State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.
Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.
DNA Res. 2018 Oct 1;25(5):465-476. doi: 10.1093/dnares/dsy017.
Fruit ripening is a developmental process regulated by a complex network of endogenous and exogenous cues. Sea buckthorn is an excellent material for fruit ripening studies due to its dramatic ripening process and high contents of nutritional and anti-oxidant compounds in berries. Here, the whole transcriptome of sea buckthorn fruit at three development stages were analysed using multiple high-throughput sequencings. We assembled and annotated 9,008 long non-coding RNAs (lncRNAs) in sea buckthorn fruits, and identified 118 differentially expressed lncRNAs (DE-lncRNAs) and 32 differentially expressed microRNAs in fruit developmental process. In addition, we predicted 1,061 cis-regulated and 782 trans-regulated targets of DE-lncRNAs, and these DE-lncRNAs are specifically enriched in the biosynthesis of ascorbic acid, carotenoids and flavonoids. Moreover, the silencing of two lncRNAs (LNC1 and LNC2) in vivo and expression analysis revealed that LNC1 and LNC2 can act as endogenous target mimics of miR156a and miR828a to reduce SPL9 and induce MYB114 expression, respectively, which lead to increased and decreased anthocyanin content as revealed by high-performance liquid chromatography analysis. Our results present the first global functional analysis of lncRNA in sea buckthorn and provide two essential regulators of anthocyanin biosynthesis, which provides new insights into the regulation of fruit quality.
果实成熟是一个受内源性和外源性信号复杂网络调控的发育过程。沙棘由于其果实成熟过程迅速，且浆果中营养和抗氧化化合物含量高，是研究果实成熟的极好材料。本研究中，我们使用多种高通量测序方法对三个发育阶段的沙棘果实进行了全转录组分析。我们在沙棘果实中组装和注释了 9008 个长链非编码 RNA（lncRNA），并在果实发育过程中鉴定了 118 个差异表达的 lncRNA（DE-lncRNA）和 32 个差异表达的 microRNA。此外，我们预测了 1061 个 cis 调控和 782 个 trans 调控的 DE-lncRNA 靶标，这些 DE-lncRNA 特异性富集在抗坏血酸、类胡萝卜素和类黄酮的生物合成中。此外，体内沉默两个 lncRNA（LNC1 和 LNC2）并进行表达分析表明，LNC1 和 LNC2 可以作为 miR156a 和 miR828a 的内源性靶标模拟物，分别降低 SPL9 和诱导 MYB114 表达，从而导致高效液相色谱分析显示的花色苷含量增加和减少。我们的研究结果首次对沙棘中的 lncRNA 进行了全面的功能分析，并提供了花色苷生物合成的两个重要调控因子，为果实品质的调控提供了新的见解。
