Biased gene conversion, copy number, and apparent mutation rate differences within chloroplast and bacterial genomes

Area of Science:

• Evolutionary biology
• Molecular evolution
• Genetics

Background:

• Synonymous substitution rates can vary between genes within organelles and bacteria.
• Gene copy number differences are hypothesized to influence these rates, potentially due to conversion bias.

Purpose of the Study:

• To investigate whether conversion bias explains differences in synonymous substitution rates between organelle and bacterial genes with varying copy numbers.
• To determine the role of intracellular population parameters versus molecular mechanisms in apparent mutation rate variations.

Main Methods:

• Comparative analysis of synonymous substitution rates in organelle (chloroplast) and bacterial genes.
• Modeling the impact of gene copy number and fixation probabilities on mutation rates.

Main Results:

• A small bias against new mutants sufficiently explains rate differences in chloroplast single-copy and inverted-repeat regions.
• Differences in within-organelle fixation probabilities lead to varying apparent mutation rates.
• Conversion bias is unlikely to explain low mutation rates near bacterial replication origins.

Conclusions:

• Intracellular population parameters, not solely molecular mechanisms like conversion bias, account for observed variations in organelle gene apparent mutation rates.
• This finding has implications for understanding gene evolution in systems with variable gene copy numbers.
• The study refutes conversion bias as a primary driver for low mutation rates near bacterial replication origins.