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Comparative genome‐wide analysis of codon usage of different bacterial species infecting Oryza sativa
Author(s) -
Vasanthi S,
Dass J Febin Prabhu
Publication year - 2018
Publication title -
journal of cellular biochemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.028
H-Index - 165
eISSN - 1097-4644
pISSN - 0730-2312
DOI - 10.1002/jcb.27214
Subject(s) - codon usage bias , biology , genetics , genome , gene , oryza sativa , bacterial genome size , coding region , start codon , nucleotide
Oryza sativa is vastly affected by microbial pathogen, causing blight‐related diseases, which in turn deplete the growth and productivity of rice. In this study, we analyzed four bacterial rice pathogen genomes and reported on their codon usage that might have greater implication in mutation‐related research. Differential codon usage indices, such as codon adaptation index (CAI), codon bias index (CBI), effective number of codons (ENc), relative synonymous codon usage (RSCU), correspondence analysis (COA), and parity plots, were applied on coding sequences of Pseudomonas fuscovaginae, Pseudomonas syringae , Xanthomonas oryzae , and Pseudomonas avenae speices. The RSCU results proposed a high‐frequency usage of CUG and CGC that codes for leucine and arginine in all of the species. The CBI and CAI values between the genomes range from 0.17 to 0.3 and from 0.26 to 0.35, respectively, indicating a direct proportionality between these indexes. The mean ENc value of P. avenae coding sequence showed high codon bias compared with other genomes. The axis I variation from COA analysis shows a mean value of 42.28% codon variations in these bacterial species. Correlation studies between axis I and ENc‐GC3, along with CAI and CBI, suggested the presence of nucleotide bias and mutational pressure as major forces for codon bias within these species. Hence, certain genes with high CAI‐CBI have been correlated for better gene expression. Our study highlights the importance of nucleotide biasness, mutation pressure, and natural selection in shaping protein‐coding genes in these four rice‐affecting bacteria. This would further help in investigating the evolution of pathogenic gene families, which may direct research toward synthetic genes that could be suppressed or overrepresented based on their codon usage pattern toward pathogenicity.