Genome and evolution of the shade-requiring medicinal herb Panax ginseng
Open Access
- 1 November 2018
- journal article
- research article
- Published by Wiley in Plant Biotechnology Journal
- Vol. 16 (11), 1904-1917
- https://doi.org/10.1111/pbi.12926
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.Funding Information
- Rural Development Administration
This publication has 88 references indexed in Scilit:
- The world ginseng market and the ginseng (Korea)Journal of Ginseng Research, 2013
- Effects of Panax ginseng in Neurodegenerative DiseasesJournal of Ginseng Research, 2012
- EST-SSR Marker Sets for Practical Authentication of All Nine Registered Ginseng Cultivars in KoreaJournal of Ginseng Research, 2012
- Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0Nature Protocols, 2011
- Full-length transcriptome assembly from RNA-Seq data without a reference genomeNature Biotechnology, 2011
- A fast, lock-free approach for efficient parallel counting of occurrences of k-mersBioinformatics, 2011
- The Ectocarpus genome and the independent evolution of multicellularity in brown algaeNature, 2010
- A protocol for generating a high-quality genome-scale metabolic reconstructionNature Protocols, 2010
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics, 2009
- OrthoMCL: Identification of Ortholog Groups for Eukaryotic GenomesGenome Research, 2003