Transcriptomic landscapes of tissue-specific color transition in eggplant reveal regulatory roles of lncRNAs and alternative splicing in anthocyanin biosynthesis

Background Color transitions from green to purple in eggplant ( Solanum melongena L.) flowers and berries result from chlorophyll and anthocyanin accumulation. While structural genes ( CHS , CHI , F3’H , DFR , ANS , UGT ) and regulatory transcription factors ( MYB , bHLH , WD40 ) in the anthocyanin pathway are well characterized, fine-scale transcriptional regulation is less understood. Long non-coding RNAs (lncRNAs) contribute to pre- and post-transcriptional regulation, whereas alternative splicing (AS) events control exclusively post-transcriptional modifications. Methods Here we performed an integrated transcriptomic analysis of mRNAs, lncRNAs and AS events to investigate fine regulation of anthocyanin biosynthesis. Results A PacBio assembly of the eggplant cultivar “Black Beauty” genome allowed the computational prediction and expression analysis of all transcripts in fruit peel and flower corolla. We identified 4, 126 lncRNAs and 34, 745 novel transcript isoforms, and tissue-specific regulatory networks revealed multiple lncRNAs and protein-coding genes AS events associated with anthocyanin biosynthesis. Quantification of anthocyanins in both peel and corolla enabled the construction of putative tissue-specific models of anthocyanin transcriptional regulation. Discussion This study provides a starting point to improve the knowledge of fine-tuning anthocyanin regulation at the transcriptional level, highlighting tissue-specific lncRNAs and AS events linked to regulatory genes, and offering, to our knowledge, the first evidence of lncRNA involvement in anthocyanin biosynthesis in eggplant.