Table_7_The gastrodin biosynthetic pathway in Pholidota chinensis Lindl. revealed by transcriptome and metabolome profiling.xls

Pholidota chinensis Lindl. is an epiphytic or lithophytic perennial herb of Orchidaceae family used as a garden flower or medicinal plant to treat high blood pressure, dizziness and headache in traditional Chinese medicine. Gastrodin (GAS) is considered as a main bioactive ingredient of this herb but the biosynthetic pathway remains unclear in P. chinensis. To elucidate the GAS biosynthesis and identify the related genes in P. chinensis, a comprehensive analysis of transcriptome and metabolome of roots, rhizomes, pseudobulbs and leaves were performed by using PacBio SMART, Illumina Hiseq and Ultra Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS/MS). A total of 1,156 metabolites were identified by UPLC-MS/MS, of which 345 differential metabolites were mainly enriched in phenylpropanoid/phenylalanine, flavone and flavonol biosynthesis. The pseudobulbs make up nearly half of the fresh weight of the whole plant, and the GAS content in the pseudobulbs was also the highest in four tissues. Up to 23,105 Unigenes were obtained and 22,029 transcripts were annotated in the transcriptome analysis. Compared to roots, 7,787, 8,376 and 9,146 differentially expressed genes (DEGs) were identified in rhizomes, pseudobulbs and leaves, respectively. And in total, 80 Unigenes encoding eight key enzymes for GAS biosynthesis, were identified. Particularly, glycosyltransferase, the key enzyme of the last step in the GAS biosynthetic pathway had 39 Unigenes candidates, of which, transcript28360/f2p0/1592, was putatively identified as the most likely candidate based on analysis of co-expression, phylogenetic analysis, and homologous searching. The metabolomics and transcriptomics of pseudobulbs versus roots showed that 8,376 DEGs and 345 DEMs had a substantial association based on the Pearson’s correlation. This study notably enriched the metabolomic and transcriptomic data of P. chinensis, and it provides valuable information for GAS biosynthesis in the plant.

中国石仙桃（Pholidota chinensis Lindl.）为兰科（Orchidaceae）附生或石生多年生草本植物，既可作为园林花卉栽培，亦可在传统中医药中用于治疗高血压、眩晕及头痛。天麻素（Gastrodin，GAS）被认为是该草药的主要生物活性成分，但中国石仙桃中天麻素的生物合成途径仍不明晰。为阐明中国石仙桃中天麻素的生物合成过程并鉴定相关功能基因，本研究采用PacBio SMART、Illumina Hiseq及超高效液相色谱-串联质谱（Ultra Performance Liquid Chromatography Tandem Mass Spectrometry，UPLC-MS/MS）技术，对其根、根状茎、假鳞茎和叶片开展了全面的转录组与代谢组联合分析。通过UPLC-MS/MS共鉴定出1156种代谢物，其中345种差异代谢物主要富集于苯丙烷类/苯丙氨酸、黄酮及黄酮醇生物合成通路。假鳞茎占整株鲜重的近一半，且其天麻素含量在四种组织中最高。转录组分析共获得23105个Unigene，注释得到22029条转录本。与根组织相比，在根状茎、假鳞茎和叶片中分别鉴定出7787、8376和9146个差异表达基因（differentially expressed genes，DEGs）。总计鉴定出80个编码天麻素生物合成所需8种关键酶的Unigene。尤为关键的是，天麻素生物合成通路最后一步的关键酶糖基转移酶，拥有39个候选Unigene；其中，经共表达分析、系统发育分析及同源序列检索后，transcript28360/f2p0/1592被推测为最具可能性的候选基因。对假鳞茎与根组织的代谢组和转录组联合分析显示，8376个DEGs与345种差异代谢物（differential metabolites，DEMs）之间存在显著的皮尔逊相关性关联。本研究显著丰富了中国石仙桃的代谢组与转录组数据，为该植物中天麻素的生物合成研究提供了宝贵的参考信息。