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Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus

Anuj Tyagi1, Niraj K Singh2, Volker Gurtler3

  • 1College of Fisheries, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, 141004, Punjab, India. anujtyaagi@yahoo.co.in.

Archives of Virology
|November 21, 2015
PubMed

Insights

Penaeus monodon nudivirus (PmNV) exhibits codon usage bias influenced by compositional constraints. Despite antagonism with its host, Penaeus monodon, selective pressures shape PmNV gene expression.

Area of Science:

  • Virology
  • Genomics
  • Molecular Biology

Background:

  • Penaeus monodon nudivirus (PmNV) is a significant viral pathogen affecting shrimp aquaculture.
  • Understanding viral gene expression mechanisms is crucial for disease management.

Purpose of the Study:

  • To analyze the codon usage patterns of PmNV.
  • To investigate the factors influencing codon usage bias in PmNV.
  • To compare PmNV codon usage with its host, Penaeus monodon.

Main Methods:

  • Analysis of effective number of codons (ENC) values.
  • Nucleotide composition-ENC correlation analysis.
  • GC3 versus ENC relationship analysis.
  • Relative synonymous codon usage (RSCU) analysis.
  • Codon adaptive index (CAI) calculations.

Main Results:

  • PmNV genes display a range of codon usage bias, from strong to low.
  • Compositional constraints significantly impact PmNV codon usage.
  • A strong antagonistic codon usage pattern exists between PmNV and Penaeus monodon at the whole-genome level.
  • Selective and translational constraints have partially overcome this antagonism in specific PmNV genes.

Conclusions:

  • Compositional constraints are a primary driver of codon usage bias in PmNV.
  • Despite host-virus codon usage conflict, adaptive forces influence viral gene expression.
  • These findings provide insights into PmNV's molecular evolution and host-pathogen interactions.
Keywords:
Codon adaptation indexCodon usage biasCorrespondence analysisPenaeus monodon nudivirusShrimp

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