State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China.
School of Science, Anhui Agricultural University, Hefei, 230036, China.
Planta. 2018 Dec;248(6):1417-1429. doi: 10.1007/s00425-018-2983-x. Epub 2018 Aug 20.
Circular RNA (circRNA) discovery, expression patterns and experimental validation in developing tea leaves indicates its correlation with circRNA-parental genes and potential roles in ceRNA interaction network. Circular RNAs (circRNAs) have recently emerged as a novel class of abundant endogenous stable RNAs produced by circularization with regulatory potential. However, identification of circRNAs in plants, especially in non-model plants with large genomes, is challenging. In this study, we undertook a systematic identification of circRNAs from different stage tissues of tea plant (Camellia sinensis) leaf development using rRNA-depleted circular RNA-seq. By combining two state-of-the-art detecting tools, we characterized 3174 circRNAs, of which 342 were shared by each approach, and thus considered high-confidence circRNAs. A few predicted circRNAs were randomly chosen, and 20 out of 24 were experimental confirmed by PCR and Sanger sequencing. Similar in other plants, tissue-specific expression was also observed for many C. sinensis circRNAs. In addition, we found that circRNA abundances were positively correlated with the mRNA transcript abundances of their parental genes. qRT-PCR validated the differential expression patterns of circRNAs between leaf bud and young leaf, which also indicated the low expression abundance of circRNAs compared to the standard mRNAs from the parental genes. We predicted the circRNA-microRNA interaction networks, and 54 of the differentially expressed circRNAs were found to have potential tea plant miRNA binding sites. The gene sets encoding circRNAs were significantly enriched in chloroplasts related GO terms and photosynthesis/metabolites biosynthesis related KEGG pathways, suggesting the candidate roles of circRNAs in photosynthetic machinery and metabolites biosynthesis during leaf development.
环状 RNA (circRNA) 在发育中的茶叶中的发现、表达模式和实验验证表明，它与 circRNA-母基因相关，并在 ceRNA 相互作用网络中具有潜在作用。环状 RNA (circRNAs) 最近作为一类新型的丰富的内源性稳定 RNA 出现，具有调节潜力，由环状化产生。然而，在植物中，特别是在基因组较大的非模式植物中，circRNA 的鉴定具有挑战性。在这项研究中，我们使用 rRNA 耗尽的环状 RNA-seq 从茶树（Camellia sinensis）叶片发育的不同阶段组织中系统地鉴定了 circRNAs。通过结合两种最先进的检测工具，我们鉴定了 3174 个 circRNAs，其中 342 个是每种方法共有的，因此被认为是高可信度的 circRNAs。随机选择了一些预测的 circRNAs，其中 24 个中的 20 个通过 PCR 和 Sanger 测序得到了实验验证。与其他植物相似，许多 C. sinensis circRNAs 的组织特异性表达也观察到了。此外，我们发现 circRNA 的丰度与它们母基因的 mRNA 转录本丰度呈正相关。qRT-PCR 验证了芽和嫩叶之间 circRNAs 的差异表达模式，这也表明与母基因的标准 mRNA 相比，circRNAs 的表达丰度较低。我们预测了 circRNA- microRNA 相互作用网络，发现 54 个差异表达的 circRNAs 具有潜在的茶树 miRNA 结合位点。编码 circRNAs 的基因集在叶绿体相关 GO 术语和光合作用/代谢物生物合成相关 KEGG 途径中显著富集，表明 circRNAs 在叶片发育过程中参与光合作用机制和代谢物生物合成的候选作用。
