Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya
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RESEARCH ARTICLE
Open Access
Integrated sRNAome and RNA-Seq analysis reveals miRNA effects on betalain biosynthesis in pitaya Canbin Chen1, Fangfang Xie1, Qingzhu Hua1, Noemi Tel Zur2, Lulu Zhang1, Zhike Zhang1, Rong Zhang1, Jietang Zhao1, Guibing Hu1 and Yonghua Qin1*
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. Thirty-four candidate miRNAs related to betalain biosynthesis were differentially expressed. The expression patterns of those differential expressed miRNAs were analyzed in various pitaya tissues 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. Hmo-miR157b-HmSPL6-like, Hmo-miR160a-Hpcyt P450-like3, Hmo-miR6020-HmCYP71A8-like, Hmo-novel-2HmCYP83B1-like, Hmo-novel-15-HmTPST-like, Hmo-miR828a-HmTT2-like, Hmo-miR858-HmMYB12-like, Hmo-miR858HmMYBC1-like and Hmo-miR858-HmMYB2-like were verified by 5′RACE and transient expression system in tobacco. Conclusions: Hmo-miR157b, Hmo-miR160a, Hmo-miR6020 Hmo-novel-2, Hmo-novel-15, Hmo-miR828a and HmomiR858 play important roles in pitaya fruit coloration and betalain accumulation. Our findings provide new insights into the roles of miRNAs and their target genes of regulatory functions involved in betalain biosynthesis of pitaya. Keywords: Hylocereus, Betalain biosynthesis, sRNAome and RNA-Seq, miRNA, Gene expression, 5′RACE
Background Mature microRNAs (miRNAs) are a type of endogenous non-coding small RNAs with 20–24 nucleotide (nt) length. miRNAs regulate their target genes by mRNA at the posttranscriptional level via the RNA-induced silencing complex (RISC) by binding with the Argonaute (AGO) protein * Correspondence: [email protected] 1 State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, P. R. China Full list of author information is available at the end of the article
to cleavage target mRNA or repress translation of target mRNA [1]. miRNAs play vital roles in plant growth and development, (a)biotic stress response, post-transcriptional regulation, and pigment regulation [2–4]. miRNAs are involved in chlorophyll, carotenoid, and anthocyanin biosynthesis. miRNAs can regulate coloration and chlorophyll accumulation [3, 5–7]. Overexpression of osa-miR171b by an artificial miRNA could enhance chlorophyll accum
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