Identification of cell‐type specificity, trans‐ and cis‐acting functions of plant lincRNAs from single‐cell transcriptomes

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.