Ginseng genome examination for ginsenoside biosynthesis

Ginseng, which contains ginsenosides characterized as bioactive compounds, has been regarded as an important traditional medicine for several millennia. Howerver, the genetic background of ginseng remains poorly understood partly because of the plant's large and complex genome composition.
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We report the entire genome sequence of Panax ginseng using next-generation sequencing. The 3.5 Gb nucleotide sequence contained more than 60% repeats and encoded 42,006 predicted genes. Twenty-two transcriptome datasets and mass spectrometry images of ginseng roots were adopted to precisely quantify the functional genes. Thirty-one genes were identified to be involved in the mevalonic acid pathway. Eight of these genes were annotated as 3-hydroxy-3-methylglutaryl-CoA reductases, which displayed diverse structures and expression characteristics. A total of 225 UDP-glycosyltransferase (UGTs) were identified, and these UGTs accounted for one of the largest gene families of ginseng. Tandem repeats contributed to the duplication and divergence of UGTs. Molecular modeling of UGTs in the 71, 74, and 94 families revealed a regiospecific conserved motif located at the N-terminus. Molecular docking predicted that this motif captured ginsenoside precursors.
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The panorama of ginseng genome represents a valuable resource for understaning and improving the breeding, cultivation, and synthesis biology of this key herb.

人参含有被称为生物活性化合物的人参皂苷，数千年来一直被视为重要的传统药材。然而，由于人参基因组庞大且结构复杂，其遗传背景仍知之甚少。

我们利用下一代测序技术报道了人参（Panax ginseng）的全基因组序列。该3.5 Gb核苷酸序列包含超过60%的重复序列，编码42006个预测基因。我们采用22个转录组数据集和人参根的质谱图像，对功能基因进行精准量化。共鉴定出31个参与甲羟戊酸途径的基因，其中8个被注释为3-羟基-3-甲基戊二酰辅酶A还原酶，这些酶具有多样的结构和表达特征。共鉴定出225个UDP-糖基转移酶（UDP-glycosyltransferase, UGTs），该家族是人参最大的基因家族之一。串联重复促成了UGTs的复制与分化。对71、74和94家族UGTs的分子建模揭示了位于N端的区域特异性保守基序。分子对接预测该基序可结合人参皂苷前体。

人参基因组全景为理解和改进这一关键草本植物的育种、栽培及合成生物学研究提供了宝贵资源。