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. 2013 Sep 30:2:492.
doi: 10.1186/2193-1801-2-492. eCollection 2013.

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

Rahul Raveendran Nair  1 , Manivasagam Bharatha Nandhini, Thilaga Sethuraman, Ganesh Doss
Affiliations

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

Rahul Raveendran Nair et al. Springerplus. .

Abstract

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.

Keywords: Chromatophore; Mutational pressure; Paulinella chromatophora; Synechococcus elongatus; Synonymous codon usage.

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Figures

Figure 1
Figure 1
Diagrammatic representation of three clades in the Prochlorococcus / Synechococcus clade. SCU variation in marine Synechococcus is shaped by selection but in marine Prochlorococcus, mutational pressure shapes the SCU pattern. SCU: Synonymous codon usage.
Figure 2
Figure 2
Relationship between SCUO and GC composition in P. chromatophora . (a) Relationship between SCUO and the overall GC composition, (b) Relationship between SCUO and GC1, (c) Relationship between SCUO and GC2, (d) Relationship between SCUO and GC3. SCUO: Synonymous codon usage order.
Figure 3
Figure 3
Relationship between SCUO and GC composition in S. elongatus. (a) Relationship between SCUO and the overall GC composition, (b) Relationship between SCUO and GC1, (c) Relationship between SCUO and GC2, (d) Relationship between SCUO and GC3.
Figure 4
Figure 4
ENC Vs GC 3 plots. (a) ENC Vs GC3 plot of 768 PCG in P. chromatophora. (b) ENC vs GC3 plot of 2342 PCG in S. elongatus genome. ENC: Effective number of codons.
Figure 5
Figure 5
Neutrality plots. (a) Neutrality plot of 768 PCG in P. chromatophora. (b) Neutrality plot of 2342 PCG in S. elongatus.
Figure 6
Figure 6
PR2 bias plots. (a) PR2 bias plot of 768 PCG in P. chromatophora. (b) PR2 bias plot of 2342 PCG in S. elongatus genome.
Figure 7
Figure 7
Correspondence analysis. Correspondence analysis on RSCU values of 768 PCG in the chromatophore genome of P. chromatophora.
Figure 8
Figure 8
Correspondence analysis. Correspondence analysis on RSCU values of 2342 PCG in S. elongatus.
See this image and copyright information in PMC

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