Summary Long noncoding RNAs, including intergenic lncRNAs (lincRNAs), play a key role in various biological processes throughout the plant life cycle, and the advent of single‐cell RNA sequencing (scRNA‐seq) technology has opened up a valuable avenue for scrutinizing the intricate roles of lincRNAs in cellular processes. Here, we identified a new batch of lincRNAs using scRNA‐seq data from diverse tissues of plants (rice, Arabidopsis, tomato, and maize). Based on well‐annotated single‐cell transcriptome atlases, plant lincRNAs were found to possess the same level of cell‐type specificity as mRNAs and to be involved in the differentiation of certain cell types based on pseudo‐time analysis. Many lincRNAs were predicted to play a hub role in the cell‐type‐specific co‐expression networks of lincRNAs and mRNAs, suggesting their trans‐acting abilities. Besides, plant lincRNAs were revealed to have potential cis‐acting properties based on their genomic distances and expression correlations with the neighboring mRNAs. Furthermore, an online platform, PscLncRNA (http://ibi.zju.edu.cn/psclncrna/), was constructed for searching and visualizing all identified plant lincRNAs with annotated potential functions. Our work provides new insights into plant lincRNAs at single‐cell resolution and an important resource for understanding and further investigation of plant lincRNAs.

中文翻译：

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从单细胞转录组中鉴定植物 lincRNA 的细胞类型特异性、反式和顺式作用功能


摘要长链非编码 RNA，包括基因间 lncRNA （lincRNA），在整个植物生命周期的各种生物过程中起着关键作用，单细胞 RNA 测序 （scRNA-seq） 技术的出现为仔细研究 lincRNA 在细胞过程中的复杂作用开辟了一条有价值的途径。在这里，我们使用来自植物不同组织（水稻、拟南芥、番茄和玉米）的 scRNA-seq 数据鉴定了一批新的 lincRNA。基于注释良好的单细胞转录组图谱，发现植物 lincRNA 具有与 mRNA 相同水平的细胞类型特异性，并且基于伪时间分析参与某些细胞类型的分化。预计许多 lincRNAs 在 lincRNAs 和 mRNA 的细胞类型特异性共表达网络中发挥枢纽作用，表明它们的反式作用能力。此外，根据植物 lincRNAs 的基因组距离和与邻近 mRNA 的表达相关性，发现植物 lincRNAs 具有潜在的顺式作用特性。此外，构建了一个在线平台 PscLncRNA （http://ibi.zju.edu.cn/psclncrna/），用于搜索和可视化所有已鉴定的具有注释潜在功能的植物 lincRNA。我们的工作为单细胞分辨率的植物 lincRNAs 提供了新的见解，并为理解和进一步研究植物 lincRNA 提供了重要资源。