Genome-wide identification and characterization of SET domain family genes in Neopyropia yezoensis

Neopyropia yezoensis is a significant economically important macroalga in China, primarily thriving on intertidal zone rocky reefs where it encounters various biotic and abiotic stresses. Consequently, it serves as an ideal model organism for studying tolerance mechanisms in intertidal algae. Genes with the SET domain are widely recognized for their involvement in histone lysine methyltransferase activity, playing crucial roles in diverse biological processes such as gene regulation and development. To date, a comprehensive investigation of SET domain genes (SDGs) in Neopyropia yezoensis has not been undertaken. Eighteen NySDGs were identified and categorized into five distinct classes (Ⅰ, Ⅱ, Ⅲ, Ⅶ and UN) through an integrative approach comprising phylogenetic analysis, domain configuration assessments, and motif distribution patterns. In addition, dispersed duplication played a role in the evolution of this family, and the duplicated genes were subject to strong purifying selection. The NySDG promoter sequences include diverse cis-acting elements associated with growth, hormones, and stress. The silico expression analysis at two life cycle stages revealed a broad and stage-specific expression pattern. The expression analysis under abiotic and biotic stresses supports the crucial role of NySDGs in stress environments. The reverse transcription-quantitative PCR for 6 target NySDGs in two life cycle stages was performed. And our findings agree with the computational expression data, underscoring the significance of these genes in laver development. This study established a groundwork for future investigations into the functional aspects of SDGs in N. yezoensis, contributing novel insights to the existing knowledge based on current literature and online resources.