Genome-Wide View and Characterization of Natural Antisense Transcripts in Cannabis Sativa L.

Abstract Natural Antisense Transcripts (NATs) are a kind of complex regulatory RNAs that play vitriol roles in gene expression and regulation. In recent years, due to the tremendous economic and medicinal values of cannabinoids, the genome of Cannabis Sativa L. was sequenced and the the biosynthetic pathway of cannabinoids was deciphered. Moreover, the regulation of non-coding RNAs, including microRNAs and long non-coding RNAs involved in the biosynthesis of cannabinoids were predicted. However, the NATs in C. sativa remain unknown. In this study, we predicted C. sativa NATs genome-wide by a computational pipeline using strand-specific RNA sequencing (ssRNA-Seq) data. Then, we performed a comprehensive analysis and validated the expression profiles by strand-specific quantitative reverse transcription PCR (ssRT-qPCR). As a result, 260 NATs were predicted in C. sativa, including 92 cis- and 168 trans-NATs. The primary type of cis-NATs was sense transcripts (STs) containing NATs. The expression profiles of 92% of transcripts of ssRNA-Seq were consistent with those of the ssRT-qPCR. Functional enrichment analysis demonstrated that the C. sativa NATs potentially participated in growth and development, stress resistance, and the biosynthesis of compounds. Finally, 12 cis- and 278 trans- NAT-ST pairs were predicted to produce 476 cis- and 2342 trans- small interfering RNA (nat-siRNAs), respectively. These nat-siRNAs were potentially involved in the biosynthesis of cannabinoids, fatty acids, and cellulose. All these results will shed light on the regulation of NATs and nat-siRNAs in C. sativa.