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

  • Xiaoqing Meng
  • Ge Li
  • Lingya Gu
  • Yu Sun
  • Zongyun Li
  • Jingran Liu
  • Xiaoqing Wu
  • Tingting DongEmail author
  • Mingku ZhuEmail author


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.


Anthocyanin biosynthesis Differentially expressed genes Metabolomic analysis Phalaenopsis amabilis Transcriptome sequencing 



Phenylalanine ammonia lyase


Cinnamate 4-hydroxylase


4-CoumarateCoA ligase


Chalcone synthase


Chalcone isomerase


Flavone 3-hydroxylase


Flavonoid 3′,-hydroxylase


Flavonoid 3′,5′-hydroxylase


Dihydroflavonol reductase


Anthocyanidin synthase


UPD glucose: flavonoid-3-O-glucosyltransferase








Flavonol synthase


Flavone synthase


High-performance liquid chromatography


Quantitative real-time PCR



The authors thank Mingzhi Li (Genepioneer Biotechnologies, Nanjing, China) for the assistance in transcriptome data analysis. This work was supported by National Natural Science Foundation of China (31700226), Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD), Natural Science Foundation of Jiangsu Province (BK20160215), Graduate Innovation Project of Jiangsu Normal University (KYCX17-1619), and Science and Technology Program of Ministry of Housing and Urban–Rural Development of China (2016-K1-028).

Author Contributions

MZ and XM designed the experiments, analyzed the data and wrote the manuscript. TD and ZL analyzed the data and improved manuscript quality. XM, GL, LG, YS, JL and XW analyzed the data and performed the experiments. All authors have read and approved the final manuscript.

Compliance with Ethical Standards

Conflict of interest

The authors declare no conflict of interest.

Supplementary material

344_2019_10025_MOESM1_ESM.pdf (1.2 mb)
Supplementary file1 (PDF 1189 kb)
344_2019_10025_MOESM2_ESM.xlsx (1.2 mb)
Supplementary file2 (XLSX 1228 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Xiaoqing Meng
    • 1
    • 2
  • Ge Li
    • 1
    • 2
  • Lingya Gu
    • 1
  • Yu Sun
    • 1
  • Zongyun Li
    • 1
    • 2
  • Jingran Liu
    • 1
    • 2
  • Xiaoqing Wu
    • 3
  • Tingting Dong
    • 1
    • 2
    Email author
  • Mingku Zhu
    • 1
    • 2
    Email author
  1. 1.School of Life SciencesJiangsu Normal UniversityXuzhouChina
  2. 2.Jiangsu Key Laboratory of Phylogenomics & Comparative GenomicsJiangsu Normal UniversityXuzhouChina
  3. 3.Jiangsu Vocational Institute of Architectural TechnologyXuzhouChina

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