Identification of MicroRNAs and Their Target Genes Related to the Accumulation of Anthocyanins in Litchi chinensis by High-Throughput Sequencing and Degradome Analysis

Abstract

Litchi (Litchi chinensis Sonn.) is an important subtropical fruit in southern China and the fruit pericarp has attractive red skin at maturity, which is provided by anthocyanins accumulation. To understand the anthocyanin biosynthesis at post-transcriptional level, we investigated the roles of microRNAs (miRNAs) during fruit coloring. In the present study, four small RNA libraries and a mixed degradome library from pericarps of ‘Feizixiao’ litchi at different developmental phases were constructed and sequenced by Solexa technology. A total of 78 conserved miRNAs belonging to 35 miRNA families and 41 novel miRNAs were identified via high-throughput sequencing, and 129 genes were identified as their targets by the recently developed degradome sequencing. miR156a and a novel microRNA (NEW41) were found to be differentially expressed during fruit coloring, indicating they might affect anthocyanin biosynthesis through their target genes in litchi. qRT-PCR analysis confirmed the expression changes of miR156a and the novel microRNA (NEW41) were inversely correlated with the expression profiles of their target genes LcSPL1/2 and LcCHI, respectively, suggesting regulatory roles of these miRNAs during anthocyanin biosynthesis. The target genes of miR156a, LcSPL1/2, encode transcription factors, as evidenced by a localization in the nucleus, that might play roles in the regulation of transcription. To further explore the relationship of LcSPL1/2 with the anthocyanin regulatory genes, yeast two-hybrid and BiFC analyses showed that LcSPL1 proteins could interact with LcMYB1, which is the key regulatory gene in anthocyanin biosynthesis in litchi. This study represents a comprehensive expression profiling of miRNAs in anthocyanin biosynthesis during litchi fruit maturity and confirmed that the miR156- SPLs module was conserved in anthocyanin biosynthesis in litchi.

Systematic identification of long noncoding RNAs expressed during light‐induced anthocyanin accumulation in apple fruit

“…In litchi (Litchi chinensis Sonn. ), miR156a abundance was reported to be inversely correlated with the expression profiles of its target genes LcSPL1/2 and LcCHI, and increased expression of miR156a was shown to lead to a decrease in LcSPL1 transcript levels, which downregulate anthocyanin biosynthesis via interaction with LcMYB1 (Liu et al, 2016). miR858a functions as a positive regulator of anthocyanin biosynthesis in A. thaliana seedlings, with increased miR858a activity resulting in high levels of anthocyanins due to the inhibition of MYBL2 expression (Wang et al, 2016).…”

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

“…In different rose cultivars, miRNAs may negatively regulate target genes to prevent carotenoid accumulation resulting in white owers according to expression analyses of ve miRNAs [9]. miRNAs can also regulate anthocyanin accumulation through their target genes [13][14][15][16][17][18][19][20][21][22][23][24][25].…”

Integrated transcriptome, small RNA and degradome sequencing approaches proffer insights into chlorogenic acid (CGA) biosynthesis in leafy sweet potato

“…For instance, SPLs played important roles in plant growth and development. The miR156/SPL module was reported to participate in the biosynthesis of phenylpropanoids by destabilizing the MYB-bHLH-WD (MBW) complex and directly preventing the expression of anthocyanin biosynthetic genes in Litchi chinensis [51]; as HD-ZIP TFs played crucial roles in shoot apical meristem and organ polarity, the blockage of miRNA165/166 caused the upregulation of HD-ZIP TFs and increased IAA content accompanied by enhanced anthocyanin [41]. In this research, the analyses of degradome sequencing demonstrated that SPLs were targeted by miR156, HD-ZIP by miR166, MYB by miR159.…”