Ginseng, which contains ginsenosides characterized as bioactive compounds, has been regarded as an important traditional medicine for millennia. However, the size and complexity of its genome has hindered the ginseng industry, including its cultivation and the metabolic engineering of ginsenosides.
Here, we report the whole genome sequence of Panax ginseng. Its 3.5-Gb nucleotide sequence, which contains more than 60% repeats, encodes 42,006 predicted genes encompassing 488 cytochrome P450s, 2556 transcription factors and 3745 transporter genes.
Twenty-nine genes involved in the mevalonic acid (MVA) pathway were identified, of which eight were annotated as HMGRs. To precisely quantify the functional genes, 27 transcriptomes and desorption electrospray ionization mass spectrometry (DESI-MS) imaging of ginseng root were employed. The analysis showed that HMGR2.2 played a functional role in ginsenoside synthesis. Furthermore, 1652 resistance genes were identified, some of which were co-expressed with HMGR2.2, implicating a coordination between microbe resistance and secondary metabolism in P. ginseng. A total of 208 UDP-glycosyltransferase genes were detected, indicating a large amount of gene expansion compared with other plants. Tandem repeats contributed to the duplication and divergence of UGTs. Molecular modeling of UGT 71, 74 and 94 revealed a conserved motif located at the N-terminus that was predicted to capture ginsenoside precursors via molecule docking. Three predicted functional UGTs (UGT166, UGT212 and UGT47) were cloned and expressed in E. coli, and their ability to modify ginsenosides was confirmed. This research will contribute to ginseng breeding, cultivation and synthetic biology, and it also offers a powerful solution for plant functional genomic analysis with increased throughput, precision and sensitivity.