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Codon usage and codon context bias in Xanthophyllomyces dendrorhous.

Marcelo Baeza1, Jennifer Alcaíno2, Salvador Barahona3

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Gene expression levels in Xanthophyllomyces dendrorhous correlate with codon usage and codon pair bias, crucial for optimizing protein production. Totiviral genes showed no such bias relative to the host.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Codon usage bias and codon pair bias influence translation accuracy and rate.
  • Understanding these biases is key for optimizing heterologous protein expression.
  • Xanthophyllomyces dendrorhous is a valuable yeast for astaxanthin production.

Purpose of the Study:

  • Analyze codon usage and codon context bias in X. dendrorhous open reading frames (ORFs).
  • Determine the relationship between bias, gene expression levels, GC%, and sequence length.
  • Investigate biases in totiviral ORFs within X. dendrorhous.

Main Methods:

  • Genomic and transcriptomic data analysis of X. dendrorhous ORFs.
  • Identification and determination of intron-exon structures for 1,695 ORFs.
  • Comparison of codon usage and codon pair bias across different growth conditions and carbon sources.

Main Results:

  • Highly expressed genes in X. dendrorhous exhibited strong codon usage and 3' codon context bias.
  • Bias was independent of culture conditions, GC%, and sequence length.
  • Totiviral ORFs displayed highly variable biases unrelated to host ORFs.

Conclusions:

  • Gene expression levels are directly related to codon usage and 3' context bias in X. dendrorhous.
  • This relationship is most pronounced in highly expressed ORFs.
  • Totiviral ORF biases are not directly related to host ORF biases.