Hongliang Ji

Sepal doubling in Punica granatum (pomegranate), characterized by calyx splitting and bilayered structure formation, confers distinctive ornamental value but its developmental mechanisms remain poorly understood. Elucidating the molecular mechanisms of sepal doubling and screening for associated genes and proteins in pomegranate are of theoretical and practical significance. Herein, transcriptomic and proteomic analyses were performed on sepals from single, double, and proliferated flowers. Overall, 23,630 genes and 5803 proteins were identified, with 5634 quantified at both levels. Pairwise comparisons revealed stronger correlations between differentially expressed genes (DEGs) and differentially abundant proteins (DAPs) than between the total gene and protein sets. Because SeSi and SeDo/SePr were obtained from different cultivars, SeSi comparisons are partly confounded by genotype, whereas SeDo vs. SePr is the least cultivar-affected comparison. Cell wall-related terms were detected in the transcriptomic, proteomic and integrated datasets, alongside dominant photosynthesis-related terms in the transcriptomic comparisons. Eleven cell wall metabolism-related DEGs and three cell wall metabolism-related DAPs were identified, including ten concordant DEG–DAP pairs. These candidates included both concordant DEG–DAP pairs and those supported at a single omics level. Among them, cellulose synthase A (CESA), extensin-2 (EXT2), endo-1,4-β-D-glucanase (EG), and xyloglucan endotransglucosylase/hydrolase 16 (XTH16) were associated with bilayered calyx formation, whereas pectinesterase (PE), alpha-galactosidase (α-Gal), xylan α-glucuronyltransferase (α-GLU), and polygalacturonase (PG) were associated with calyx splitting. Two protein-modifying enzymes, serine/threonine-protein kinase (STPK) and serine carboxypeptidase (SCP), were associated with calyx splitting. Additionally, two transcription factors, basic helix–loop–helix (bHLH) and cold-shock domain protein (CSD), were associated with sepal doubling. These findings provide a molecular basis for further studies of floral development and type improvement in pomegranate.

Background: The ATP-binding cassette (ABC) G subfamily, a key member of the ABC protein family, mediates plant stress responses by transporting metabolites across membranes, but its mechanism of action in tomato (Solanum lycopersicum L.) remains poorly understood. Methods: We systematically analyzed the evolutionary relationships, structural characteristics, stress-responsive expression patterns, and functional roles in response to saline-alkali stress of the SlABCG gene family in tomato, using a combination of approaches including phylogenetic analysis (MEGA), gene structure and motif analysis (GSDS, MEME), cis-acting element prediction, homology analysis, transcriptome analysis, protein-protein interaction prediction, and qRT-PCR validation. Results: We identified a total of 41 SlABCG genes from the tomato genome. These genes, together with 43 ABCG genes from Arabidopsis thaliana, were clustered into five distinct clades. There are 35 collinear gene pairs between the SlABCG gene family in tomato and the ABCG gene family in Arabidopsis, while 39 collinear gene pairs exist among ABCG genes within the tomato genome itself.The promoter regions of SlABCG genes contain cis-acting elements associated with responses to salicylic acid, low temperature, and gibberellin stresses. Transcriptome sequencing revealed that six SlABCG genes responded to saline-alkali stress. Gene regulatory network prediction revealed that multiple genes related to saline-alkali stress were regulated. Expression profile analysis of the 25 upregulated genes revealed that all of them were significantly upregulated during the saline-alkali stress treatment. Conclusions: In summary, our results provide deep insights into the characteristics of the SlABCG subfamily, facilitate the design of effective analysis strategies, and offer data support for exploring the roles of ABCG transporters under different stress conditions.