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Background  Bagging is commonly used to enhance red pigmentation and thereby improve fruit quality of apples ( Malus domestica ). The green-skinned apple cultivar ‘Granny Smith’ develops red pigmentation after bagging removal, but the signal transduction pathways mediating light-induced anthocyanin accumulation in apple peel are yet to be defined. The aim of this study was to identify the mechanisms underpinning red pigmentation in ‘Granny Smith’ after bag removal based on transcriptome sequencing.    Results  The anthocyanin content in apple peel increased considerably after bag removal, while only trace amounts of anthocyanins were present in the peel of unbagged and bagged fruits. RNA sequencing identified 18,152 differentially expressed genes (DEGs) among unbagged, bagged, and bag-removed fruits at 0, 4, and 10 days after bag removal. The DEGs were implicated in light signal perception and transduction, plant hormone signal transduction, and antioxidant systems. Weighted gene co-expression network analysis of DEGs generated a module of 23 genes highly correlated with anthocyanin content. The deletion of − 2026 to − 1870 bp and − 1062 to − 964 bp regions of the  MdMYB1  (LOC103444202) promoter induced a significant decrease in glucuronidase activity and anthocyanin accumulation in apple peel.    Conclusions  Bagging treatment can induce red pigmentation in ‘Granny Smith’ via altering the expression patterns of genes involved in crucial signal transduction and biochemical metabolic pathways. The − 2026 to − 1870 bp and − 1062 to − 964 bp regions of the  MdMYB1  promoter are essential for  MdMYB1 -mediated regulation of anthocyanin accumulation in the ‘Granny Smith’ apple cultivar. The findings presented here provide insight into the mechanisms of coloration in the peel of ‘Granny Smith’ and other non-red apple cultivars.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5730-1) contains supplementary material, which is available to authorized users.

Transcriptome profiling of anthocyanin biosynthesis in the peel of ‘Granny Smith’ apples (Malus domestica) after bag removal