Genome Streamlining: Effect of Mutation Rate and Population Size on Genome Size Reduction

Area of Science:

• Evolutionary biology
• Genomics
• Computational biology

Background:

• Genome streamlining, a reduction in genome size, is observed across diverse bacteria, including endosymbiotic and marine species.
• The evolutionary drivers and mechanisms behind genome streamlining remain unclear due to confounding environmental factors.
• Computational modeling offers a robust approach to test hypotheses regarding genome size reduction.

Purpose of the Study:

• To computationally investigate the impact of increased population size (N) and mutation rate (μ) on bacterial genome streamlining.
• To differentiate the effects of population size and mutation rate on genome structure and coding density.

Main Methods:

• Utilized the Aevol platform, a computational tool for studying genome architecture evolution.
• Simulated bacterial evolution under conditions of elevated population size and/or mutation rate.
• Analyzed changes in genome size, noncoding sequences, and coding sequences.

Main Results:

• Both increased population size and increased mutation rate led to genome streamlining.
• Elevated population size resulted in the loss of noncoding sequences, increasing coding density.
• Elevated mutation rate caused the loss of both coding and noncoding sequences, decreasing coding density.
• The product of population size and mutation rate (N×μ) was found to determine genome coding density.

Conclusions:

• Genome streamlining is influenced by the interplay of population size and mutation rate.
• Different combinations of N and μ can produce a wide spectrum of genome sizes and densities.
• These findings suggest genome size and density are shaped by selection for adaptation and robustness.