Reports concerning the regulation of anthocyanin synthesis and the structural and regulatory genes in the anthocyanin biosynthetic pathway in L. ruthenicum are limited.</p><p>In response to this limitation, the current study evaluated anthocyanin biosynthesis at three different development or ripeness stages in the fruits of L. ruthenicum using RNA-Seq. The RNA-Seq data allowed us to investigate the structural genes and TFs related to anthocyanin biosynthesis throughout fruit coloration. Our findings offer insight into the molecular mechanisms of anthocyanin biosynthesis in L. ruthenicum and provide a foundation for the future genetic engineering of improved anthocyanin content in plants.