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Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne
Jyoti Chandan1,2, Suruchi Gupta3, Vikash Babu1,2
1CSIR-Indian Institute of Integrative Medicine, Jammu, 18000, India.
Abstract:
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.
Insights
This study reveals that codon usage bias in Withania somnifera, its root-knot nematode (Meloidogyne incognita), and fungal parasite (Alternaria alternata) is weakly biased. Evolutionary forces like mutation and natural selection shape this bias, influencing pathogen adaptability.
Area of Science:
- Genomics
- Evolutionary Biology
- Plant Pathology
Background:
- Withania somnifera is a vital medicinal plant susceptible to parasites like Meloidogyne incognita (root-knot nematode) and Alternaria alternata (fungus).
- Understanding the evolutionary adaptation of these pathogens to their host is crucial for managing infections.
Purpose of the Study:
- To analyze the evolutionary patterns and codon usage bias (CUB) in Withania somnifera, Meloidogyne incognita, and Alternaria alternata.
- To investigate the influence of evolutionary forces on CUB in the host-pathogen system.
Main Methods:
- Nucleotide analysis to determine genome bias (A-T vs. GC).
- Codon Usage Bias (CUB) analysis.
- Neutrality plots and Correspondence analysis to infer evolutionary forces (mutation vs. natural selection).
Main Results:
- Weak CUB was observed across all three organisms.
- Withania somnifera and Meloidogyne incognita exhibited A-T biased genomes, while Alternaria alternata showed a GC-biased genome.
- A higher similarity in CUB patterns was found between the host and nematode compared to the host and fungus.
- Mutation predominantly influenced CUB in W. somnifera and M. incognita, whereas natural selection was the primary driver for A. alternata.
Conclusions:
- Both evolutionary forces and CUB play significant roles in the adaptability of pathogens to the host environment.
- The findings provide insights into the establishment of parasitic relationships through pathogen adaptation mechanisms.
