Comprehensive in silico characterization of proteins associated with light responses, transport, and stress-related processes in the gametophyte of the fern Dryopteris affinis ssp. affinis

Background . Fern gametophytes represent a key phase in the fern life cycle and play an essential role in establishment and persistence. Despite their ecological and developmental relevance, the molecular basis of gametophyte function remains poorly characterised, particularly in apogamous ferns. The growing availability of transcriptomic resources offers new opportunities to investigate the functional organisation of this life stage. Results . We conducted an in silico analysis of a previously published RNA-seq dataset obtained from gametophytes of the apogamous fern Dryopteris affinis ssp. affinis , focusing on the functional annotation of high-confidence protein candidates. Following stringent filtering, 1,160 proteins were identified and assigned to light-related processes, transport functions and stress responses. Light-associated proteins were primarily linked to photosynthesis, photorespiration, xanthophyll metabolism and photomorphogenesis, including components involved in photosystem assembly, chloroplast function and photoreceptor-mediated signalling. Transport-related proteins comprised a diverse set of membrane- and cytoplasm-associated transporters mediating the movement of sugars, amino acids, ions and other metabolites. In addition, numerous proteins associated with biotic and abiotic stress responses and plant immunity were detected. Protein–protein interaction analysis identified a small number of highly connected nodes, with MODIFIED TRANSPORT TO THE VACUOLE 17 (MTV17) emerging as the most connected protein, mainly supported by database- and text-mining-based evidence. Conclusions . This study presents a curated, high-confidence protein dataset that extends current knowledge of fern gametophyte molecular organisation. The functional categories and interaction patterns identified highlight core processes underlying gametophyte physiology and stress adaptation, and provide a resource for future functional, comparative and experimental studies in ferns and other early-diverging land plants.