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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 262-271 |
| Number of pages | 10 |
| Journal | Genome Biology and Evolution |
| Volume | 7 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 1 2014 |
| Externally published | Yes |
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Keywords
- mutation hotspots
- Neutral evolution
- nonrandom mutations
- phage evolution
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Genetics
Cite this
Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948. / Long, Hongan; Sung, Way; Miller, Samuel F.; Ackerman, Matthew S.; Doak, Thomas G.; Lynch, Michael.
In: Genome Biology and Evolution, Vol. 7, No. 1, 01.01.2014, p. 262-271.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Mutation rate, spectrum, topology, and context-dependency in the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948
AU - Long, Hongan
AU - Sung, Way
AU - Miller, Samuel F.
AU - Ackerman, Matthew S.
AU - Doak, Thomas G.
AU - Lynch, Michael
PY - 2014/1/1
Y1 - 2014/1/1
N2 - 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.
AB - 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.
KW - mutation hotspots
KW - Neutral evolution
KW - nonrandom mutations
KW - phage evolution
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UR - http://www.scopus.com/inward/citedby.url?scp=84928236984&partnerID=8YFLogxK
U2 - 10.1093/gbe/evu284
DO - 10.1093/gbe/evu284
M3 - Article
C2 - 25539726
AN - SCOPUS:84928236984
VL - 7
SP - 262
EP - 271
JO - Genome Biology and Evolution
JF - Genome Biology and Evolution
SN - 1759-6653
IS - 1
ER -