Genome-wide analysis and expression profiling of the phenylalanine ammonia-lyase gene family in Chrysanthemum morifolium.

Background

Chrysanthemum morifolium, a perennial herb of the genus Chrysanthemum (Asteraceae), is highly valued for its ornamental, edible and medicinal properties, primarily attributed to its abundant flavonoids. Phenylalanine ammonia-lyase (PAL) is the rate-limiting enzyme initiating the phenylpropanoid pathway, which synthesizes lignin, flavonoids, and phytoalexins, key metabolites for plant growth, development, and stress adaptation. Despite the availability of the chromosome-level C. morifolium genome, the PAL gene family remains insufficiently characterized. Specifically, the expression patterns of CmPAL genes across floral developmental stages, floret types, and various abiotic stresses have not been elucidated.

Results

In this study, 19 CmPAL genes were identified from C. morifolium. Systematic analyses of their molecular evolutionary characteristics, including gene/protein structures, chromosomal localization, phylogenetic relationships, and genome-wide synteny were performed. CmPAL genes were found to be unevenly distributed across 8 of 27 chromosomes, and phylogenetically clustered members exhibited similar gene/protein structures, reflecting evolutionary conservation and functional importance. Expression profiles revealed that CmPAL genes were preferentially expressed in ray florets and at the color-emerging/blooming stages, indicating their involvement in floral pigmentation. Additionally, several CmPALs were significantly upregulated/downregulated under cold, salt, drought, and heavy metal stresses, suggesting roles in abiotic stress responses.

Conclusions

This study provides a comprehensive characterization and expression profiles of the C. morifolium PAL gene family. These findings provide a valuable genomic resource for functional studies of CmPAL genes, as well as identify candidate genes for molecular breeding to improving flower quality and environmental adaptability of chrysanthemums. Specifically, CmPAL1, 6, 11, and 13 are prioritized as major candidate genes for floral pigmentation, while CmPAL3, 5, 9, 10, and 15 are highlighted for their broad-spectrum stress adaptation roles.