Evolutionary insights from the pangenome and pigment profiles of Parasynechococcus

Parasynechococcus is one of the two essential alongside Prochlorococcus photosynthetic cyanobacteria that contribute primary productivity in the ocean. Despite its global importance its specie delimitation remains controversial. Herein, a pangenome analysis of 39 high-quality genomes was conducted to delineate Parasynechococcus species. Core-gene phylogram revealed the classification of these genomes into 18 well-defined putative genospecies, which was corroborated by ANI index and GTDB classification. Moreover, numerous interspecies and intraspecies HGT events were detected, some of which may be responsible for the inconsistencies between core-gene and pan-gene phylograms. Besides, the profiling of phycobilisome rod region in Parasynechococcus genomes unraveled intriguing diversity of their genomic organization, pigment type and genomic cluster variants. The diversification process was hypothesized to be mediated by the putative mobile elements located in these regions. Moreover, phylogeny incongruence between the genes within phycobilisome rod region and the core genome indicate distinct evolutionary history, which could be ascribed to lateral gene transfer. Conclusively, the results provide insights into the diversity and evolution of Parasynechococcus from the perspective of pangenome and pigment type, facilitating the evolutionary research and exploration of this important taxon.