Transcriptome analysis reveals long noncoding RNAs involved in the tuber anthocyanin synthesis of potato (Solanum tuberosum L.)

Anthocyanin plays an important role in improving the overall appearance and nutritional value of plants, and its has physiological functions of anti-cancer, aging prevention, cardiovascular disease on humans. Although the molecular mechanism has been described by genome-wide association studies (GWAS), metabolomics analysis, proteome and transcriptomic analysis, the mechanism by which the long non-coding RNA manipulates the anthocyanin biosynthesis in potato remains unknown. In present study, we using white potato (Atlantic) and purple potato (Huasong66) as materials, and detection of anthocyanin content showed that there were significant differences between the two materials. Three development stage tubers, include formation, bulking and the maturity, of Atlantic (D1, D2, D3) and Huasong66 (H1, H2, H3) were collected and used for deep transcriptome sequencing. A total of 15,191 long non-coding RNAs (lncRNAs) were identified, including 8,124 lincRNAs, 1,959 antisense-lncRNA, 2,302 intronic-lncRNA and 2,806 sense overlapping lncRNAs. Among them, 990 lncRNAs were preferentially expressed in the Huasong 66 and 679 lncRNAs were preferentially expressed in the Atlantic. A total of 1,831 lncRNAs were common differential expression across three tuber development periods between Atlantic and Huasong 66. And partly of their target genes mainly participate in phenylalanine metabolism, anthocyanin biosynthesis, flavone and flavonol biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis. We found the lncRNA TCONS00021404 and its target genes, C88_C11H1G019590 and C88_C10H3G081620, which encode flavonoid 3’,5’-hydroxylase and anthocyanidin 3-O-glucosyltransferase, were all showed higher expression patterns in Huasong 66 rather than in Atlantic, not only during the tuber formation and bulking stages, but also during the maturity stage. In addition, we found there were 243 lncRNAs act as precursors of 53 known miRNAs, 917 lncRNAs were targeted by 205 miRNAs, and part of lncRNAs could acted as eTMs of miR172b and miR482b respectively. This study established the transcriptomic repertoires in tuber development and provided evidence for the potential functions of lncRNAs in anthocyanin synthesis in potato.