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Related Experiment Videos

Codon usage bias amongst plant viruses.

M J Adams1, J F Antoniw

  • 1Plant Pathogen Interactions Division, Rothamsted Research, Harpenden, Herts, UK. mike.adams@bbsrc.ac.uk

Archives of Virology
|December 23, 2003
PubMed
Summary
This summary is machine-generated.

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Plant viruses exhibit significant codon usage bias, primarily driven by genome nucleotide composition, not host adaptation. This variation in codon preferences is mainly influenced by mutational bias rather than translational selection.

Area of Science:

  • Virology
  • Bioinformatics
  • Genomics

Background:

  • Plant viruses, viroids, and satellites possess diverse genetic sequences.
  • Understanding viral gene expression and evolution requires analyzing codon usage patterns.

Purpose of the Study:

  • To establish a comprehensive database (DPVweb) for plant pathogen sequences.
  • To analyze codon usage bias in plant viruses and identify factors influencing it.

Main Methods:

  • Developed DPVweb database with >4600 plant virus, viroid, and satellite sequences.
  • Created client software for sequence selection and codon usage analysis.
  • Analyzed codon bias in genes of fully-sequenced plant viruses.

Main Results:

Related Experiment Videos

  • Significant differences in codon preferences were observed among plant viruses.
  • Codon bias correlated with genome nucleotide composition, especially GC content at the third codon position.
  • No correlation found between gene size and codon bias.
  • Viral codon usage did not consistently align with host plant preferences or transmission type.
  • Mutational bias, not translational selection, was the primary driver of codon usage variation.

    • Conclusions:

    • Plant virus codon usage is largely shaped by mutational biases and intrinsic genomic properties.
    • Viruses do not appear to adapt their codon usage to match host plants.
    • DPVweb provides a valuable resource for analyzing viral sequence data and codon usage.