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 a curated subset of protein candidates defined by stringent filtering criteria (E-value < 1 × 10⁻¹⁰⁰ and minimum sequence length > 450 bp). Following filtering, 1,160 proteins were retained and classified into three main functional categories-light-related processes, transport functions, and stress responses-representing key processes underlying gametophyte physiology and environmental adaptation. 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 1 (MTV17) emerging as the most connected protein, mainly supported by database- and text-mining-based evidence, suggesting a potential central role in intracellular transport-related processes. 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.