Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents

Area of Science:

• Genetics
• Evolutionary Biology
• Bioinformatics

Background:

• Human mitochondrial protein-coding genes are crucial for energy production (ATP) via the electron transport chain.
• Understanding codon usage and phylogenetic relationships aids in deciphering gene evolution.
• No prior studies have investigated mitochondrial codon usage across six continents.

Purpose of the Study:

• To analyze codon usage patterns in human mitochondrial protein-coding genes across six continents.
• To investigate the factors (natural selection vs. mutation pressure) driving codon usage bias.
• To explore the evolutionary relationships of these genes in a global context.

Main Methods:

• Bioinformatic analysis of 13 human mitochondrial protein-coding genes.
• Assessment of codon usage bias using metrics like ENC (Effective Number of Codons).
• Phylogenetic analysis to infer evolutionary relationships across continents.

Main Results:

• Low codon usage bias was observed, indicated by high ENC values.
• GC3 content showed varied correlations with codon usage, with exceptions in ND4L and ND5 genes.
• Neutrality plots suggested a dominant role of natural selection for some genes (e.g., ATP6, CYB) and mutation pressure for others (e.g., ND1, ND6).
• Phylogenetic analysis revealed distinct evolutionary patterns for each gene across continents, with geographical distance as a significant factor.

Conclusions:

• Codon usage in human mitochondrial genes exhibits low bias globally.
• Both natural selection and mutation pressure contribute to codon usage patterns, varying by gene and potentially by region.
• Geographical distance plays a role in the evolutionary divergence of human mitochondrial protein-coding genes across continents.