National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China.
State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan Agricultural University, Kunming, China.
Mol Ecol Resour. 2021 Oct;21(7):2204-2220. doi: 10.1111/1755-0998.13403. Epub 2021 Jul 29.
Siberian ginseng (Eleutherococcus senticosus, also known as ciwujia) belongs to the Araliaceae family, which contains more than 1,500 species in 41 genera with diverse chromosome numbers and genome sizes. General consensus posits that ancient whole-genome duplication events and rapid evolutionary radiation are the driving forces for this variation in genome properties. In an attempt to generate more genomic information for the Araliaceae family, we report a 1.30 Gb high-quality draft genome assembly (contig N50 = 309.43 kb) of E. senticosus via PacBio long reads and Hi-C chromatin interaction maps. We found that transposable elements accounted for 72.82% of the genome and a total of 36,372 protein-coding genes were predicted. Comparative analyses of the E. senticosus, Panax notoginseng and Daucus carota genomes revealed a burst expansion of Tekay chromoviral elements in Araliaceae after its divergence with Apiaceae. We also found that E. senticosus underwent a lineage-specific whole-genome duplication event Es-α and a whole-genome duplication event Araliaceae-β that was probably shared by all Araliaceae species. Even though the rediploidization of the E. senticosus genome is evident, pathway analyses show that these two whole-genome duplication events may have contributed to the adaptation of E. senticosus to a cold environment. Taken together, the high-quality genome assembly of E. senticosus provides a valuable genomic resource for future research on the evolution of Araliaceae.
西伯利亚人参（刺五加，也称为刺五加）属于五加科，该科包含超过 1500 种，分布在 41 个属中，具有不同的染色体数目和基因组大小。普遍认为，古老的全基因组复制事件和快速的进化辐射是导致基因组特性变化的驱动力。为了为五加科家族生成更多的基因组信息，我们通过 PacBio 长读和 Hi-C 染色质互作图谱报告了刺五加的 13 亿高质量基因组草图组装（contig N50 = 309.43 kb）。我们发现转座元件占基因组的 72.82%，共预测了 36372 个蛋白质编码基因。对刺五加、三七和胡萝卜基因组的比较分析表明，在与伞形科分化后，五加科中的 Tekay 染色质病毒元件发生了爆发性扩张。我们还发现，刺五加经历了一个谱系特异性的全基因组复制事件 Es-α和一个可能被所有五加科物种共享的全基因组复制事件 Araliaceae-β。尽管刺五加基因组的加倍化是明显的，但通路分析表明，这两个全基因组复制事件可能有助于刺五加适应寒冷环境。总之，高质量的刺五加基因组组装为未来对五加科的进化研究提供了有价值的基因组资源。
