Systematic Analysis and Expression Profiles of the 4-Coumarate: CoA Ligase (4CL) Gene Family in Pomegranate ( L.).

(, EC6.2.1.12), located at the end of the phenylpropanoid metabolic pathway, regulates the metabolic direction of phenylpropanoid derivatives and plays a pivotal role in the biosynthesis of flavonoids, lignin, and other secondary metabolites. In order to understand the molecular characteristics and potential biological functions of the gene family in the pomegranate, a bioinformatics analysis was carried out on the identified . In this study, 12 were identified in the pomegranate genome, which contained two conserved amino acid domains: AMP-binding domain Box I (SSGTTGLPKGV) and Box II (GEICIRG). During the identification, it was found that was missing Box II. The gene cloning and sequencing verified that this partial amino acid deletion was caused by genome sequencing and splicing errors, and the gene cloning results corrected the sequence information in the 'Taishanhong' genome. According to the phylogenetic tree, were divided into three subfamilies, and each subfamily had 1, 1, and 10 members, respectively. Analysis of cis-acting elements found that all the upstream sequences of contained at least one phytohormone response element. An RNA-seq and protein interaction network analysis suggested that was highly expressed in different tissues and may participate in lignin synthesis of pomegranate. The expression of in developing pomegranate fruits was analyzed by quantitative real-time PCR (qRT-PCR), and the expression level of demonstrated a decreasing trend, similar to the trend of flavonoid content, indicating may involve in flavonoid synthesis and pigment accumulation. , , , and were almost not expressed or lowly expressed, the expression level of was higher in the later stage of fruit development, suggesting that played a crucial role in fruit ripening. The expression levels of genes were significantly different in various fruit development stages. The results laid the foundation for an in-depth analysis of pomegranate gene functions.