NEW YORK (GenomeWeb) – Researchers have sequenced the genome of the ginseng plant for the first time.
Ginseng has been used as a traditional medicine for millennia in East Asia and modern pharmacological research has focused on its major bioactive compounds, the ginsenosides.
Researchers led by China Academy of Chinese Medical Sciences' Shilin Chen reported in GigaScience this week that they sequenced Panax ginseng and found that its 3.4-gigabase genome is highly repetitive. By folding in transcriptome data from various plant tissues, the researchers also began to investigate the genes involved in the synthesis of ginsenosides.
"The ginseng genome represents a valuable resource for understanding and improving the breeding, cultivation, and synthesis biology of this key herb," Chen and his colleagues wrote in their paper.
The researchers extracted genomic DNA from a four-year-old P. ginseng line with low heterozygosity for paired-end sequencing on the Illumina HiSeq X platform. After filtering, they assembled the 91X high-quality reads into a 3.43-gigabase draft genome.
Some 62 percent of the P. ginseng genome is predicted to be repeats, the researchers reported, which is higher than sorghum, rice, and grape, and similar to orchid. They also estimated that the P. ginseng genome harbors slightly more than 42,000 protein-coding genes.
Chen and his colleagues zeroed their analyses in on the ginsenosides. Using desorption electrospray ionization mass spectrometry, they examined the distribution of ginsenosides within ginseng roots. Certain types of ginsenosides, they found, were concentrated in the outer bark or core of the roots, while others were more widespread. This led them to separate out different parts of the root for their gene expression analyses.
The transcriptome data they generated found thousands of genes that were differentially expressed between various root regions. Many of these genes, they noted, were involved in metabolic processes and stimulus response.
Many of the enzymes in the mevalomic acid (MVA) pathway through which ginsenosides are synthesized were present in multiple copies and isoforms in the ginseng genome, Chen and his colleagues noted. For instance, there are eight genes in the P. ginseng genome that encode 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), which helps catalyzed HMG-CoA into MVA. Four of these HMGR genes are highly similar to the previously reported PgHMGR1, while the others were similar to PgHMGR2. The researchers found that the expression of the PgHMGR2s varied more than that of the PgHMGR1s, suggesting to them that PgHMGR2s might have a regulatory role during ginseng development.
Similarly, the researchers uncovered 225 UDP-glycosyltransferases (UGTs) within the ginseng genome, making them one of the largest ginseng gene families. The UGTs, which aid in the glycosylation of ginsenosides, also exhibited tissue-specific expression patterns, with some being highly expressed in root and others not present in the root at all, but in the fruit. Molecular modeling of a subset of the UGTs indicated that they had a conserved three-dimensional structure and had a general regiospecificity.
The researchers said that the P. ginseng genome and analysis of ginsenoside synthesis pathways would help inform ginseng breeding, cultivation, and synthesis. It also "provides an effective resource for plant functional genomic analysis with increased throughput, precision, and sensitivity," they added.