Analysis of synonymous codon usage patterns in the genus Rhizobium

Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha

Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman’s rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC₃) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC₃ and cumulative GC content at first and second codon positions (GC₁₂) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from mutational pressure and selection, certain unknown selective forces might be acting on the PCGs in the analyzed mitogenomes as the phenomenon of SCUB could not be explained by mutational pressure, by selection, or by both.

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

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.