GreenCells: A comprehensive resource for single-cell analysis of plant lncRNAs

Long non-coding RNAs (lncRNAs) play crucial roles in plant growth, development, and stress responses. With the advancement of single-cell RNA sequencing (scRNA-seq) technology, it is now possible to investigate lncRNA expression and function at single-cell resolution. Although several plant single-cell transcriptome databases have been established, they predominantly focus on protein-coding genes while largely overlooking lncRNAs. To bridge this gap, we developed GreenCells (http://greencells.liu-lab.com/), a comprehensive database specifically designed to explore plant lncRNAs at the single-cell level. By integrating scRNA-seq data from eight plant species, GreenCells has identified 2177 lncRNA marker genes and 68,869 protein-coding marker genes across diverse cell types. The database also features cell type-specific co-expression networks that reveal the regulatory potential of lncRNAs, many of which function as hub genes. For example, co-expression network analysis suggests that lncCOBRA5 may be involved in transmembrane processes. In addition, by comparing bulk and single-cell transcriptome profiles, we identified a set of lncRNAs uniquely expressed in specific cell types that are undetectable in root bulk RNA-seq data. We also observed a strong correlation between tissue-specific and cell type-specific expression patterns of lncRNAs. Overall, GreenCells provides detailed annotations, high-quality visualizations, advanced search functions, and practical analytical tools. It offers a valuable platform for investigating the regulation and expression of plant lncRNAs at single-cell resolution, thereby contributing a new resource to plant functional genomics research.