Long Hongan, Sung Way, Miller Samuel F, Ackerman Matthew S, Doak Thomas G, Lynch Michael
Department of Biology, Indiana University, Bloomington
Department of Biology, Indiana University, Bloomington.
Genome Biol Evol. 2014 Dec 23;7(1):262-71. doi: 10.1093/gbe/evu284.
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 the mutation rate varies around the chromosome, with the lowest mutation rate found near the origin of replication. Consistent with observations from other studies, we find that site-specific mutation rates are heavily influenced by the immediately flanking nucleotides, indicating that mutations are context dependent.
荧光假单胞菌的自然分离株存在高度的遗传多样性，在基因组复制终点附近尤其明显，那里存在菌株特异性基因。为了了解遗传变异在假单胞菌进化中的作用，我们分析了荧光假单胞菌ATCC948的45个突变积累系中的31106个碱基替换，该菌株天然缺乏错配修复功能，产生的碱基替换突变率为每代每个位点2.34×10⁻⁸（标准误差：0.01×10⁻⁸），小插入缺失突变率为每代每个位点1.65×10⁻⁹（标准误差：0.03×10⁻⁹）。我们发现，原噬菌体区域（通常包含毒力因子和抗生素抗性）的突变谱与宿主基因组基因间区域的突变谱高度相似。我们的结果表明，突变率在染色体上各不相同，在复制起点附近发现突变率最低。与其他研究的观察结果一致，我们发现位点特异性突变率受紧邻核苷酸的严重影响，这表明突变依赖于上下文。
