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Lycoris  is used as a garden flower due to the colorful and its special flowers. Floral coloration of  Lycoris  is a vital trait that is mainly regulated via the anthocyanin biosynthetic pathway. In this study, we performed a comparative transcriptome analysis of  Lycoris radiata  petals at four different flower development stages. A total of 38,798 differentially expressed genes (DEGs) were identified by RNA sequencing, and the correlation between the expression level of the DEGs and the anthocyanin content was explored. The identified DEGs are significantly categorized into ‘flavonoid biosynthesis,’ ‘phenylpropanoid biosynthesis,’ ‘Tropane, piperidine and pyridine alkaloid biosynthesis,’ ‘terpenoid backbone biosynthesis’ and ‘plant hormone signal transduction’ by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The candidate genes involved in anthocyanin accumulation in  L. radiata  petals during flower development stages were also identified, which included 56 structural genes (especially  LrDFR1  and  LrFLS ) as well as 27 key transcription factor DEGs (such as  C3H ,  GATA ,  MYB , and  NAC ). In addition, a key structural gene namely  LrDFR1  of anthocyanin biosynthesis pathway was identified as a hub gene in anthocyanin metabolism network. During flower development stages, the expression level of  LrDFR1  was positively correlated with the anthocyanin content. Subcellular localization revealed that LrDFR1 is majorly localized in the nucleus, cytoplasm and cell membrane. Overexpression of  LrDFR1  increased the anthocyanin accumulation in tobacco leaves and  Lycoris  petals, suggesting that  LrDFR1  acts as a positively regulator of anthocyanin biosynthesis. Our results provide new insights for elucidating the function of anthocyanins in  L. radiata  petal coloring during flower development.

Comparative Transcriptome Analysis Identifies Key Regulatory Genes Involved in Anthocyanin Metabolism During Flower Development in Lycoris radiata