Manually Annotated Gene Prediction of the Apple Genome and Identification of Anthocyanin Biosynthesis Mechanisms in Apple.

Fruit color is a crucial biological trait of apple and is closely correlated with its nutritional value. The coloration of apple fruit is primarily determined by the anthocyanin accumulation in the peel. Nevertheless, the molecular mechanisms underlying peel anthocyanin accumulation in apple remain poorly understood. In the present study, we updated the apple genome annotation, which provides a valuable resource for the identification of novel genes and further functional studies on apple peel coloration. Using RNA-seq transcriptome analysis, we systematically characterized the regulatory mechanisms governing anthocyanin biosynthesis and color formation in apple. Particular attention was given to newly identified genes with potential regulatory roles in anthocyanin accumulation. By integrating mRNA and small RNA transcriptomic data, we uncovered a core miR858-MdMYB regulatory module that participates in apple anthocyanin metabolism. Furthermore, comparative transcriptomic analysis revealed that the photosystem I center gene MdPSAEA is involved in the regulation of apple anthocyanin biosynthesis. Collectively, our study provides an updated genome annotation and offers novel insights into the molecular basis of anthocyanin accumulation in apple.