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Differential genomic variation between short- and long-term bacterial evolution revealed by ultradeep sequencing
Ye Feng1, Hsiu-Ling Chen, Cheng-Hsun Chiu
1Genomics Research Center, Harbin Medical University, People's Republic of China. chchiu@adm.cgmh.org.tw
Genome Biology and Evolution
|March 28, 2013
Summary
Spontaneous mutation patterns in Staphylococcus aureus differ from those observed between closely related strains. Ultradeep sequencing reveals A → G substitutions and 1 bp deletions as predominant, suggesting prior selection influences comparisons of related strains.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- Bacterial genome nucleotide composition is shaped by mutation and selection.
- Previous studies assumed minimal selection impact on closely related strains to infer mutation patterns.
Purpose of the Study:
- To characterize spontaneous mutation patterns in Staphylococcus aureus using ultradeep sequencing.
- To investigate whether genomic differences between closely related strains reflect true spontaneous mutation rates.
Main Methods:
- Sequencing of Staphylococcus aureus genome using a SOLiD autosequencer with over 5,000× mapping coverage.
- Direct counting of variations from ultradeep sequencing reads to identify single-base substitutions and small indels.
Main Results:
- A → G was the predominant single-base substitution.
- 1 bp deletions were identified as the major small indel.
- Observed mutation patterns differed significantly from those in comparisons of closely related strains (where C → T was more common and deletions/insertions were equally frequent).
Conclusions:
- Genomic differences between closely related bacterial strains are influenced by selection.
- Comparisons of closely related strains do not accurately represent spontaneous mutation patterns.
- Ultradeep sequencing provides a more accurate method for determining true mutation rates.
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