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Analysis of codon usage pattern of mitochondrial protein-coding genes in different hookworms
Bornali Deb1, Arif Uddin2, Gulshana Akthar Mazumder1
1Department of Biotechnology, Assam University, Silchar 788011, Assam, India.
Molecular and Biochemical Parasitology
|November 22, 2017
Summary
Codon usage bias (CUB) analysis in hookworm mitochondrial genes reveals high bias in most species. Both mutation pressure and natural selection influence CUB, with mutation pressure dominant in A. ceylanicum and natural selection in other hookworms.
Area of Science:
- Molecular Biology
- Evolutionary Biology
- Genomics
Background:
- Codon usage bias (CUB) describes the non-uniform use of synonymous codons, varying by species.
- Understanding CUB is crucial for insights into molecular evolution, mRNA translation, transgene design, and gene discovery.
Purpose of the Study:
- To analyze the synonymous codon usage patterns in mitochondrial protein-coding genes of six hookworm species.
- To investigate the factors, including natural selection and mutation pressure, that influence CUB in these genes.
Main Methods:
- Analysis of codon usage patterns using the effective number of codons (ENC).
- Nucleotide composition analysis, including composition at the third codon position.
- Correspondence analysis and neutrality plots to infer the roles of natural selection and mutation pressure.
Main Results:
- High codon usage bias was observed in the mitochondrial genes of most studied hookworm species.
- Mitochondrial genes were found to be AT-rich, with lower GC content.
- Both natural selection and mutation pressure were identified as factors affecting CUB, with varying dominance across species.
Conclusions:
- Mutation pressure appears to be the primary driver of CUB in *Ancylostoma ceylanicum*.
- Natural selection plays a more dominant role in shaping CUB in *Ancylostoma duodenale*, *Necator americanus*, *Ancylostoma tubaeforme*, *Ancylostoma caninum*, and *Uncinaria sanguinis*.
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