Transcriptome Analysis Reveals the Crucial Role of Phenylalanine Ammonia-Lyase in Low Temperature Response in Ammopiptanthus mongolicus

<b>Background</b>: <i>Ammopiptanthus mongolicus</i> is a rare temperate evergreen shrub with high tolerance to low temperature, and understanding the related gene expression regulatory network can help advance research on the mechanisms of plant tolerance to abiotic stress. <b>Methods:</b> Here, time-course transcriptome analysis was applied to investigate the gene expression network in <i>A. mongolicus</i> under low temperature stress. <b>Results</b>: A total of 12,606 differentially expressed genes (DEGs) were identified at four time-points during low temperature stress treatment, and multiple pathways, such as plant hormones, secondary metabolism, and cell membranes, were significantly enriched in the DEGs. Trend analysis found that the expression level of genes in cluster 19 continued to upregulate under low temperatures, and the genes in cluster 19 were significantly enriched in plant hormone signaling and secondary metabolic pathways. Based on the transcriptome data, the expression profiles of the genes in abscisic acid, salicylic acid, and flavonoid metabolic pathways were analyzed. It was found that biosynthesis of abscisic acid and flavonoids may play crucial roles in the response to low temperature stress. Furthermore, members of the phenylalanine ammonia-lyase (PAL) family in <i>A. mongolicus</i> were systematically identified and their structures and evolution were characterized. Analysis of cis-acting elements showed that the <i>PAL</i> genes in <i>A. mongolicus</i> were closely related to abiotic stress response. Expression pattern analysis showed that <i>PAL</i> genes responded to various environmental stresses, such as low temperature, supporting their involvement in the low temperature response in <i>A. mongolicus</i>. <b>Conclusions</b>: Our study provides important data for understanding the mechanisms of tolerance to low temperatures in <i>A. mongolicus.</i>