We present a high-quality genome assembly of the Japanese peach cultivar Akatsuki, a leading commercial and breeding parent. Using PacBio long-read sequencing and Bionano optical mapping, we generated chromosome-scale sequences totaling 241.9 Mbp, anchored to the reference Lovell genome. The Akatsuki genome assembly demonstrated excellent completeness, with a complete BUSCO score of 99.3%, comparable to the high-quality Lovell assembly. Comparative analysis of 38 Japanese cultivars identified genome-wide polymorphisms, which have been incorporated into the TASUKE+ database to facilitate public access and comparative genomic studies. Transcriptome profiling of twelve tissues revealed distinct gene expression patterns associated with fruit development, ripening, and organ identity, providing insights into the molecular basis of tissue-specific functions. Together, these genomic and transcriptomic resources offer a valuable foundation for understanding agronomically important traits in Japanese peaches and will accelerate marker-assisted breeding and cultivar improvement.