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.
Rubber tree is an economically important woody plant, whereas the cellular heterogeneity and regulatory networks underlying its xylem differentiation remain poorly characterised. Here, we built a protocol to isolate differentiating xylem protoplasts and performed scRNA-seq on two rubber tree cultivars (RK525 and RY73397) with distinct rates of girth growth. The first single-cell transcriptional atlas of differentiating xylem in the rubber tree was established, providing a cellular basis for growth variations. Ten distinct cell clusters were identified, with cell types-including vessel element, libriform fibre, and ray parenchyma-determined by established marker genes. Pseudotime analysis revealed two clearly developmental trajectories, underscoring fusiform lineages (fibres and vessels) being crucial for growth differences. Specifically, the fast-growing cultivar RK525 exhibited a cluster of upregulated genes in fibre and vessel cells. Subsequently, differentially expressed genes (DEGs) in fusiform cell clusters between the two cultivars were intersected with subcluster-upregulated genes and pseudotime-core DEGs in RK525, highlighting secondary cell wall (SCW) biosynthesis genes that regulate xylem development and promote rapid growth. WGCNA further identified a specific module significantly correlated with fibre cells, which includes six key transcription factors. Moreover, ATAC-seq revealed variety-specific chromatin accessibility patterns and transcription factor binding motifs associated with xylem development. Functional validation using Arabidopsis mutants of rubber tree homologues confirmed their crucial roles in vascular development. These findings reveal intricate regulatory programmes in differentiating xylem, and provide valuable resources and targets for genetic improvement of the rubber tree.
Chaofeng Zhang, Yuan Yao, Miaomiao Zhou et al.· Plant, Cell and Environment· 0 citations
