Genome-wide identification and characterisation of phenylalanine ammonia-lyase gene family in grapevine

Phenylalanine ammonia-lyase (PAL) is a rate-limiting enzyme of phenylpropanoid biosynthesis in plants that synthesise many ubiquitous key compounds, including phenolic acids, flavonoids, lignins, and stilbenes. The first draft of the full grape genome assembly was released, but systematic analysis of the PAL family has not been completed in detail. In this study, 15 PALs were identified in the grape genome. Grape PALs are distributed on 6 chromosomes, and 9 PALs are distributed on chromosome 16, in which most of the 2 downstream genes, including chalcone synthase (CHS) and stilbene synthase (STS). Promoter analysis revealed that there were many cis-acting elements in the promoter regions to respond to light, phytohormone, and stress. According to transcriptome-data analysis, VvPALs have extensive expression patterns in various tissues and developmental stages in response to various stresses. Dynamic expression patterns of PAL1/2/3/5 were observed in different developmental stages of 4 grape varieties on the basis of qRT-PCR analysis, and suggested that PALs are involved in a complex mechanism to modulate in anthocyanin biosynthesis. Comprehensive analysis of PALs offers a basis for further understanding the physiological functions of PALs during grape development and their potential role to respond the various stimuli.