Phylogenomic diversity and chromatic acclimation in phycoerythrin-containing Microcystis aeruginosa

Microcystis aeruginosa is a bloom-forming cyanobacterium widely distributed in eutrophic freshwater systems. Most strains are blue-green due to the presence of the photosynthetic pigments phycocyanin and chlorophyll a. Less commonly, brownish strains have been reported, reflecting the presence of the red pigment phycoerythrin (PE). However, the genomic basis, phylogeny and evolutionary origin of PE pigmentation in M. aeruginosa remain poorly understood. Here, we characterized PE-containing M. aeruginosa strains, including six newly sequenced genomes. All genomes harboured putative PE synthesis and regulatory genes (the cpe cluster). Phylogenomic analysis further revealed that these PE-containing strains are distributed across three distinct phylogenetic groups. In contrast, the genomic organization of the cpe cluster was largely conserved. Spectroscopic analyses further indicated that strains belonging to different phylogenetic groups exhibit the same type of chromatic acclimation. Moreover, the phylogenetic relationships inferred for each PE gene were congruent and consistent with the whole-genome phylogeny. Our findings support a single origin of PE genes, with the observed distribution best explained by two independent horizontal transfer events rather than repeated gene loss during intraspecific diversification in M. aeruginosa.