Genome-Wide Identification Analysis of the 4-Coumarate: Coa Ligase (4CL) Gene Family in Brassica U’s Triangle Species and Its Potential Role in the Accumulation of Flavonoids in Brassica napus L.

4-Coumarate: CoA ligase (4CL) is a key branch point enzyme at the end of the phenylpropanoid metabolic pathway. It regulates the synthesis of various metabolites and participates in plant growth and development by catalyzing the formation of CoA ester compounds. However, <i>4CL</i> family members have not been identified and analyzed among U's triangle species in <i>Brassica</i>. In this study, 53 <i>4CL</i> genes were identified in <i>Brassica</i> U's triangle species and divided into 4 groups (group I, II, III and IV) according to phylogenetic relationship. Based on phylogenetics, gene structure, conserved motifs, chromosome localization and collinearity analysis, <i>4CLs</i> were relatively conserved in the evolution of <i>Brassica</i> U's triangle species. The promoter region contains a large number of cis-acting elements, implying the functional diversity of <i>4CLs</i>. Further combining transcriptome data and reverse transcription quantitative PCR (RT-qPCR), we found that <i>Bna4CLs</i> have tissue specificity and can not only respond to exogenous phytohormone changes but also regulate the flavonoid biosynthetic pathway in the yellow- and black-seeded <i>B. napus</i>. Our results complement the lack of research on the <i>4CL</i> gene family in <i>Brassica</i>, clarify the sequence characteristics and functional diversity of these genes and lay a foundation for further exploration of <i>4CL</i> genes in response to abiotic stress and regulation of seed coat flavonoid accumulation.