Evolutionary patterns of codon usage in the chloroplast gene rbcL

Area of Science:

• Evolutionary Biology
• Molecular Evolution
• Genomics

Background:

• Chloroplast gene rbcL is crucial for photosynthesis.
• Codon usage bias (CUB) can be influenced by mutation bias, GC content, and selection.
• Previous studies predicted low CUB in chloroplasts due to low GC content.

Purpose of the Study:

• To reconstruct the evolutionary history of CUB in the rbcL gene across 92 green-plant taxa.
• To investigate the roles of selection and drift in shaping CUB patterns.
• To identify factors driving CUB evolution in chloroplast genomes.

Main Methods:

• Phylogenetic analysis of 92 green-plant taxa.
• Development of a CUB measure accounting for chloroplast genomic nucleotide content.
• Maximum likelihood-ratio tests to compare models of codon overrepresentation (single vs. double codons).

Main Results:

• Significant variation in CUB extent across different plant lineages, indicating clade-specific selection.
• Independent evolution of low CUB in seed plants and liverworts, suggesting relaxed selection.
• Frequent transitions from single- to double-codon overrepresentation, potentially driven by biochemical selection.
• Strong influence of twofold degenerate amino acids on total CUB, despite their minority presence.

Conclusions:

• CUB in rbcL is shaped by clade-specific selection, not solely by GC content.
• Specific amino acids, particularly those functionally important, appear to constrain CUB.
• CUB patterns in rbcL may serve as a predictor of functionally critical amino acid residues.