State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, People's Republic of China.
Funct Integr Genomics. 2020 Jul;20(4):591-607. doi: 10.1007/s10142-020-00737-w. Epub 2020 Mar 25.
Non-coding RNAs with lengths greater than 200 bp are known as long non-coding RNAs (lncRNAs), and these RNAs play important role in gene regulation and plant development. However, to date, little is known regarding the role played by lncRNAs during flowering in hickory (Carya cathayensis). Here, we performed whole transcriptome RNA-sequencing of samples from hickory female and male floral buds, in which three samples (H0311PF, H0318PF, and H0402PF) represent pre-flowering, flowering, and post-flowering, respectively, while eight male samples collected from May 8th to June 13th as this time course are the key stage for male floral bud differentiation. We identified 2163 lncRNAs in hickory during flowering, containing 213 intronic, 1488 intergenic, and 462 antisense lncRNAs. We noticed that 510 and 648 lncRNAs were differentially expressed corresponding to female and male floral buds, respectively. And some of the lncRNAs were in a tightly tissue-specific or stage-specific manner. To further understand the roles of the lncRNAs, we predicted the function of the lncRNAs in cis- and trans-acting modes. The results showed that 924 lncRNAs were cis-correlated with 1536 protein-coding genes, while 1207 lncRNAs co-expressed (trans-acting) with 7432 protein-coding genes (R > 0.95 or R < - 0.95). These lncRNAs were all enriched in flower development-associated biological processes, i.e., circadian rhythm, vernalization response, response to gibberellin, inflorescence development, floral organ development, etc. To further understand the relationships between lncRNAs and floral-core genes, we build a co-expressing lncRNA-mRNA flowering network. We classified these floral genes into different pathway (photoperiod, vernalization, gibberellin, autonomous, and sucrose pathway) according to their particular functions. We found a set of lncRNAs that preferentially expressed in these pathways. The network showed that some lncRNAs (i.e., XLOC_038669, XLOC_017938) functioned in a particular flowering time pathway, while others (i.e., XLOC_011251, XLOC_04110) were involved in multiple pathway. Furthermore, some lncRNAs (i.e., XLOC_038669, XLOC_009597, and XLOC_049539) played roles in single or multiple pathways via interaction with each other. This study provides a genome-wide survey of hickory flower-related lncRNAs and will contribute to further understanding of the molecular mechanism underpinning flowering in hickory.
长度大于 200bp 的非编码 RNA 被称为长非编码 RNA（lncRNA），这些 RNA 在基因调控和植物发育中发挥重要作用。然而，迄今为止，人们对山核桃（Carya cathayensis）开花过程中 lncRNA 的作用知之甚少。在这里，我们对山核桃雌性和雄性花芽的样本进行了全转录组 RNA-seq 分析，其中 H0311PF、H0318PF 和 H0402PF 分别代表开花前、开花中和开花后，而从 5 月 8 日到 6 月 13 日收集的 8 个雄性样本作为这一时序的关键阶段是雄性花芽分化的关键阶段。我们在山核桃开花过程中鉴定了 2163 个 lncRNA，其中包括 213 个内含子、1488 个基因间和 462 个反义 lncRNA。我们注意到，有 510 个和 648 个 lncRNA 分别对应雌性和雄性花芽差异表达。并且一些 lncRNA 以紧密的组织特异性或阶段特异性方式存在。为了进一步了解 lncRNA 的作用，我们预测了 lncRNA 在顺式和反式作用模式下的功能。结果表明，924 个 lncRNA 与 1536 个蛋白编码基因呈顺式相关，而 1207 个 lncRNA 与 7432 个蛋白编码基因（R>0.95 或 R<-0.95）共表达（反式作用）。这些 lncRNA 均富集在与花发育相关的生物学过程中，如花芽发育、花器官发育等。为了进一步了解 lncRNA 与花核心基因之间的关系，我们构建了一个共表达的 lncRNA-mRNA 开花网络。我们根据特定功能将这些花基因分类到不同的途径（光周期、春化、赤霉素、自主和蔗糖途径）中。我们发现了一组在这些途径中优先表达的 lncRNA。该网络显示，一些 lncRNA（例如 XLOC_038669、XLOC_017938）在特定的开花时间途径中发挥作用，而其他 lncRNA（例如 XLOC_011251、XLOC_04110）则参与多个途径。此外，一些 lncRNA（例如 XLOC_038669、XLOC_009597 和 XLOC_049539）通过相互作用在单个或多个途径中发挥作用。本研究提供了山核桃花相关 lncRNA 的全基因组调查，将有助于进一步了解山核桃开花的分子机制。
