Background The tree peony (Paeonia suffruticosa Andr.) cultivar ‘Er Qiao’ is appreciated for its unstable variegated flower coloration, with cyanic and acyanic flowers appearing on different branches of the same plant and occasionally in a single flower or petal. However, the variegation mechanism is still unclear. Results In this study, we found significantly higher contents and more diverse sets of anthocyanins in the cyanic petals than in the acyanic petals. Comparative transcriptome analysis between the two flower types revealed 477 differentially expressed genes (DEGs). Quantitative real-time PCR results verified that the transcript levels of the flavonol synthase (FLS) gene were significantly increased in the acyanic petals. Furthermore, we found that a GCGGCG insertion at 246 bp in the flavonoid 3′-hydroxylase (F3’H) gene-coding region constitutes a duplication of the 241–245 bp section and was consistently found only in acyanic flowers. Sequence alignment of the F3’H gene from different plant species indicated that only the acyanic petals of ‘Er Qiao’ contained the GCGGCG insertion. The transformation of Arabidopsis tt7–1 lines demonstrated that the ectopic expression of F3’H-cyanic, but not F3’H-acyanic, could complement the colors in the hypocotyl and seed coat. Conclusion In summary, we found that an indel in F3’H and the upregulation of FLS drastically reduced the anthocyanin content in acyanic petals. Our results provide molecular candidates for a better understanding of the variegation mechanisms in tree peony.

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The complete nucleotide sequence of the Astragalus membranaceus (Fisch.) Bunge var. membranaceus chloroplast genome was reported and characterized in this study. The chloroplast genome is a circular molecule of 123623 bp that belongs to the inverted repeat-lacking clade (IRLC). It comprises 110 genes, including 76 protein-coding genes, four unique rRNAs and 30 tRNAs. Similar to the plastomes of A. membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P. K. Hsiao and other closely related species, rpl22 and rps16 are absent. The phylogenetic analysis of 67 proteins from 29 chloroplast genomes belonging to IRLC provided strong support for the non-monophyly of Galegeae. This genome has provided a wealth of information for distinguishing varieties of A. membranaceus.