Background Pueraria lobata (Willd.) Ohwi is a valuable herb used in traditional Chinese medicine. Isoflavonoids are the major bioactive compounds in P. lobata, namely puerarin, daidzin, glycitin, genistin, daidzein, and glycitein, which have pharmacological properties of anti-cardiovascular, anti-hypertension, anti-inflammatory, and anti-arrhythmic. Methods To characterize the corresponding genes of the compounds in the isoflavonoid pathway, RNA sequencing (RNA-Seq) analyses of roots, stems, and leaves of P. lobata were carried out on the BGISEQ-500 sequencing platform. Results We identified 140,905 unigenes in total, of which 109,687 were annotated in public databases, after assembling the transcripts from all three tissues. Multiple genes encoding key enzymes, such as IF7GT and transcription factors, associated with isoflavonoid biosynthesis were identified and then further analyzed. Quantitative real-time PCR (qRT-PCR) results of some genes encoding key enzymes were consistent with our RNA-Seq analysis. Differentially expressed genes (DEGs) were determined by analyzing the expression profiles of roots compared with other tissues (leaves and stems). This analysis revealed numerous DEGs that were either uniquely expressed or up-regulated in the roots. Finally, quantitative analyses of isoflavonoid metabolites occurring in the three P. lobata tissue types were done via high-performance liquid-chromatography and tandem mass spectrometry methodology (HPLC-MS/MS). Our comprehensive transcriptome investigation substantially expands the genomic resources of P. lobata and provides valuable knowledge on both gene expression regulation and promising candidate genes that are involved in plant isoflavonoid pathways.

中文翻译：

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葛根、茎和叶的比较转录组分析：鉴定参与异黄酮生物合成的基因


背景 葛根 (Pueraria lobata (Wild.) Ohwi) 是一种珍贵的中药草本植物。异黄酮是葛根中的主要生物活性化合物，即葛根素、大豆苷、黄豆黄素、染料木苷、黄豆苷元、黄豆黄素等，具有抗心血管、抗高血压、抗炎、抗心律失常等药理作用。方法为了表征异黄酮途径中化合物的相应基因，在BGISEQ-500测序平台上对白花根、茎、叶进行RNA测序（RNA-Seq）分析。结果 在组装所有三种组织的转录本后，我们总共鉴定了 140,905 个 unigene，其中 109,687 个在公共数据库中进行了注释。鉴定出编码与异黄酮类生物合成相关的关键酶（例如 IF7GT 和转录因子）的多个基因，然后进行进一步分析。一些编码关键酶的基因的定量实时 PCR (qRT-PCR) 结果与我们的 RNA-Seq 分析一致。通过分析根与其他组织（叶和茎）的表达谱来确定差异表达基因（DEG）。该分析揭示了许多在根中独特表达或上调的 DEG。最后，通过高效液相色谱和串联质谱方法 (HPLC-MS/MS) 对三种 P. lobata 组织类型中的异黄酮代谢物进行定量分析。我们全面的转录组研究极大地扩展了 P. lobata 的基因组资源，并提供了有关基因表达调控和参与植物异黄酮途径的有希望的候选基因的宝贵知识。