Table3_Transcriptome and metabolome profiling unveil the accumulation of chlorogenic acid in autooctoploid Gongju.xlsx

BackgroundGongju is recognized as one of the four traditional Chinese medicinal herbs, and its main constituents are chlorogenic acid (CGA) and its derivative material. CGA content in autooctoploid Gongju are considerably elevated compared with those in parental tetraploid Gongju at different flowering stages. However, the underlying molecular mechanisms governing the regulation CGA content remain poorly understood.
MethodsTherefore, we conducted integrated transcriptome and metabolome analyses of different flowering stages in autooctoploid and tetraploid Gongju to elucidate the underlying molecular mechanisms governing CGA biosynthesis.
ResultsTranscriptome analysis showed that the number of differentially expressed genes in the budding stage (BS), early flowering stage (EF), and full flowering stage (FF) of tetraploid and octoploid Gongju were 3859, 11,211, and 6837, respectively. A total of 563, 466, and 394 differential accumulated metabolites were respectively identified between the bud stages of tetraploid and octoploid Gongju (4BS vs. 8BS), between the early flowering stages of tetraploid and octoploid Gongju (4EF vs. 8EF), and the full flowering stages of tetraploid and octoploid Gongju (4FF vs. 8FF) groups. The integrated analysis of transcriptomics and metabolomics revealed that the expression of pma6460 and mws0178, which are key enzymes involved in the CGA synthesis pathway, increased during the flowering stages of octoploid Gongju relative to that of tetraploid Gongju. The expression levels of CmHQT and CmC3H genes associated with CGA synthesis were higher in octoploid plants than in tetraploid plants at various flowering stages. To investigate the potential regulation of transcription factors involved in CGA synthesis, we analyzed the coexpression of CmC3H and CmHQT with CmMYBs and CmbHLHs. Results indicated that transcription factors, such as CmMYB12 (Cluster-30519.0), CmMYB26 (Cluster-75874.0), CmMYB5 (Cluster-94106.0), CmMYB1 (Cluster-71968.7), CmbHLH62 (Cluster-32024.1), CmbHLH75 (Cluster-62341.0), CmbHLH62 (Cluster-32024.8), CmbHLH75 (Cluster-60210.0), and CmbHLH16 (Cluster-90665.1) play a pivotal role in CGA synthesis regulation. The present study provides novel insights into the molecular mechanisms underlying CGA accumulation in autopolyploid Gongju.

背景 贡菊（Gongju）是中国四大传统药用草本之一，其主要活性成分为绿原酸（chlorogenic acid, CGA）及其衍生物。相较于亲本四倍体贡菊，同源八倍体贡菊在不同开花时期的CGA含量均显著升高，但调控CGA积累的潜在分子机制仍不甚明晰。
方法 为此，本研究对同源八倍体与四倍体贡菊的不同开花时期样本开展整合转录组与代谢组分析，以阐明调控CGA生物合成的潜在分子机制。
结果 转录组分析显示，四倍体与八倍体贡菊的现蕾期（BS）、始花期（EF）、盛花期（FF）的差异表达基因数量分别为3859、11211和6837。在四倍体与八倍体贡菊的现蕾期组（4BS vs 8BS）、始花期组（4EF vs 8EF）、盛花期组（4FF vs 8FF）中，分别鉴定得到563、466和394种差异积累代谢物。转录组与代谢组整合分析发现，相较于四倍体贡菊，八倍体贡菊开花阶段中参与CGA合成通路的关键酶基因pma6460和mws0178的表达水平显著上调。在各开花时期，八倍体植株中与CGA合成相关的CmHQT和CmC3H基因的表达量均高于四倍体植株。为探究参与CGA合成的转录因子的潜在调控作用，本研究分析了CmC3H、CmHQT与CmMYBs及CmbHLHs的共表达关系。结果表明，CmMYB12（Cluster-30519.0）、CmMYB26（Cluster-75874.0）、CmMYB5（Cluster-94106.0）、CmMYB1（Cluster-71968.7）、CmbHLH62（Cluster-32024.1）、CmbHLH75（Cluster-62341.0）、CmbHLH62（Cluster-32024.8）、CmbHLH75（Cluster-60210.0）及CmbHLH16（Cluster-90665.1）等转录因子在CGA合成调控中发挥关键作用。本研究为同源多倍体贡菊中CGA积累的分子机制提供了全新的研究见解。