Nucleotide composition and codon usage bias of SRY gene

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• The SRY gene on the Y chromosome determines maleness in mammals.
• Codon Usage Bias (CUB) refers to the non-uniform use of synonymous codons.
• Understanding CUB is vital for gene expression, primer design, and synthetic gene creation.

Purpose of the Study:

• To analyze the codon usage bias of the SRY gene across various mammalian species.
• To investigate the factors influencing the codon usage patterns in the SRY gene.

Main Methods:

• Utilized bioinformatic tools for analyzing SRY gene codon usage.
• Calculated Codon Bias Index (CBI) and Relative Synonymous Codon Usage (RSCU).
• Employed Correspondence Analysis (CA) and Neutrality plots to assess nucleotide constraints and evolutionary pressures.

Main Results:

• The SRY gene exhibits a weak overall codon usage bias.
• Frequently used codons in SRY mRNA often end with 'A' or 'C' at the third position.
• Compositional constraints, influenced by both mutation pressure and natural selection, play a role in SRY's codon usage.

Conclusions:

• Natural selection appears to be the dominant force shaping SRY gene codon usage in mammals, with mutation pressure playing a lesser role.
• This study provides the first comprehensive analysis of codon usage bias in the mammalian SRY gene.