Comprehensive genomic identification and expression analysis 4CL gene family in apple

• Published in: Gene 2023-03, Vol.858, p.147197-147197, Article 147197
• Main Authors: Ma, Zong-Huan, Nan, Xin-Tong, Li, Wen-Fang, Mao, Juan, Chen, Bai-Hong
• Format: Article
• Language: English
• Subjects: 4-coumarate CoA ligase; Anthocyanins; Apple; Expression profile; Fruit - genetics; Fruit - metabolism; Gene Expression; Gene Expression Regulation, Plant; Genomics; Malus - genetics; Malus - metabolism; Plant Proteins - genetics; Plant Proteins - metabolism
• ISSN: 0378-1119; 1879-0038
• DOI: 10.1016/j.gene.2023.147197

•A total of 69 4CL family members were cloned from apple and divided into four subclasses according to their evolutionary relationships.•The subcellular localization prediction showed that the 4CL family members were mainly distributed in the cytoplasm, chloroplast, nucleus and cell membrane, and the secondary structures were mainly α-helices and irregular coils.•Microarray data analysis showed that the expression levels of each 4CL family member in apple were related to fruit variety and tissue structure, and the expression levels were mainly higher in fruit, flower and leaf.•qRT-PCR analysis showed that the expression of each member was related to the degree of fruit coloring. The expression of apple 4CL was significantly up-regulated, of which Md4CL10 and Md4CL23 were the most significant. To clarify the structural characteristics, phylogeny, biological function and regulation of 4-coumarate-CoAligase (4CL) in anthocyanin synthesis, the 4CL gene family members in apples were identified and bioinformatic analysis was performed. qRT-PCR was used to analyze the expression levels of this gene family members in different apple varieties, and the role of the 4CL gene in apple anthocyanin synthesis was preliminaries clarified, which provided a certain theoretical basis for the regulatory network of apple anthocyanin synthesis. The results showed that a total of 69 members of the 4CL gene family were identified in the apple (Malus domestica Brokh.), encoding amino acids ranging from 97 to 2310 with theoretical isoelectric points ranging from 5.28 to 9.84. The 69 4CL family members were distributed on 17 chromosomes in the apple, among which chromosome 17 had the largest distribution (9 members), followed by chromosome 9 (7 members), chromosomes 16 and 14 (6 members each), and chromosomes 15 and 13 (5 members each). The subcellular localization prediction showed that apple 4CL gene family members were mainly expressed in cytoplasm, chloroplast, nucleus and cell membrane, with a small amount of expression in mitochondria, vacuoles, peroxisomes, cytoskeleton, golgi and cell matrix, but not in endoplasmic reticulum. The secondary structures are mainly α-helices and irregular coils. Microarray expression profile analysis showed that the expression levels of each member in apple were related to fruit variety and tissue structure, and the expression levels were mainly higher in fruit, flower and leaf. Real-time PCR analysis showed that the expression level of each mem