Genome-wide characterization of the LAC gene family in five fern species reveals evolutionary diversification and putative roles in lignin biosynthesis in Alsophila spinulosa

Abstract Background Laccases (LACs) are multicopper oxidases that play vital roles in lignin polymerization, cell wall formation, and various stress responses in plants. Despite their importance, genome-wide investigations of the LAC gene family in ferns remain limited. As the earliest lineage of vascular plants, ferns offer a unique perspective for understanding the evolution of lignification and the development of vascular systems. Among them, the tree fern Alsophila spinulosa is the only extant woody fern with a distinct trunk structure, providing an ideal model for exploring the molecular basis of lignin biosynthesis and secondary growth in primitive vascular plants. Results In this study, we performed a comprehensive genome-wide analysis of the LAC gene family in five fern species. A total of 160 LAC genes were identified and classified into five phylogenetic subfamilies. Comparative analysis revealed marked variation in family size among the five species, with A. spinulosa possessing the largest repertoire. Integrated transcriptomic analysis, WGCNA, qRT-PCR validation, and subcellular localization assays identified several vascular tissue–enriched AspiLAC genes potentially associated with lignin deposition and secondary cell wall formation. Notably, AspiLAC7, AspiLAC29, and AspiLAC42 were localized to the plasma membrane. Conclusion This study provides the first genome-wide characterization of the LAC gene family in ferns, revealing its evolutionary diversification, duplication patterns, and expression dynamics. The results indicate that gene duplication has driven the expansion and functional specialization of LAC genes in A. spinulosa. The identification of xylem-specific AspiLAC genes and their potential regulatory roles in lignin synthesis offer valuable insights into the molecular mechanisms of lignification, vascular tissue evolution, and secondary metabolism in early land plants.