SRP095506 PRJNA358304 Prunus mume Transcriptome or Gene expression Detection of differentially expressed genes (DEGs) from both two coloured flowers is an essential step to elucidate mechanisms of variegated pigmentation. Here, we used next-generation high-throughput sequencing technology to investigate these mechanisms. DEGs were identified as candidate genes related to variegated pigmentation at the transcriptional level in Japanese apricot. Our data presented here may be a useful resource for further study. Prunus mume