Multidimensional analysis of long noncoding RNAs function in Solanaceae plants.

Long noncoding RNAs (lncRNAs) have been gradually verified as functional regulators in plants, yet their functions remain underexplored, especially in the Solanaceae family. While substantial progress has been made in identifying lncRNAs in different Solanaceae species, systematic functional annotations are lacking. In this study, we uniformly identified and systematically characterized lncRNAs from seven Solanaceous species using large-scale strand-specific RNA-seq (ssRNA-seq). About 113 700 lncRNA genes were obtained and analyzed for their sequence, conservation, expression profile, epigenetic signals, and genetic mutants. In tomato, 97.4% of lncRNAs have been annotated with basic characteristics. Also, 25.7% of lncRNAs were further predicted to be involved in stress response, development, and metabolism. Comparisons between lncRNAs and protein-coding genes (PCGs) highlighted unique characteristics in tissue expression, stress responses, sequence composition, and epigenetic signal distribution. We shared our datasets on Solanaceous lncRNAs at http://solanaceae-lncrna-source.liu-lab.com/. Taking fruit development and ripening as an example, we further mined the data resources and predicted a total of 1158 lncRNAs associated with this process, presenting how our curated data can be utilized to discover the functions of plant lncRNAs. Overall, this study provides a comprehensive multidimensional framework for lncRNA functional research, which serves as a valuable reference for understanding lncRNA functions in other plants.