Comparative genomics and transcriptomics reveal a restricted but immune-relevant IRF repertoire in bivalve molluscs

Interferon regulatory factors (IRFs) are DNA-binding transcription factors involved in immune regulation, yet the composition and physiological relevance of IRF repertoires in bivalve molluscs remain incompletely understood. In this study, comparative genomic, phylogenetic, structural and transcriptomic analyses were integrated to examine IRF evolution and immune-associated expression in bivalves. IRF genes were identified from representative bivalve proteomes and analyzed together with IRFs from model animals and previously characterized molluscan sequences. The dataset comprised 29 bivalve species from 12 families. Within this sampled dataset, IRF copy number ranged from two to four per species, with most species retaining three members, indicating a restricted IRF repertoire. Phylogenetic analysis of 113 IRF proteins from 34 species resolved four major subfamilies. Bivalve IRFs were mainly assigned to IRF1/2-like and IRF4/8/9-related lineages, whereas in the present dataset, clear bivalve representatives of vertebrate IRF3/7 and IRF5/6 clades were not detected. Motif and gene-structure analyses indicated conservation of the N-terminal IRF DNA-binding region, while the middle and C-terminal regions were more variable, particularly in IRF4/8-like members. In the noble scallop Mimachlamys nobilis, IRF genes and selected IRF-related genes, including MyD88, TRAF6-like, TBK1/IKKε-like and IKKα/β-like candidates, showed gene-specific expression patterns across tissues, with several genes reaching their highest mean expression in the gill, and showed distinct temporal expression profiles over 72 h of Vibrio parahaemolyticus exposure. Re-analysis of oyster and mussel transcriptomes further showed that IRF genes were expressed together with adaptor and kinase genes under bacterial exposure or in gill-associated immune contexts. These findings suggest that bivalves maintain a restricted but immune-relevant IRF repertoire, and that the potential functional diversification of molluscan IRFs is likely shaped by structural divergence, tissue-biased deployment and differential association with upstream innate immune signaling components rather than by extensive gene-family expansion.