Comparative transcriptome analysis of mulberry reveals anthocyanin biosynthesis mechanisms in black (Morus atropurpurea Roxb) and white (Morus alba L) fruit genotypes

To better understand anthocyanin biosynthesis in mulberry fruit, we analyzed the transcriptome of Da 10 (Morus atropurpurea Roxb, black fruit) and Baisang (Morus alba L., white fruit). Although Da 10 had high levels of cyanidin 3-O-glucoside (Cy) and pelargonidin 3-O-glucoside (Pg), Baisang contained only Cy, at low levels. Comparative transcriptome analysis resulted in the annotation of more than 27,085 genes (including 1,735 new genes). Differentially expressed genes (DEGs) were detected at three developmental stages—S1 (4,256 genes, 10 DPA), S2 (5,612 genes, 19 DPA), and S3 (5,226 genes, 28 DPA)—when comparing Da 10 and Baisang. Anthocyanin biosynthesis was associated with the expression of 15 core genes and 5 transcription factors. Relative to Baisang, Da 10 showed significant upregulation of the genes involved in the early stages (production of the intermediate compounds, chalcone and dihydroflavonol) and late stages (production of Cy and Pg) of anthocyanin biosynthesis. Baisang showed significant downregulation of the genes involved in the early stages of anthocyanin biosynthesis, and overexpression of flavanone 3-hydroxylase, resulting in the generation of quercetin and/or myricetin but not anthocyanins. Anthocyanin biosynthesis in mulberry fruit was fueled by the precursor, phenylalanine, the intermediates, chalcone and dihydroflavonol, and the products, Cy and Pg, involving the anthocyanin biosynthesis pathways.