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 <i>PAL</i> family has not been completed in detail. In this study, 15 <i>PAL</i>s were identified in the grape genome. Grape <i>PAL</i>s are distributed on 6 chromosomes, and 9 <i>PAL</i>s are distributed on chromosome 16, in which most of the 2 downstream genes, including <i>chalcone synthase</i> (<i>CHS</i>) and <i>stilbene synthase</i> (<i>STS</i>). Promoter analysis revealed that there were many <i>cis</i>-acting elements in the promoter regions to respond to light, phytohormone, and stress. According to transcriptome-data analysis, <i>VvPALs</i> have extensive expression patterns in various tissues and developmental stages in response to various stresses. Dynamic expression patterns of <i>PAL1/2/3/5</i> were observed in different developmental stages of 4 grape varieties on the basis of qRT-PCR analysis, and suggested that <i>PAL</i>s are involved in a complex mechanism to modulate in anthocyanin biosynthesis. Comprehensive analysis of <i>PAL</i>s offers a basis for further understanding the physiological functions of <i>PAL</i>s during grape development and their potential role to respond the various stimuli.

苯丙氨酸解氨酶（Phenylalanine ammonia-lyase, PAL）是植物苯丙烷类生物合成途径的限速酶，该途径可合成多种广泛存在的关键化合物，包括酚酸类、黄酮类、木质素以及芪类化合物。首个葡萄全基因组组装草图已公布，但目前针对PAL基因家族的详细系统分析尚未完成。本研究在葡萄基因组中共鉴定到15个PAL基因。葡萄PAL基因分布于6条染色体上，其中9个PAL基因定位于16号染色体，该染色体上存在包括查尔酮合酶（chalcone synthase, CHS）与芪合酶（stilbene synthase, STS）在内的2个下游基因。启动子分析结果显示，其启动子区域存在多种顺式作用元件，可响应光照、植物激素与逆境胁迫。转录组数据分析表明，葡萄PAL基因家族（VvPALs）在不同组织与发育阶段均具有广泛的表达模式，且可响应多种逆境胁迫。基于实时定量聚合酶链反应（qRT-PCR）分析，本研究观察了4个葡萄品种不同发育阶段中PAL1/2/3/5的动态表达模式，结果提示PAL基因参与调控花青素生物合成的复杂机制。对PAL基因家族的综合分析，可为进一步阐明PAL基因在葡萄发育过程中的生理功能，以及其响应各类外界刺激的潜在作用提供理论基础。