Genome-wide identification and functional analysis of the Caffeoylshikimate esterase (CSE) gene family in five fern species

Abstract Background Ferns, comprising epiphytic, aquatic, and terrestrial varieties, are good models to investigate plant terrestrialization. Vascular tissue represents a significant development in the terrestrial adaptation of plants. Lignin is a crucial biomolecule of vascular tissue, especially in xylem. Caffeoylshikimate esterase (CSE) serves as a crucial enzyme in the biosynthesis of lignin monomers. However, the comprehensive understanding of CSE in ferns remains unclear. Results This study performed a genome-wide analysis of CSE genes across five fern species, identifying 95 unique members. Phylogenetic analysis, chromosome distribution studies, and gene duplication investigations indicated notable gene expansion during plant terrestrialization, especially in Alsophila spinulosa. Promoter analysis revealed multiple cis-acting elements related to stress and hormone responses, suggesting an integration of environmental signals in regulating CSE gene expressions. This study further identified two genes, AspiCSE19 and AspiCSE35, that are specifically highly expressed in the xylem and are potentially implicated in the biosynthesis of A. spinulosa lignin. Overexpression experiments suggested that AspiCSE19 and AspiCSE35 promotes lignin synthesis. Conclusions This study offers insights into the evolutionary diversification and functional specialization of fern CSE genes, establishing a basis for understanding lignin biosynthesis in early vascular plants.