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Anthocyanins play many roles in plants, including providing protection from biotic and abiotic stresses. Japanese apple rust (Gymnosporangium yamadae Miyabe ex G. Yamada) causes serious diseases in plants of the genus Malus and results in reduced fruit production and quality. However, few studies have been done to unravel the molecular mechanisms of anthocyanin formation in rust-infected apple leaves. To identify new regulatory genes in apple leaves that may be involved in regulating rust-induced anthocyanin biosynthesis, we measured anthocyanin content and sequenced the transcriptomes of rust-infected and uninfected tissues of Malus ‘Profusion’ leaves. Significant color changes and anthocyanin enrichment (especially cyanidin-3-galactoside chloride) occurred in infected tissues, whereas no significant color change and a low anthocyanin level were observed in uninfected tissue. We identified 10,045 differentially expressed genes (DEGs) in these two tissue types, including 6021 genes that were upregulated in the infected tissue and 4024 genes that were downregulated. We also identified five structural genes that are putative regulators of anthocyanin biosynthesis. In addition, 56 MYB genes, 36 bHLH genes, and one WD40 gene were identified among the obtained DEGs. According to the phylogeny of the amino acid sequences of transcription factors known to be involved in anthocyanin biosynthesis, one MYB gene (MYB114-like) and two bHLH genes (bHLH33 and bHLHA-like) may relate to anthocyanin biosynthesis in rust-infected apple leaves. These data will provide insights into the molecular mechanisms underlying anthocyanin accumulation upon rust infection.

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Transcriptome Sequencing and Expression Analysis of Genes Related to Anthocyanin Biosynthesis in Leaves of Malus ‘Profusion’ Infected by Japanese Apple Rust