Divergent Codon Usage in Rice (Oryza sativa) and Its Blast Pathogen Magnaporthe oryzae Reveals Species-Specific Translational Selection and Host–Pathogen Co-evolution

Natural selection for translational precision and efficiency as well as mutational pressure both affect codon use bias (CUB), which is the non-random use of synonymous codons. Key information about the co-evolutionary dynamics of host-pathogen systems can be obtained by analyzing CUB. Using a range of statistical and computational techniques, we carried out a thorough comparison of codon use between rice ( Oryza sativa ) and its fungal blast pathogen, Magnaporthe oryzae . Coding sequences (CDS) between the pathogen and host were clearly separated, showing different codon preferences, according to principal component analysis (PCA) and correspondence analysis (CA). Permutational multivariate analysis of variance (PERMANOVA) showed significant divergence in codon usage profiles (pseudo-F = 8.94, p = 0.001), whereas silhouette analysis showed significant species-specific clumping. Quantitative measurements were used to identify biologically meaningful differences: Although the effective number of codons (ENC) did not differ significantly between species, the codon adaptation index (CAI), which was calculated using rice as the reference, was much higher in rice CDS than in M. oryzae CDS. This implies that fungal genes may function under distinct translational restrictions and are less tailored for the host's translational machinery. Analysis of neutrality plots showed that natural selection shapes codon usage in both organisms more strongly than mutational drift. All of these findings point to different translational selection in rice and the fungus that causes it. While M. oryzae has a unique codon usage pattern, which most likely reflects evolutionary adaptation to its pathogenic lifestyle, rice genes seem to be optimized for efficiency under their own codon preference regime. The significance of translational control in host-pathogen interactions is highlighted by this difference.