Genome-wide identification, evolution, and expression characterization
of the pepper MADS-box gene family
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
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
(CaMADS26/CbMADS31/CcMADS11). This study provides the basis for an
in-depth study of the evolutionary features and biological functions of
pepper MADS-box genes.