Dataset Information

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.

SUBMITTER: Liu R

PROVIDER: S-EPMC5223483 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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

Liu Rui R Lai Biao B Hu Bing B Qin Yonghua Y Hu Guibing G Zhao Jietang J

Frontiers in plant science 20170110

Litchi (<i>Litchi chinensis</i> 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 con ...[more]

PMID: 28119728

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Project description:BackgroundMicroRNAs (miRNAs) are a class of noncoding small RNAs (sRNAs) that are 20-24 nucleotides (nt) in length. Extensive studies have indicated that miRNAs play versatile roles in plants, functioning in processes such as growth, development and stress responses. Chilling is a common abiotic stress that seriously affects plants growth and development. Recently, chilling-responsive miRNAs have been detected in several plant species. However, little is known about the miRNAs in the model plant tomato. 'LA1777' (Solanum habrochaites) has been shown to survive chilling stress due to its various characteristics.ResultsHere, two small RNA libraries and two degradome libraries were produced from chilling-treated (CT) and non-chilling-treated (NT) leaves of S. habrochaites seedlings. Following high-throughput sequencing and filtering, 161 conserved and 236 novel miRNAs were identified in the two libraries. Of these miRNAs, 192 increased in the response to chilling stress while 205 decreased. Furthermore, the target genes of the miRNAs were predicted using a degradome sequencing approach. It was found that 62 target genes were cleaved by 42 conserved miRNAs, while nine target genes were cleaved by nine novel miRNAs. Additionally, nine miRNAs and six target genes were validated by quantitative real-time PCR (qRT-PCR). Target gene functional analysis showed that most target genes played positive roles in the chilling response, primarily by regulating the expression of anti-stress proteins, antioxidant enzyme and genes involved in cell wall formation.ConclusionsTomato is an important model plant for basic biological research. In this study, numerous conserved and novel miRNAs involved in the chilling response were identified using high-throughput sequencing, and the target genes were analyzed by degradome sequencing. The work helps identify chilling-responsive miRNAs in tomato and increases the number of identified miRNAs involved in chilling stress. Furthermore, the work provides a foundation for further study of the regulation of miRNAs in the plant response to chilling stress.

Project description:Litchi has diverse fruit color phenotypes, yet no research reflects the biochemical background of this diversity. In this study, we evaluated 12 litchi cultivars for chromatic parameters and pigments, and investigated the effects of abscisic acid, forchlorofenron (CPPU), bagging and debagging treatments on fruit coloration in cv. Feizixiao, an unevenly red cultivar. Six genes encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP-glucose: flavonoid 3-O-glucosyltransferase (UFGT) were isolated from the pericarp of the fully red litchi cv. Nuomici, and their expression was analyzed in different cultivars and under the above mentioned treatments. Pericarp anthocyanin concentration varied from none to 734 mg m(-2) among the 12 litchi cultivars, which were divided into three coloration types, i.e. non-red ('Kuixingqingpitian', 'Xingqiumili', 'Yamulong'and 'Yongxing No. 2'), unevenly red ('Feizixiao' and 'Sanyuehong') and fully red ('Meiguili', 'Baila', Baitangying' 'Guiwei', 'Nuomici' and 'Guinuo'). The fully red type cultivars had different levels of anthocyanin but with the same composition. The expression of the six genes, especially LcF3H, LcDFR, LcANS and LcUFGT, in the pericarp of non-red cultivars was much weaker as compared to those red cultivars. Their expression, LcDFR and LcUFGT in particular, was positively correlated with anthocyanin concentrations in the pericarp. These results suggest the late genes in the anthocyanin biosynthetic pathway were coordinately expressed during red coloration of litchi fruits. Low expression of these genes resulted in absence or extremely low anthocyanin accumulation in non-red cultivars. Zero-red pericarp from either immature or CPPU treated fruits appeared to be lacking in anthocyanins due to the absence of UFGT expression. Among these six genes, only the expression of UFGT was found significantly correlated with the pericarp anthocyanin concentration (r?=?0.84). These results suggest that UFGT played a predominant role in the anthocyanin accumulation in litchi as well as pericarp coloration of a given cultivar.

Dataset Information

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

Publications

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

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