Transcriptome Analysis Identifies the Key Genes Responsible for High Anthocyanin Content in the Fruits of Lycium ruthenicum Murray

Lycium ruthenicum Murray (black wolfberry) is an important economic plant producing black fruit with high anthocyanin content. The transcriptome of its fruits was compared with that of Lycium barbarum L. (wolfberry), which produces orange-red fruits, with its pigmentation depending largely on carotenoids, with the aim of identifying the key genes responsible for anthocyanin accumulation through RNA sequencing. A total of 32.05 and 28.52 Gb clean reads was obtained after filtering in L. barbarum and L. ruthenicum respectively. Altogether 192,869 unigenes were assembled with an average length of 1064 bp. These unigenes were predicted to encode 152,209 specific proteins with the help of protein databases. Compared with L. barbarum, 733,070 genes were upregulated while 25,779 genes appeared downregulated in the fruits of L. ruthenicum. The genes of the anthocyanin biosynthesis pathway exhibited more differences between the two species than did those of any other biosynthetic pathway. All structural genes in connection with anthocyanin biosynthesis had higher expression level in L. ruthenicum than in L. barbarum, except F3′H and 3GT. The downregulation of F′H and 3GT in L. ruthenicum would be responsible for the absence of cyanidin and glycosylation in this species. The MYB and bHLH genes regulating anthocyanin biosynthesis also displayed higher transcript levels in L. ruthenicum than in L. barbarum, especially the MYB transcription factor gene, which should be the reason for the activation of the anthocyanin biosynthesis structural genes. More work should be carried out to isolate the MYB and bHLH transcription factor genes, and to confirm their functions in producing the pigments found in the black fruits of L. ruthenicum.