Salt stress is one of the main abiotic stresses that strongly affects plant growth. Clarifying the molecular regulatory mechanism in ornamental plants under salt stress is of great significance for the ecological development of saline soil areas. Aquilegia vulgaris is a perennial with a high ornamental and commercial value. To narrow down the key responsive pathways and regulatory genes, we analyzed the transcriptome of A. vulgaris under a 200 mM NaCl treatment. A total of 5600 differentially expressed genes were identified. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis pointed out that starch and sucrose metabolism and plant hormone signal transduction were significantly improved. The above pathways played crucial roles when A. vulgaris was coping with salt stress, and their protein–protein interactions (PPIs) were predicted. This research provides new insights into the molecular regulatory mechanism, which could be the theoretical basis for screening candidate genes in Aquilegia.

Salt stress has a considerable impact on the development and growth of plants. The soil is currently affected by salinisation, a problem that is becoming worse every year. This means that a significant amount of salt-tolerant plant material needs to be added. Aquilegia vulgaris has aesthetically pleasing leaves, unique flowers, and a remarkable tolerance to salt. In this study, RNA-seq technology was used to sequence and analyse the transcriptome of the root of Aquilegia vulgaris seedlings subjected to 200 mM NaCl treatment for 12, 24, and 48 h. In total, 12 Aquilegia vulgaris seedling root transcriptome libraries were constructed. At the three time points of salt treatment compared with the control, 3888, 1907, and 1479 differentially expressed genes (DEGs) were identified, respectively. Various families of transcription factors (TFs), mainly AP2, MYB, and bHLH, were identified and might be linked to salt tolerance. Gene Ontology (GO) analysis of DEGs revealed that the structure and composition of the cell wall and cytoskeleton may be crucial in the response to salt stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs showed a significant enrichment of the pentose and glucuronate interconversion pathway, which is associated with cell wall metabolism after 24 and 48 h of salt treatment. Based on GO and KEGG analyses of DEGs, the pentose and glucuronate interconversion pathway was selected for further investigation. AP2, MYB, and bHLH were found to be correlated with the functional genes in this pathway based on a correlation network. This study provides the groundwork for understanding the key pathways and gene networks in response to salt stress, thereby providing a theoretical basis for improving salt tolerance in Aquilegia vulgaris.

Cgr-miR166 was observed to be significantly enhanced in Chrysanthemum under 200 mM NaCl treatment. Here, ten family members were identified by aligning cgr-miR166 with scaffold sequences from the Chrysanthemum nankingense genome database, naming them from cgr-miR166a to cgr-miR166j, and their precursors could form stable stem-loop structures. The mature regions were observed to be highly conserved, with the 3′ end being more conserved than the 5′ end. miR166s promoters have been found to contain cis-acting elements responsive to diverse stimuli like the phytohormones ABA and IAA. qRT-RCR results demonstrated that the transcriptome sequencing results were reliable and miR166 was present at different levels in the roots, stems, leaves and flowers of Chrysanthemum. Furthermore, the HD-ZipIII transcription factor was validated to be the target gene of Chrysanthemum miR166s by degradome sequencing. Taken together, the cgr-miR166 family exhibited both evolutionary conservation and diversification. The expression level of miR166 was upregulated in root under salt stress, while the expression level of the target gene HD-ZipIII was downregulated. These findings established the foundation for further understanding the mechanism of miR166-HD-ZipIII modules in salt response and tolerance.

Low-temperature stress is a major factor limiting the development of the chrysanthemum industry. Chrysanthemum indicum L., wild germplasm with strong cold tolerance within the genus, is an ideal material for mining cold resistance genes. Through preliminary transcriptome analysis of C. indicum under low-temperature stress (PRJNA1391062), we found that multiple R2R3-MYB family members were significantly differentially expressed (|log₂FC| ≥ 1, p < 0.05), suggesting that this family may play important roles in cold stress responses. Within the C. indicum genome, we identified 63 R2R3-MYB members (CiMYBs) through HMMER and BLAST searches combined with domain validation. Phylogenetic analysis classified these genes into 19 subgroups, with most key nodes supported by bootstrap values > 80%. Promoter cis-element analysis revealed enrichment of elements related to light responsiveness, hormone signaling, and stress responses, including 41 low-temperature responsive elements distributed across 28 genes and 32 drought-induced MYB-binding sites present in 23 genes. Synteny analysis identified 13 duplicated gene pairs within the C. indicum genome and 41 collinear gene pairs between C. indicum and Arabidopsis thaliana L. Transcriptome data under low-temperature stress showed that 22 of the 63 CiMYB members were differentially expressed under 4 °C acclimation and −4 °C freezing stress, and they could be classified into three response patterns: acute stress-responsive (rapid upregulation upon initial stress), acclimation-induced (significant activation after 4 °C acclimation), and freezing-suppressed (downregulation after −4 °C freezing). Six differentially expressed genes were randomly selected for RT-qPCR validation, and the results showed consistent trends with the transcriptome data. This study provides a comprehensive identification of R2R3-MYB family members in C. indicum and reveals their expression divergence under low-temperature stress, offering candidate gene resources for deciphering the cold adaptation mechanisms of C. indicum and breeding new cold-resistant chrysanthemum cultivars.