Dataset Information

Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

ABSTRACT: 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.

SUBMITTER: Kim NH

PROVIDER: S-EPMC6181221 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

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Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

Kim Nam-Hoon NH Jayakodi Murukarthick M Lee Sang-Choon SC Choi Beom-Soon BS Jang Woojong W Lee Junki J Kim Hyun Hee HH Waminal Nomar E NE Lakshmanan Meiyappan M van Nguyen Binh B Lee Yun Sun YS Park Hyun-Seung HS Koo Hyun Jo HJ Park Jee Young JY Perumal Sampath S Joh Ho Jun HJ Lee Hana H Kim Jinkyung J Kim In Seo IS Kim Kyunghee K Koduru Lokanand L Kang Kyo Bin KB Sung Sang Hyun SH Yu Yeisoo Y Park Daniel S DS Choi Doil D Seo Eunyoung E Kim Seungill S Kim Young-Chang YC Hyun Dong Yun DY Park Youn-Il YI Kim Changsoo C Lee Tae-Ho TH Kim Hyun Uk HU Soh Moon Soo MS Lee Yi Y In Jun Gyo JG Kim Heui-Soo HS Kim Yong-Min YM Yang Deok-Chun DC Wing Rod A RA Lee Dong-Yup DY Paterson Andrew H AH Yang Tae-Jin TJ

Plant biotechnology journal 20180525 11

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 intercont ...[more]

PMID: 29604169

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Project description:Panax ginseng C.A. Meyer (P. ginseng) is an important medicinal plant and is often used in traditional Chinese medicine. With next generation sequencing (NGS) technology, we determined the complete chloroplast genome sequences for four Chinese P. ginseng strains, which are Damaya (DMY), Ermaya (EMY), Gaolishen (GLS), and Yeshanshen (YSS). The total chloroplast genome sequence length for DMY, EMY, and GLS was 156,354 bp, while that for YSS was 156,355 bp. Comparative genomic analysis of the chloroplast genome sequences indicate that gene content, GC content, and gene order in DMY are quite similar to its relative species, and nucleotide sequence diversity of inverted repeat region (IR) is lower than that of its counterparts, large single copy region (LSC) and small single copy region (SSC). A comparison among these four P. ginseng strains revealed that the chloroplast genome sequences of DMY, EMY, and GLS were identical and YSS had a 1-bp insertion at base 5472. To further study the heterogeneity in chloroplast genome during domestication, high-resolution reads were mapped to the genome sequences to investigate the differences at the minor allele level; 208 minor allele sites with minor allele frequencies (MAF) of ≥0.05 were identified. The polymorphism site numbers per kb of chloroplast genome sequence for DMY, EMY, GLS, and YSS were 0.74, 0.59, 0.97, and 1.23, respectively. All the minor allele sites located in LSC and IR regions, and the four strains showed the same variation types (substitution base or indel) at all identified polymorphism sites. Comparison results of heterogeneity in the chloroplast genome sequences showed that the minor allele sites on the chloroplast genome were undergoing purifying selection to adapt to changing environment during domestication process. A study of P. ginseng chloroplast genome with particular focus on minor allele sites would aid in investigating the dynamics on the chloroplast genomes and different P. ginseng strains typing.

Dataset Information

Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

Publications

Genome and evolution of the shade-requiring medicinal herb Panax ginseng.

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