about 2.39 Gb with a contig N50 of 16 kb and scaffold N50 of 96 kb and Zhang etc.’s was a ~1.85 Gb assembly with scaffold N50 of 158 kb and contig N50 of 13.2 kb 2,3 . There was a notable difference of genome assembly size (~540 Mb) between two genomes.…”

Section: Introductionmentioning

confidence: 99%

Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

Fan¹,

Fu²,

Yang

et al. 2018

Preprint

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Panax notoginseng is a traditional Chinese herb with high medicinal and economic value. There has been considerable research on the pharmacological activities of ginsenosides contained in Panax spp.; however, very little is known about the ginsenoside biosynthetic pathway. We reported the first de novo genome of 2.36 Gb of sequences from P. notoginseng with 35,451 protein-encoding genes. Compared to other plants, we found notable gene family contraction of disease-resistance genes in P. notoginseng, but notable expansion for several ATP-binding cassette (ABC) All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The 4, 2018; transporter subfamilies, such as the Gpdr subfamily, indicating that ABCs might be an additional mechanism for the plant to cope with biotic stress. Combining eight transcriptomes of roots and aerial parts, we identified several key genes, their transcription factor binding sites and all their family members involved in the synthesis pathway of ginsenosides in P. notoginseng, including dammarenediol synthase, CYP716 and UGT71. The complete genome analysis of P. notoginseng, the first in genus Panax, will serve as an important reference sequence for improving breeding and cultivation of this important nutraceutical and medicinal but vulnerable plant species.copyright holder for this preprint (which . http://dx.doi.org/10.1101/362046 doi: bioRxiv preprint first posted online Jul.All rights reserved. No reuse allowed without permission.was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

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The Medicinal Herb Panax notoginseng Genome Provides Insights into Ginsenoside Biosynthesis and Genome Evolution

Cited by 86 publications

References 11 publications

Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

SMRT- and Illumina-based RNA-seq analyses unveil the ginsinoside biosynthesis and transcriptomic complexity in Panax notoginseng

Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

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