Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948. Long, H., Sung, W., Miller, S., F., Ackerman, M., S., Doak, T., G., & Lynch, M. Genome Biology and Evolution, 7(1):262-271, Oxford University Press, 2014.
Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948 [link]Website  abstract   bibtex   
High levels of genetic diversity exist among natural isolates of the bacterium Pseudomonas fluorescens, and are especially elevated around the replication terminus of the genome, where strain-specific genes are found. In an effort to understand the role of genetic variation in the evolution of Pseudomonas, we analyzed 31,106 base substitutions from 45 mutation accumulation lines of P. fluorescens ATCC948, naturally deficient for mismatch repair, yielding a base-substitution mutation rate of 2.34×10-8 per site per generation (SE: 0.01×10-8) and a small-insertion-deletion mutation rate of 1.65×10-9 per site per generation (SE: 0.03×10-9). We find that the spectrum of mutations in prophage regions, which often contain virulence factors and antibiotic resistance, is highly similar to that in the intergenic regions of the host genome. Our results show that themutation rate varies around the chromosome, with the lowest mutation rate foundnear the originof replication. Consistent with observations fromother studies, wefind that site-specificmutation rates are heavily influenced by the immediately flanking nucleotides, indicating thatmutations are context dependent. © 2014 The Author(s).
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 title = {Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948},
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 year = {2014},
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 keywords = {Bacteria (microorganisms); Pseudomonas; Pseudomona,Bacterial; Genetic Variation; Host-Pathogen Inter,DNA Mismatch Repair; DNA Replication; Drug Resist,antibiotic resistance; DNA replication; genetic v},
 pages = {262-271},
 volume = {7},
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 abstract = {High levels of genetic diversity exist among natural isolates of the bacterium Pseudomonas fluorescens, and are especially elevated around the replication terminus of the genome, where strain-specific genes are found. In an effort to understand the role of genetic variation in the evolution of Pseudomonas, we analyzed 31,106 base substitutions from 45 mutation accumulation lines of P. fluorescens ATCC948, naturally deficient for mismatch repair, yielding a base-substitution mutation rate of 2.34×10-8 per site per generation (SE: 0.01×10-8) and a small-insertion-deletion mutation rate of 1.65×10-9 per site per generation (SE: 0.03×10-9). We find that the spectrum of mutations in prophage regions, which often contain virulence factors and antibiotic resistance, is highly similar to that in the intergenic regions of the host genome. Our results show that themutation rate varies around the chromosome, with the lowest mutation rate foundnear the originof replication. Consistent with observations fromother studies, wefind that site-specificmutation rates are heavily influenced by the immediately flanking nucleotides, indicating thatmutations are context dependent. © 2014 The Author(s).},
 bibtype = {article},
 author = {Long, H and Sung, W and Miller, S F and Ackerman, M S and Doak, T G and Lynch, M},
 journal = {Genome Biology and Evolution},
 number = {1}
}

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