Differential transcriptome analysis is an effective method for gene selection of triterpene saponin biosynthetic pathways. MeJA-induced differential transcriptome of Panax notoginseng has not been analyzed yet. In this study, comparative transcriptome analysis of P. notoginseng roots and methyl jasmonate (MeJA)-induced roots revealed 83,532 assembled unigenes and 21,947 differentially expressed unigenes. Sixteen AP2/ERF transcription factors, which were significantly induced by MeJA treatment in the root of P. notoginseng, were selected for further analysis. Real-time quantitative PCR (RT-qPCR) and co-expression network analysis of the 16 AP2/ERF transcription factors showed that PnERF2 and PnERF3 had significant correlation with dammarenediol II synthase gene (DS) and squalene epoxidase gene (SE), which are key genes in notoginsenoside biosynthesis, in different tissues and MeJA-induced roots. A phylogenetic tree was conducted to analyze the 16 candidate AP2/ERF transcription factors and other 38 transcription factors. The phylogenetic tree analysis showed PnERF2, AtERF3, AtERF7, TcERF12 and other seven transcriptional factors are in same branch, while PnERF3 had close evolutionary relationships with AtDREB1A, GhERF38 and TcAP2. The results of comparative transcriptomes and AP2/ERF transcriptional factors analysis laid a solid foundation for further investigations of disease resistance and notoginsenoside biosynthesis in P. notoginseng.

差异转录组分析是三萜皂苷生物合成途径基因选择的有效方法。MeJA诱导的三七的差异转录组尚未进行分析。在这项研究中，对三七参根和茉莉酸甲酯（MeJA）诱导的根进行的转录组比较分析揭示了83,532个组装的单基因和21,947个差异表达的单基因。选择16种AP2 / ERF转录因子进行进一步分析，这些因子通过MeJA处理在三七根中显着诱导。实时定量PCR（RT-qPCR）和16个AP2 / ERF转录因子的共表达网络分析表明PnERF2和PnERF3与三七皂苷生物合成中的关键基因丹豆二醇II合酶基因（DS）和角鲨烯环氧酶基因（SE）在不同的组织和MeJA诱导的根中具有显着的相关性。进行系统进化树分析16个候选AP2 / ERF转录因子和其他38个转录因子。系统进化树分析显示，PnERF2，AtERF3，AtERF7，TcERF12和其他七个转录因子位于同一分支，而PnERF3与AtDREB1A，GhERF38和TcAP2有着密切的进化关系。比较转录和AP2 / ERF转录因子分析的结果为抗病进一步调查和三七在生物合成奠定了基础三七。