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Background  Comparative study of synonymous codon usage variations and factors influencing its diversification in α - cyanobacterial descendant  Paulinella chromatophora  and β - cyanobacterium  Synechococcus elongatus  PCC6301 has not been reported so far. In the present study, we investigated various factors associated with synonymous codon usage in the genomes of  P .  chromatophora  and  S .  elongatus  PCC6301 and findings were discussed.    Results  Mutational pressure was identified as the major force behind codon usage variation in both genomes. However, correspondence analysis revealed that intensity of mutational pressure was higher in  S .  elongatus  than in  P .  chromatophora . Living habitats were also found to determine synonymous codon usage variations across the genomes of  P .  chromatophora  and  S .  elongatus .    Conclusions  Whole genome sequencing of α-cyanobacteria in the cyanobium clade would certainly facilitate the understanding of synonymous codon usage patterns and factors contributing its diversification in presumed ancestors of photosynthetic endosymbionts of  P .  chromatophora .

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Mutational pressure dictates synonymous codon usage in freshwater unicellular α - cyanobacterial descendant Paulinella chromatophora and β - cyanobacterium Synechococcus elongatus PCC6301