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Related Experiment Video

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Codon usage pattern in human SPANX genes.

Monisha Nath Choudhury1, Supriyo Chakraborty1

  • 1Department of Biotechnology, Assam University, Silchar-788011, Assam, India.

Bioinformation
|December 15, 2015
PubMed
Summary

Human SPANX genes show low codon usage bias, with natural selection playing a more significant role than mutation pressure in shaping their genetic code.

Area of Science:

  • Genetics
  • Molecular Biology
  • Human Reproduction

Background:

  • SPANX (sperm protein coupled with the nucleus in the X chromosome) genes are vital for human spermatogenesis.
  • Codon usage bias (CUB) is a genome-specific phenomenon influenced by mutation and selection.
  • Analyzing SPANX gene composition and CUB aids in understanding its molecular biology.

Purpose of the Study:

  • To investigate the codon usage bias in human SPANX genes.
  • To determine the relative contributions of mutation pressure and natural selection on SPANX gene codon usage.

Main Methods:

  • Retrieved human SPANX gene variants from NCBI.
  • Utilized a Perl script for analyzing nucleotide composition and CUB parameters.
  • Employed correspondence analysis (COA) and neutrality plots.
Keywords:
SPANX genecodon usagemutation pressurenatural selectionsynonymous codon

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Main Results:

  • Human SPANX genes exhibit low codon usage bias (low Codon Bias Index - CBI).
  • GC content bias (GC3) correlated positively with GC-ending codons.
  • Neutrality plots indicated natural selection has a greater influence than mutation pressure on SPANX genes.

Conclusions:

  • Codon usage bias in human SPANX genes is not pronounced.
  • Natural selection is the dominant force over mutation pressure in regulating codon usage for SPANX genes.