MADS domain transcription factors play roles throughout the whole lifecycle of plants from seeding to flowering and fruitbearing. However, systematic research into MADS-box genes of the economically important vegetable crop pepper (Capsicum spp.) is still lacking. We identified 174, 207, and 72 MADS-box genes from the genomes of C. annuum, C. baccatum and C. chinense, respectively. These 453 MADS-box genes were divided into type I (Mα, Mβ, Mγ) and type II (MIKC* and MIKCC) based on their phylogenetic relationships. Collinearity analysis identified 144 paralogous genes and 195 orthologous genes in the three pepper species, and 70, 114, and 10 MADS-box genes specific to C. annuum, C. baccatum and C. chinense, respectively. Comparative genomic analysis highlighted functional differentiation among homologous MADS-box genes during pepper evolution. Tissue expression analysis revealed three main expression patterns: highly expressed in roots, stems, leaves and flowers (CaMADS93/CbMADS35/CcMADS58); only expressed in roots; and specifically expressed in flowers (Ca-MADS26/CbMADS31/CcMADS11). This study provides the basis for an in-depth study of the evolutionary features and biological functions of pepper MADS-box genes. Hosted fileessoar.10512212.1.docx available at https://authorea.com/users/542768/articles/601054genome-wide-identification-evolution-and-expression-characterization-of-the-pepper-madsbox-gene-family Core Ideas:• Genome-wide identification identified 454 MADS-box genes from Capsicum spp. Genomes.• Genome-wide identification revealed the evolutionary relationship of MADSbox gene family in Capsicum spp.• Most of the Capsicum MADS-box genes have been amplified on a large scale.• Most of the Capsicum MADS-box genes have undergone purification selection during evolution.• Tissue specific expression patterns of most MADS-box genes indicated their functional diversity. Genome-wide identification, evolution, and expression characterization of the pepper MADS-box gene familyZhicheng Gan,

MADS domain transcription factors play roles throughout the whole lifecycle of plants from seeding to flowering and fruit-bearing. However, systematic research into MADS-box genes of the economically important vegetable crop pepper (Capsicum spp.) is still lacking. We identified 174, 207, and 72 MADS-box genes from the genomes of C. annuum, C. baccatum, and C. chinense, respectively. These 453 MADS-box genes were divided into type I (Mα, Mβ, Mγ) and type II (MIKC* and MIKCC) based on their phylogenetic relationships. Collinearity analysis identified 144 paralogous genes and 195 orthologous genes in the three Capsicum species, and 70, 114, and 10 MADS-box genes specific to C. annuum, C. baccatum, and C. chinense, respectively. Comparative genomic analysis highlighted functional differentiation among homologous MADS-box genes during pepper evolution. Tissue expression analysis revealed three main expression patterns: highly expressed in roots, stems, leaves, and flowers (CaMADS93/CbMADS35/CcMADS58); only expressed in roots; and specifically expressed in flowers (CaMADS26/CbMADS31/CcMADS11). Protein interaction network analysis showed that type II CaMADS mainly interacted with proteins related to flowering pathway and flower organ development. This study provides the basis for an in-depth study of the evolutionary features and biological functions of pepper MADS-box genes.