Noncoding and coding transcriptome analysis reveals the regulation roles of long noncoding RNAs in fruit development of hot pepper (Capsicum annuum L.)

Long non-coding RNAs (lncRNAs) have been shown to play critical regulatory roles in diverse biological processes in plants. However, the presence of lncRNAs and their potential functions in hot pepper are still unknown. Using strand-specific RNA-sequencing, a total of 2505 putative lncRNAs were identified in the fruits of hot pepper. The lncRNAs were transcribed from all pepper chromosomes and 95.37% of them originated from intergenic regions. And 1066 lncRNAs were differentially expressed among the four samples during pepper fruit development. Many potential protein-coding (PC) genes targeted by lncRNAs with cis or trans-acting were also identified. Six of them and their target genes were further validated by quantitative RT-PCR. Some of these target genes were involved in plant hormone signal transduction, cell wall formation and carotenoid biosynthesis, indicating the roles of lncRNAs in the regulation of fruit development and quality. This study identified a large number of lncRNAs in hot pepper, thereby providing some insights into the fruit development of hot pepper.