Insertion of a novel transposable element disrupts the function of an anthocyanin biosynthesis-related gene in Echinacea purpurea

•The white-flowered E. purpurea cultivar ‘Virgin’ had higher flavonol content than the reddish-flowered wild-type plants.•Two anthocyanin biosynthesis-related genes (DFR and ANS) were isolated from E. purpurea.•Insertion of a novel transposable element was observed in the ANS coding region.•This insertion had interrupted the gene function in ‘Virgin’ plants. Echinacea purpurea is a popular medical and ornamental flower. The ray florets in E. purpurea are naturally reddish purple, and several colored varieties of ray florets have been produced. The main components responsible for flower coloration in wild-type E. purpurea are two cyanidin-derived anthocyanins. The E. purpurea cultivar ‘Virgin,’ however, possesses white ray florets and is thought to be an anthocyanin-devoid mutant. To determine the mechanisms underlying ray floret pigmentation between E. purpurea wild-type and ‘Virgin,’ we carried out a comprehensive comparison of the flavonoid composition of their tissues. Moreover, we isolated two genes, encoding dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS), that are related to anthocyanin biosynthesis in E. purpurea. Structural and expression analyses showed that both the nucleotide sequences and expression of DFR genes were similar between wild-type and ‘Virgin’ plants. However, we observed insertion of a novel 349-bp non-autonomous miniature-inverted repeat transposable element in the ANS coding region of the ‘Virgin’ cultivar only. This inserted element may interrupt gene expression, as it was succeeded by a premature stop codon, and could form secondary structures in hairpin RNA that could then be processed into a mature miRNA. Collectively, these results indicate that the insertion in the ANS gene was responsible for the generation of anthocyanin-devoid ray florets in E. purpurea.