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.

中文翻译：

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山核桃（山核桃）开花过程中lncRNA的全基因组鉴定。

长度大于200 bp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起重要作用。然而，迄今为止，关于山核桃（山核桃）中lncRNA在开花过程中所起的作用鲜为人知）。在这里，我们对山核桃雌花和雄花芽的样品进行了全转录组RNA测序，其中三个样品（H0311PF，H0318PF和H0402PF）分别代表开花前，开花和开花后，同时收集了八个雄性样品从5月8日到6月13日是这个时间过程，是雄性花芽分化的关键阶段。我们在开花期间在山核桃中鉴定了2163个lncRNA，其中包含213个内含子，1488个基因间和462个反义lncRNA。我们注意到分别对应于雌性和雄性花芽的510和648个lncRNA被差异表达。而且某些lncRNAs具有紧密的组织特异性或阶段特异性方式。为了进一步了解lncRNA的作用，我们预测了lncRNA在顺式和反式中的功能。交易模式。结果显示924个lncRNA与1536个蛋白质编码基因顺式相关，而1207个lncRNA与7432个蛋白质编码基因共表达（反式作用）（R  > 0.95或R <-0.95）。这些lncRNA都富含与花发育相关的生物过程，即昼夜节律，春化反应，对赤霉素的反应，花序发育，花器官发育等。为了进一步了解lncRNA与花芯基因之间的关系，我们构建了一个共表达lncRNA-mRNA开花网络。根据它们的特定功能，我们将这些花卉基因分为不同的途径（光周期，春化，赤霉素，自主和蔗糖途径）。我们发现了一组在这些途径中优先表达的lncRNA。该网络显示，某些lncRNA（即XLOC_038669，XLOC_017938）在特定的开花时间途径中起作用，而其他lncRNA（即XLOC_011251，XLOC_04110）则参与了多种途径。此外，一些lncRNA（例如，XLOC_038669，XLOC_009597和XLOC_049539）通过相互影响在单个或多个路径中发挥作用。这项研究提供了全基因组的山核桃花相关lncRNA的调查，将有助于进一步了解山核桃开花的分子机制。