Hainan Provincial Key Laboratory of Tropical Crops Cultivation and Physiology, Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
Tree Physiol. 2022 Mar 9;42(3):629-645. doi: 10.1093/treephys/tpab120.
Noncoding RNAs (ncRNAs) play pivotal roles in various biological processes in plants. However, the role of ncRNAs in tapping panel dryness (TPD) of rubber tree (Hevea brasiliensis Muell. Arg.) is largely unknown. Here, the whole transcriptome analyses of bark tissues from healthy and TPD trees were performed to identify differentially expressed long ncRNAs (DELs), microRNAs/miRNAs (DEMs), genes (DEGs) and their regulatory networks involved in TPD. A total of 263 DELs, 174 DEMs and 1574 DEGs were identified in the bark of TPD tree compared with that of healthy tree. Kyoto Encyclopedia of Genes and Genomes analysis revealed that most of the DEGs and targets of DELs and DEMs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Additionally, the majority of DEGs and DELs related to rubber biosynthesis were downregulated in TPD trees. Furthermore, 98 DEGs and 44 DELs were targeted by 54 DEMs, 190 DEGs were identified as putative targets of 56 DELs, and 2 and 44 DELs were predicted as precursors and endogenous target mimics of 2 and 6 DEMs, respectively. Based on these, the DEL-DEM-DEG regulatory network involved in TPD was constructed, and 13 hub DELs, 3 hub DEMs and 2 hub DEGs were identified. The results provide novel insights into the regulatory roles of ncRNAs underlying TPD and lay a foundation for future functional characterization of long ncRNAs, miRNAs and genes involved in TPD in rubber tree.
非编码 RNA（ncRNA）在植物的各种生物学过程中发挥着关键作用。然而，ncRNA 在橡胶树（Hevea brasiliensis Muell. Arg.）割胶排胶中的作用在很大程度上尚不清楚。本研究对健康和排胶橡胶树树皮组织进行了全转录组分析，以鉴定与排胶相关的差异表达长 ncRNA（DEL）、microRNA/miRNA（DEM）、基因（DEG）及其调控网络。与健康树相比，排胶树树皮中共鉴定到 263 个 DEL、174 个 DEM 和 1574 个 DEG。京都基因与基因组百科全书（KEGG）分析显示，大多数 DEG 和 DELs、DEMs 的靶基因主要富集在代谢途径、次生代谢物的生物合成和植物激素信号转导途径中。此外，与橡胶生物合成相关的大多数 DEG 和 DEL 在排胶树中下调表达。进一步分析发现，98 个 DEG 和 44 个 DEL 受 54 个 DEM 的靶向调控，190 个 DEG 被鉴定为 56 个 DEL 的潜在靶基因，2 个和 44 个 DEL 分别被预测为 2 个和 6 个 DEM 的前体和内源性靶 mimics。基于此，构建了与排胶相关的 DEL-DEM-DEG 调控网络，鉴定到 13 个 DEL 枢纽基因、3 个 DEM 枢纽基因和 2 个 DEG 枢纽基因。该研究结果为 ncRNA 参与排胶的调控作用提供了新的见解，为进一步研究橡胶树中与排胶相关的长 ncRNA、miRNA 和基因的功能特性奠定了基础。
