To better understand the molecular mechanism of color formation in different varieties of the mulberry fruit, we investigated the functional genes related to anthocyanin and betulinic acid biosynthesis using high-throughput transcriptome sequencing and detected the primary and secondary metabolites in the white (Morus alba L. cv. ‘Turkey’) and red (Morus alba L. cv. ‘Cheongil’) mulberry cultivars. We obtained 171,702,058 high-quality reads with an average read length of 125 bp. These reads were assembled into 51,272 and 51,159 unigenes in Turkey and Cheongil, respectively. We also identified the genes related to anthocyanin and triterpene biosynthesis and investigated their expression and metabolite profiles. Overall, our transcriptome sequencing provides valuable information that could be used in gene discovery, marker-assisted selection, and investigation of metabolic pathways in mulberry. Additionally, gene expression and metabolite profiles provide new insights into the underlying mechanism of anthocyanin and betulinic acid biosynthesis and relationship between primary and secondary metabolites.
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