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Meloidogyne incognita  (Root-knot nematode) and  Alternaria alternata  (fungus) were among the dominant parasites of the medicinal plant  Withania somnifera . Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation is lacking. The present study elucidates evolutionary and codon usage bias analysis of  W. somnifera  (host plant),  M. incognita  (root-knot nematode) and  A. alternata  (fungal parasite). The results of the present study revealed a weak codon usage bias prevalent in all the three organisms. Based on the nucleotide analysis, genome of  W. somnifera  and  M. incognita  was found to be A-T biased while  A. alternata  had GC biased genome. We found high similarity of CUB pattern between host and its nematode pathogen as compared to the fungal pathogen. Inclusively, both the evolutionary forces influenced the CUB in host and its associated pathogens. However, neutrality plot indicated the pervasiveness of natural selection on CUB of the host and its pathogens. Correspondence analysis revealed the dominant effect of mutation on CUB of  W. somnifera  and  M. incognita  while natural selection was the main force affecting CUB of  A. alternata . Taken together the present study would provide some prolific insight into the role of codon usage bias in the adaptability of pathogens to the host’s environment for establishing parasitic relationship.

Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne incognita and Alternaria alternata