Genome-wide identification of in Brassicaceae, with a focus on the expression pattern of regulating anthocyanin synthesis in crops.

The Brassicaceae family includes the model plant , along with various vegetables and oil crops, which possess significant economic and scientific value. Notably, three diploid species within the U's Triangle of have undergone natural hybridization, resulting in the formation of three allotetraploid species, which provides an excellent model for investigating the phylogenetic, evolutionary, and functional differentiation of plant homologous genes. In this study, we systematically identified homologous genes within the 31 Brassicaceae species, with a total of 48 homologous genes identified from 30 species, and phylogenetic analysis revealed the presence of six subfamilies, Ka/Ks analysis showed that only 10 homologous gene were positively selected during evolution. We subsequently concentrated on the evolution, gene structure, and conserved domain analysis of 16 homologous genes across six crops found in U's Triangle. Our findings indicated that these 16 homologous genes predominantly clustered into two branches and exhibited a high degree of evolutionary conservation. Further RNA-seq analysis of various tissues and organs from crops demonstrated that homologous genes were significantly up-regulated in tissues with anthocyanin accumulation. Concurrently, we employed Weighted Gene Co-expression Network Analysis (WGCNA) to identify hub genes regulated by anthocyanin in different tissues of , revealing that exhibited a strong repressor with anthocyanin biosynthetic genes (ABGs) in petals. Finally, quantitative reverse transcription PCR (qRT-PCR) analysis of leaves, stems, and petals indicated that four homologous genes were significantly up-regulated in leaves and petals, with expression patterns consistent with those of ABGs. Our results contribute new insights into the transcriptional regulatory mechanisms of anthocyanin in crops.