Long noncoding RNAs (lncRNAs) are widely present in different species and play critical roles in response to abiotic stresses. However, the functions of lncRNAs in Chinese cabbage under heat stress remain unknown. Here, we first conducted a global comparative analysis of 247,242 lncRNAs among 37 species. The results indicated that lncRNAs were poorly conserved among different species, and only 960 lncRNAs were homologous to 524 miRNA precursors. We then carried out lncRNA sequencing for a genome-wide analysis of lncRNAs and their target genes in Chinese cabbage at different stages of heat treatment. In total, 18,253 lncRNAs were identified, of which 1229 differentially expressed (DE) lncRNAs were characterized as being heat-responsive. The ceRNA network revealed that 38 lncRNAs, 16 miRNAs, and 167 mRNAs were involved in the heat response in Chinese cabbage. Combined analysis of the cis- and trans-regulated genes indicated that the targets of DE lncRNAs were significantly enriched in the “protein processing in endoplasmic reticulum” and “plant hormone signal transduction” pathways. Furthermore, the majority of HSP and PYL genes involved in these two pathways exhibited similar expression patterns and responded to heat stress rapidly. Based on the networks of DE lncRNA-mRNAs, 29 and 22 lncRNAs were found to interact with HSP and PYL genes, respectively. Finally, the expression of several critical lncRNAs and their targets was verified by qRT-PCR. Overall, we conducted a comparative analysis of lncRNAs among 37 species and performed a comprehensive analysis of lncRNAs in Chinese cabbage. Our findings expand the knowledge of lncRNAs involved in the heat stress response in Chinese cabbage, and the identified lncRNAs provide an abundance of resources for future comparative and functional studies.

中文翻译：

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被子植物长链非编码RNA的比较分析及长链非编码RNA响应大白菜热应激的特性

长链非编码 RNA (lncRNA) 广泛存在于不同物种中，并在应对非生物胁迫中发挥关键作用。然而，热应激下大白菜中lncRNA的功能仍不清楚。在这里，我们首先对 37 个物种中的 247,242 个 lncRNA 进行了全球比较分析。结果表明，lncRNA在不同物种之间的保守性较差，只有960个lncRNA与524个miRNA前体同源。然后，我们对大白菜中不同热处理阶段的 lncRNA 及其靶基因进行了全基因组分析。总共鉴定了 18,253 个 lncRNA，其中 1229 个差异表达 (DE) lncRNA 被表征为热响应性。ceRNA 网络揭示了 38 个 lncRNA、16 个 miRNA、167个mRNA参与了大白菜的热反应。综合分析顺式- 和反式调节基因表明DE lncRNA的靶点在“内质网蛋白质加工”和“植物激素信号转导”通路中显着富集。此外，大多数热休克蛋白和PYL参与这两种途径的基因表现出相似的表达模式并且对热应激反应迅速。基于 DE lncRNA-mRNAs 的网络，发现 29 和 22 个 lncRNAs 与热休克蛋白和PYL基因，分别。最后，通过 qRT-PCR 验证了几个关键 lncRNA 及其靶标的表达。总体而言，我们对 37 个物种的 lncRNA 进行了比较分析，并对大白菜中的 lncRNA 进行了综合分析。我们的研究结果扩展了对参与大白菜热应激反应的 lncRNA 的认识，鉴定出的 lncRNA 为未来的比较和功能研究提供了丰富的资源。