Genome-Wide Identification, Evolution, and Expression Characterization of the Pepper (Capsicum spp.) 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 MAD...

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Published in:Genes 2022-11, Vol.13 (11), p.2047
Main Authors: Gan, Zhicheng, Wu, Xingxing, Biahomba, Sage Arnaud Missamou, Feng, Tingting, Lu, Xiaoming, Hu, Nengbing, Li, Ruining, Huang, Xianzhong
Format: Article
Language:English
Subjects:
Capsicum
Capsicum annuum
Evolution
Evolutionary genetics
Flowering
Flowers
Fruits
Gene expression
Genomes
Genomic analysis
MADS box proteins
Phylogenetics
Phylogeny
Proteins
Seeds
Transcription factors
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Summary: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.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes13112047