Abstract
BackgroundComparative 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.ResultsMutational 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.ConclusionsWhole 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.
Highlights
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
High negative correlation was found between A and GC content at 3rd codon position (GC3) (Table 1). This suggests that A and GC contents play important role in Synonymous codon usage (SCU) bias in the chromatophore genome
Since A3 content was in strong negative correlation with all total nucleotide contents (Table 1), it can be inferred that A3 content play an important role in shaping SCU patterns across 786 Protein coding genes (PCGs) in the chromatophore genome
Summary
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. Synonymous codon usage (SCU) bias favours the usage of specific subset of certain codons (preferred codons) within each amino acid family (Agashe et al 2013). Strength of selection appears to be varying among evolutionarily conserved amino acid residues that exhibit stronger bias. Evolutionarily variable residues often exhibit less or weaker bias (Akashi 1995; Drummond and Wilke 2008) Mutational pressure is another important factor, shaping SCU variations (Plotkin and Kudla 2011; Akashi 2001). Role of physiological processes in framing evolution of biased codon usage is yet to be unravelled (Agashe et al 2013)
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