Integrated sRNAome and RNA-Seq Analysis Reveals miRNA Effects on Betalain Biosynthesis in Pitaya

Abstract

Background: MicroRNAs (miRNAs) and their regulatory functions in anthocyanin, carotenoid, and chlorophyll accumulation have been extensively characterized in many plant species. However, the miRNA regulatory mechanism in betalain biosynthesis remains mostly unknown. Results: In this study, 126 conserved miRNAs and 41 novel miRNAs were first isolated from Hylocereus monacanthus, among which 95 conserved miRNAs belonged to 53 miRNA families. 34 candidate miRNAs related to betalain biosynthesis were found to be differentially expressed. The expression patterns of those differential expressed miRNAs were analyzed in various tissues of the pitaya by RT-qPCR. A significantly negative correlation was detected between the expression levels of half those miRNAs and corresponding target genes. Target genes of miRNAs i.e. aly-miR157d-5p_L+1_1ss4AC-comp25631_c0, aau-miR160_L-4R+ 1-comp36993_c0_seq3, nta-miR6020b-comp234190_c0, PC-5p-192_7269-comp29967_c0, PC-5p-23845_39-comp28219_c0, mdm-miR828a_1ss22AT-comp24967_c0, mdm-miR858- comp15143_c0, mdm-miR858-comp24362_c0 and mdm-miR858-comp403340_c0 were verified by 5′RACE and transient expression system in tobacco.Conclusions: aly-miR157d-5p_L+1_1ss4AC, aau-miR160_L-4R+1, nta-miR6020b PC-5p-192_7269, PC-5p-23845_39, mdm-miR828a_1ss22AT and mdm-miR858 may play important roles in pitaya fruit coloration and betalain accumulation. Our findings provide insights into the roles of miRNAs and their target genes of regulatory functions involved in betalain biosynthesis of pitaya.