Integrated Phylogenomic and Expression Analyses Reveal Lineage-Specific Loss of the Mβ Subfamily and Regulatory Diversification of MADS-Box Genes in Pepper

MADS-box transcription factors are key regulators of plant development and environmental responses. Here, we performed an integrated phylogenomic and expression analysis of the MADS-box gene family in Capsicum annuum, identifying 97 members that fall into 52 Type I and 45 Type II genes. Comparative phylogeny, exon–intron organization, conserved motifs, and chromosomal mapping allowed classification into 15 subfamilies. Gene duplication analysis revealed that segmental duplication has been a major driver of family expansion. Expression profiling across multiple tissues, together with promoter cis-element prediction and stress-responsive transcriptome data, demonstrated that Type II genes exhibit broad and dynamic expression patterns, particularly under ABA treatment and temperature stress. A key finding of this study is the complete absence of the Mβ lineage, a Type I subfamily typically associated with gametophyte and endosperm development in other angiosperms. No Mβ-like sequences were detected in the pepper genome, and Type I genes overall showed extremely low expression, suggesting that the Mβ lineage has undergone lineage-specific evolutionary loss and that its functions may be compensated by other Type I members or by expanded Type II regulatory modules. Together, this study provides the first evidence for the evolutionary disappearance of the Mβ subfamily in Capsicum and offers a comprehensive resource for dissecting the developmental and stress-responsive roles of MADS-box genes in pepper.