Cytosolic and Nucleosolic Calcium-Regulated Long Non-Coding RNAs and Their Target Protein-Coding Genes in Response to Hyperosmolarity and Salt Stresses in .

Long non-coding RNAs (lncRNAs) are involved in plant biotic and abiotic stress responses, in which Ca also plays a significant role. There is diversity in the regulation of different gene expressions by cytosolic Ca ([Ca]) and nucleosolic Ca ([Ca]). However, no studies have yet explored the interrelationship between lncRNAs and calcium signaling, nor how calcium signaling regulates the expression of lncRNAs. Here, we use transgenic materials and , which simulate [Ca]- and [Ca]-deficient mutants, respectively, and wild type (WT) materials in response to hyperosmolarity (250 mM sorbitol) or salt stresses (125 mM NaCl) at different time points to obtain RNA-seq data, respectively. Then, we proceed with the screening of lncRNAs, adding 688 new lncRNAs to the known Arabidopsis lncRNA database. Subsequently, through the analysis of differentially expressed lncRNA genes, it was found that cytosolic or nucleosolic calcium signals have distinct regulatory effects on differentially expressed lncRNAs (DElncRNAs) and differentially expressed protein-coding genes (DEPCGs) treated with high-concentration NaCl and sorbitol at different times. Furthermore, through weighted correlation network analysis (WGCNA), it is discovered that under hyperosmolarity and salt stresses, lncRNA-associated PCGs are related to the cell wall structure, the plasma membrane component, and osmotic substances through -regulation. In addition, by screening for -regulatory target PCGs of Ca-regulated lncRNAs related to osmotic stress, we obtain a series of lncRNA-PCG pairs related to water transport, cell wall components, and lateral root formation. Therefore, we expand the existing lncRNA database and obtain a series of lncRNAs and PCGs regulated by [Ca] or [Ca] in response to salt and hyperosmolarity stress, providing a new perspective for subsequent research on lncRNAs. We also explore the and -regulated target PCGs of lncRNAs regulated by calcium signaling, providing new insights for further studying salt stress and osmotic stress.