Genomic Characterization and Transcriptomic Analysis of the Phycobilisome Linker Proteins Family in Pyropia haitanensis.

Phycobiliprotein linker polypeptides (PBLPs) are essential structural components of phycobilisomes (PBS), yet their composition, evolutionary trajectories, and regulatory functions in Pyropia haitanensis remain poorly understood. Here, we performed the first genome-wide identification and functional characterization of PBLPs in P. haitanensis. Nineteen PBLP genes were identified and classified into three subfamilies (LR, LRC, LC), exhibiting substantial physicochemical diversity and distinct gene structures. Phylogenetic and synteny analyses revealed extensive paralogous diversification driven primarily by dispersed duplication, with most duplicated pairs under strong purifying selection. Notably, the LCM subfamily was absent in P. haitanensis and P. yezoensis, suggesting lineage-specific gene loss and potential neofunctionalization of LR/LRC members. Transcriptome profiling demonstrated pronounced expression divergence between the wild-type (ZD) and red pigment mutant (RED) strains, with six PBLP genes showing significant differential expression validated by qRT-PCR. Under five irradiance levels, PBLP genes displayed distinct light-responsive transcriptional patterns. Mantel tests further revealed strong associations between PBLP expression and phycobiliprotein contents, photosynthetic pigments, and chlorophyll fluorescence parameters, indicating functional specialization within the family. Overall, this study provides comprehensive insights into the evolution, expression dynamics, and regulatory potential of PBLPs in P. haitanensis, highlighting their central roles in PBS assembly, pigment metabolism, and photophysiological acclimation. These findings establish a foundation for elucidating PBS regulatory mechanisms and improving pigment-related traits in economically important red algae.