Comparative Metabolomic and Transcriptome Analysis Reveal Distinct Flavonoid Biosynthesis Regulation Between Petals of White and Purple Phalaenopsis amabilis

Orchids (Phalaenopsis amabilis), renowned for their extraordinary floral diversity which implies the complex flower color development, are one of the most valuable research materials for molecular biology studies. However, the genetic mechanisms underlying flower color formation in this non-model plant remain unclear. Here, the biochemical and molecular basis of the flavonoid/anthocyanin biosynthesis between purple petal cultivar (PP) and white petal cultivar (WP) was investigated. The results revealed that 142 differential flavonoid-related metabolites were identified using LC–MS/MS method, and the primary anthocyanins were identified as cyanidin derivatives. Moreover, RNA-seq revealed a total of 9523 upregulated and 6941 downregulated genes were detected. GO and KEGG analysis of DEGs indicated metabolic pathways were preferentially upregulated in PP. The expression of most known genes encoding the enzymes in anthocyanin and related derivative biosynthesis was significantly higher in PP than in WP, especially the downstream ones. We hypothesized that altered flavanone and flavone accumulation may lead to pigment elimination in WP, and the limited flux in cyanidin biosynthesis pathway seems to be the most likely reason for the colorless petal. Besides, 115 differentially expressed regulatory genes relating to anthocyanin biosynthesis were also detected, including MYB, bHLH, WD40, WRKY, MADS and bZIP. Subsequently, high consistency was observed between the results of qRT-PCR and those of RNA-seq. collectively, this study provides a comprehensive metabolic and transcriptional dataset for Phalaenopsis, the informative list of candidate structural and regulatory genes associated with purple trait offer a valuable opportunity to unravel the genetic mechanism underlying flower color formation in Phalaenopsis.