Genome-wide identification and characterization of the phenylalanine ammonia-lyase gene family in pecan (Carya illinoinensis)

Abstract

Pecans have high amounts of phenolics and flavonoids and are an important source of natural polyphenols. However, the molecular mechanisms of phenolic biosynthesis in this plant have not been elucidated. Phenylalanine ammonia-lyase (PAL) is the first committed enzyme in the phenylpropane metabolic pathway, is involved in phenolic metabolism, and plays crucial roles in plant growth and development. Nevertheless, knowledge about PALs in pecan has not been fully determined. In the present study, genome-wide CiPALs were identified and characterized, and their expression profiles were evaluated using transcriptome data. In total, seven CiPALs were obtained, and their amino acid lengths ranged from 615 to 760. All of them had predicted locations in the cytoplasm. The open reading frames of CiPAL1∼5 were interrupted by a single intron, while no introns existed in other CiPALs. Different types of cis-elements were identified in the promoter regions of seven CiPALs. Abscisic acid-responsive elements and MeJA-responsive elements were abundant in CiPAL4 and CiPAL5. These two genes were widely expressed in different tissues. CiPALs were differentially expressed during kernel maturation, female flower development, graft union generation and drought stress tolerance, in which CiPAL4 and CiPAL5 exhibited higher expression levels than other genes. Then, the full-length cDNAs of them were cloned. Homology analysis suggested that CiPAL4 and CiPAL5 shared identity values of 89.97% with each other and showed 89.70% and 79.12% identity with AtPAL1, respectively. Phylogenetic analysis indicated that they clustered together with JrPAL3 and JrPAL. Finally, the genetic polymorphisms of CiPAL4 and CiPAL5 were evaluated using seven pecan cultivars, and 13 and 14 mutations were observed in CiPAL4 and CiPAL5, respectively. Therefore, the two CiPALs might play crucial roles in the abiotic stress response and phenolic biosynthesis in pecan. The polymorphism mutations of CiPALs will be useful for genetic study in this plant.