Comparison of compositional constraints: Nuclear genome vs plasmid genome of Pseudomonas syringae pv. tomato DC3000

Pseudomonas syringae pathovar (pv) tomato DC3000 (PsPto) causes bacterial speck disease in Solanum lycopersicum (tomato) and Arabidopsis thaliana. This bacterium has attracted a lot of attention from researchers. Codon usage bias (CUB) analysis is a helpful tool to understand the gene and genome biology of an organism and also provides insights into the evolutionary mechanism. Several studies have been conducted on different bacteria, but seldom on PsPto. In the present study, the codon usage pattern of three transcriptomes of PsPto, i.e., nuclear genome, plasmid A and plasmid B were systematically analyzed. The PsPto transcriptomes were found to be strongly biased towards G and C nucleotides at the third codon position. ENC, neutrality plots, PR2 plot and COA analysis also suggested that the CUB of PsPto is mainly affected by natural selection. A comparative analysis based on the relative codon deoptimization index (RCDI) for adaptation of plasmid A and plasmid B to the nuclear genome revealed that plasmid B was closer to the nuclear genome.