Exploring the relationship between codon usage and gene expression in the Meloidogyne incognita genome: Implications for environmental adaptability

The present study investigates the phenomenon of codon usage bias (CUB) in Meloidogyne incognita, a parasitic nematode that infests plants. It explores the patterns of CUB, the factors that influence it, and its correlation with gene expression. Understanding codon usage bias in M. incognita is important for developing effective strategies for controlling nematode infections in plants. The results indicated a weak CUB in M. incognita, with an overall AT bias in the genome. The analysis of relative synonymous codon usage (RSCU) revealed that preferred and high-frequency codons mostly ended with G/C, indicating the influence of compositional constraints on codon usage. Further analysis using ENC plot, PR2 plot, Neutrality plot, and correspondence analysis suggested that natural selection and mutation pressure both played a role in observed CUB, with mutation pressure being the decisive factor. Amino acid composition analysis showed that glycine was the most frequently used amino acid, while histidine was the least utilized. Interestingly, the study found a negative correlation between codon usage and gene expression in M. incognita. Overall, this study provides a comprehensive understanding of codon usage bias in M. incognita and highlights its potential implications for gene expression and pathogenesis in plants by understanding preferred, avoided, and unique codons, which could further aid in the development of effective strategies for controlling nematode infections.