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

Abstract

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.

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

“…S10 ). Our results demonstrate that this WGD event occurred in the common ancestor of the studied Panax species, which is strongly supported by the tetraploid P. ginseng genome analysis that revealed such a shared WGD event in the Panax lineage at 28 MYA (Pg-β) 69 .…”

The unprecedented diversity of UGT94-family UDP-glycosyltransferases in Panax plants and their contribution to ginsenoside biosynthesis

“…Published P . ginseng genome data indicates that Pg_scaffold6708 (aligned with Scaffold8624 sequecned in another study 6 ) and Pg_scaffold2289 harbor three and two PgUGT94 homolog sequences in tandem repeat arrays, respectively 5 . Our cloning and sequencing of a 14–26 kb fragment from Pg_scaffold6708 demonstrated that it contained three PgUGT94 homolog genes, which were identical to three detected PgUGT94 units (PgUGT94Q5-V1, PgUGT94Q11-V1, and PgUGT94Q4-V1) from the P .…”

Structural variation, functional differentiation and expression characteristics of the AP2/ERF gene family and its response to cold stress and methyl jasmonate inPanax ginsengC.A. Meyer

“…Moreover, we also sequenced and established the databases for the transcriptomes of the roots of 5-, 12-, 18- and 25-year-old plants [34] and the roots of four-year-old plants of 42 genotypes (named from S1 to S42) representing the diversity of Jilin ginseng [35]. In this study, a ginseng line IR826 genome sequence database [36] and another Ginseng Genome Database (http://ginsengdb.snu.ac.kr/index.php) reported by Kim et al [37] were also used. In addition, a transcriptome database of the adventitious roots of ginseng cv.…”