Pan-genomic and transcriptomic analyses reveal subfunctionalization of CBP/p300-like histone acetyltransferases in soybean seed development.

Genome-wide characterization highlights the regulatory network rewiring of BTB genes in barley under stress condition

Genome-Wide Identification of AP2/ERF Transcription Factors in Capsicum annuum and Preliminary Functional Analysis of CaBBM

The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays essential roles in growth and development. Chili pepper, as a representative member of the Solanaceae family, is an important vegetable crop with enormous economic value. In this study, using the recently released gap-free telomere-to-telomere genome assembly of pepper, we re-annotated the AP2/ERF transcription factor family and identified 155 high-confidence members. Phylogenetic analysis classified these genes into five subfamilies: AP2 (19), ERF (82), DREB (51), RAV (1), and Soloist (2). Comprehensive analyses of gene structure, conserved motifs, chromosomal distribution, collinearity, cis-elements, and expression profiles revealed substantial structural conservation and functional diversification within the family. Expression profiling highlighted CaBBM, a key member of the AP2 subfamily, as a candidate developmental regulator, prompting further functional characterization. Expression analyses using qRT-PCR and promoter–GUS assays showed that CaBBM was preferentially expressed in stamens, while subcellular localization assays confirmed its nuclear localization. Preliminary analysis of biological functions suggests that heterologous expression of CaBBM in Arabidopsis can lead to phenotypes such as shorter primary roots, smaller leaves and floral organs, and decreased pollen number. In addition, yeast two-hybrid screening identified 12 candidate interacting proteins. These results provide a comprehensive framework for understanding the AP2/ERF family in chili pepper and lay a foundation for elucidating the function and regulatory mechanisms of CaBBM.

Genome-wide analysis of the pectin acetylesterase (PAE) gene family in tomato and SlPAE16 functional characterization associated with pedicel abscission.

Pectin acetylesterase (PAE) regulates pectin acetylation, which affects plant growth, development, and stress tolerance. While their functions are well-defined in models like Arabidopsis, we still know surprisingly little about how they operate in tomatoes (Solanum lycopersicum). We identified 17 SlPAE genes using tomato genome-wide analysis. These genes were classified phylogenetically into three conserved subfamilies, with branch members sharing domain architectures, motifs, and genomic structure. Promoter cis-element analysis identified multiple motifs related to hormone signaling, light response, and stress response. Spatiotemporal expression patterns obtained via qRT-PCR revealed the functional roles of SlPAE genes. Notably, silencing SlPAE16 effectively retarded pedicel abscission, a process mediated by the inhibition of TAPG1/2/4 expression. These findings clarify the functional diversity within the PAE gene family, providing a much-needed framework for future research into their specific biological roles in tomatoes.

Genome-wide identification of IiSPL gene family and IiSPL9 functional exploration

Pan-Genomic Dissection of GH1 β-Glucosidases in Brassica rapa Identifies BrBGLU10 as an Important Regulator of Pollen Development

Findings establish BrBGLU10 as an important regulator of pollen development and a potential target for fertility-related applications via gene editing in B. rapa and related Brassica crops.

Pan-genome-based characterization of SiGRAS transcription factors and prediction of hub genes correlated with plant height in foxtail millet (Setaria italica L.)

The GRAS gene family, a class of plant-specific transcription factors, plays pivotal roles in diverse biological processes, including plant growth, development, and stress responses. Although the SiGRAS family has been previously characterized in foxtail millet, those studies were restricted to a single reference genome, overlooking critical genetic variations. To overcome the inherent limitations of gene family analysis using a single reference, we systematically investigated the SiGRAS gene family using pan-genome data generated from 110 foxtail millet accessions together with the xiaomi and Yugu1 genomes. Based on a rigorously filtered pan-genome catalog, we identified a total of 949 SiGRAS pan-genes, comprising 1 core, 20 near-core, 50 dispensable, and 878 private genes. Phylogenetic analysis classified these genes into 9 distinct subfamilies. Evolutionary analysis based on Ka/Ks ratios revealed that 8 SiGRAS genes underwent purifying selection, while SiGRAS17 and SiGRAS2 were subjected to positive selection in the majority of accessions. Notably, we observed that structural variations (SVs) significantly influenced the expression levels of SiGRAS63 , and altered both conserved domains and gene structure in specific accessions. Furthermore, we identified four hub genes correlated with plant height by integrating RNA-seq data with gene co-expression regulatory network. This study lays a foundation for understanding the diversity of the SiGRAS gene family and provides a valuable resource for future function studies of SiGRAS genes in foxtail millet.