Patterns of codon usage bias in Silene latifolia

Area of Science:

• Evolutionary biology
• Genomics
• Molecular evolution

Background:

• Codon usage bias (CUB) reflects selection on synonymous codons, influenced by gene expression and sex chromosome evolution.
• Sex chromosomes exhibit unique evolutionary properties like genetic degeneration, dosage compensation, and hemizygosity, impacting CUB.
• Silene latifolia provides a model for studying early sex chromosome evolution and its effects on CUB.

Purpose of the Study:

• To investigate codon usage bias in Silene latifolia using a large expressed sequence tag dataset.
• To compare CUB patterns in S. latifolia with Arabidopsis thaliana to infer evolutionary stability of selection pressures.
• To examine the role of natural selection versus mutational bias in shaping CUB and to analyze CUB on sex-linked genes.

Main Methods:

• Expressed sequence tag (EST) data generation using 454 sequencing (over 1,608 fragments).
• Identification of preferred codons using three distinct methods.
• Analysis of gene expression levels, GC content in coding and intron regions, and polymorphism data.
• Comparative analysis of substitution patterns on X-linked and Y-linked genes.

Main Results:

• 21 preferred codons were identified in S. latifolia, closely matching those in Arabidopsis thaliana despite significant divergence.
• CUB is shaped by natural selection, evidenced by correlations between gene expression, GC content, and intron GC content.
• The X chromosome shows an excess of unpreferred to preferred codon substitutions, suggesting an increase in CUB.
• Y-linked genes exhibit balanced substitutions, contradicting expected genetic degeneration patterns.

Conclusions:

• The conserved CUB patterns between S. latifolia and A. thaliana suggest long-term stability in selection pressures on synonymous codons.
• Natural selection, rather than mutational bias, is the primary driver of CUB in S. latifolia.
• The X chromosome appears to be evolving towards higher CUB, while Y-linked genes do not show expected signs of degeneration related to codon usage.