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

Abstract

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.