Integrated transcriptomics and metabolomics uncover the molecular basis of flavonoid accumulation in the rhizomes of two Cymbidium tortisepalum var. longibracteatum cultivars

The rhizome is crucial for asexual propagation in plants. Green rhizome (termed as GR) and yellow rhizome (termed as YR) are the rhizomes of two Cymbidium tortisepalum var. longibracteatum cultivars with colour differences. In this study, we carried out integrated transcriptomic and metabolomic profiling to explore the pathways and key genes between them. The transcriptome assembled 134,527 unigenes and 508 unigenes (244 upregulated and 264 downregulated) with differential expression patterns. Metabolomic analysis identified 420 metabolites, and 115 were differentially accumulated metabolites, including 37 upregulated and 78 downregulated metabolites. Integration of transcriptome profiling and metabolite analysis revealed "phenylpropanoid biosynthesis" and "flavonoid biosynthesis" were significantly enriched. One R2R3 type v-myb avian myeloblastosis viral oncogene homologue (R2R3-MYB) transcription factor (c1121_g1), two basic helix-loop-helix (bHLH) transcription factors (c59082_g2 and c103838_g1), and five flavonoid biosynthesis related unigenes (c34902_g1, c82361_g1, c22242_g1, c39937_g1, c47509_g1) were highly expressed in YR, which is consistent with the flavonoid content. These findings shed light on the regulation of flavonoid biosynthesis and will contribute to the breeding of new cultivars in orchids.