Abstract
Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regia PAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.
Highlights
Phenylalanine ammonia-lyase (PAL, EC4.3.1.5), the first enzyme of the phenylpropanoid pathway, produces precursors to a variety of important secondary metabolites, such as phytoalexin, lignin, and phenolic compounds [1,2,3,4,5]
Our results show that the number of PAL genes in J. regia far exceeds the four AtPALs in modern A. thaliana, suggesting that genome duplication may have occurred in the evolution of J. regia [15,16]
The results showed that six genes (JrPAL7, JrPAL3, JrPAL9, JrPAL4-1, JrPAL2-1, and JrPAL6) have high expression in both female and male flowers; another six genes (JrPAL2-2, JrPAL5, JrPAL1, JrPAL4-2, JrPAL2-3, and JrPAL8) have a low expression pattern in both female and male flower tissues
Summary
Phenylalanine ammonia-lyase (PAL, EC4.3.1.5), the first enzyme of the phenylpropanoid pathway, produces precursors to a variety of important secondary metabolites, such as phytoalexin, lignin, and phenolic compounds [1,2,3,4,5]. PAL, first reported in 1961 [6], potentially comprises protective compounds, such as flavonoids, furanocoumarin phytoalexins, and cell wall components [7]. PAL encoding genes are generally well studied and are commonly found as small gene families comprising one to five members [10,11,12,13,14]. Some studies have reported that the PAL gene family has more than five members; for example, 13 PAL genes have been found in Cucumis sativus [20], in Citrullus lanatus [20], in Cucumis melo [21], and 16 in Vitis vinifera [22]. In Salix babylonica, PAL1, Genes 2019, 10, 46; doi:10.3390/genes10010046 www.mdpi.com/journal/genes
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