Contrasting mutation rates from specific-locus and long-term mutation-accumulation procedures.
Contrasting mutation rates from specific-locus and long-term mutation-accumulation procedures.
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DOI：
10.1534/g3.111.001842
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发表时间：
2012-04
期刊：
影响因子：
--
通讯作者：
Drake JW
中科院分区：
文献类型：
--
作者：
Drake JW
直到最近，估计突变率的两种主要方法是特定位点法和突变积累法（Bateman-Mukai）。这两种方法都涉及从一个小的、基因一致的种群中播种一些平行线，尽可能长时间地生长，但不要长到允许选择干扰突变频率，有时使用极端瓶颈来促进有害突变的保留。在特定位点法中，根据突变的特定表型选择突变，并通过测序确认。在旧版本的突变积累方法中，测量定量适应度性状方差的增加并将其转换为突变率。最近，基于表型盲基因组测序的突变积累方法的一种变体已经成为可能，这种方法可能（也可能不会）提供改进的采样广度，通常以样本量为代价。在最近的一项研究中，基因组测序应用于大肠杆菌系，繁殖4万代，每天通过500万个细胞传代。为了减轻选择的影响，用于计算速率的唯一目标是假定的中性同义突变。估计的突变率比以前用稳健的特定位点方法获得的结果低约6倍。在这里，我认为，净化选择作用于塑造大肠杆菌的强密码子偏好是较低估计的可能原因，而不是，例如，自然界中的突变率低于实验室中的突变率。
Until recently, the two predominant ways to estimate mutation rates were the specific-locus method and the mutation-accumulation (Bateman-Mukai) method. Both involve seeding a number of parallel lines from a small, genetically uniform population, growing as long as is feasible but not so long as to allow selection to perturb mutant frequencies, and sometimes using extreme bottlenecks to facilitate the retention of deleterious mutations. In the specific-locus method, mutations are selected according to their specific phenotypes and are confirmed by sequencing. In older versions of the mutation-accumulation method, the increase in variance of a quantitative fitness trait is measured and converted into a mutation rate. More recently, a variation on the mutation-accumulation method has become possible based on phenotype-blind genomic sequencing, which might (or might not) provide improved sampling breadth, usually at the expense of sample size. In a recent study, genomic sequencing was applied to Escherichia coli lines propagated for 40,000 generations and passaged daily via 5,000,000 cells. To mitigate the impact of selection, the only targets employed for rate calculations were putatively neutral synonymous mutations. The mutation rate estimate was about 6-fold lower than obtained previously with a robust specific-locus method. Here I argue that purifying selection acting to shape the strong codon preferences of E. coli is the probable cause of the lower estimate, rather than, for instance, a lower mutation rate in nature than in the laboratory.
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影响因子：
4.5
作者：
Drake JW
通讯作者：
Drake JW
DOI：
10.1534/g3.111.000406
发表时间：
2011-08-01
期刊：
G3 (Bethesda, Md.)
影响因子：
--
作者：
Wielgoss S;Barrick JE;Tenaillon O;Cruveiller S;Chane-Woon-Ming B;Médigue C;Lenski RE;Schneider D
通讯作者：
Schneider D
影响因子：
5.6
作者：
Xia, Shuangluo;Wang, Mina;Konigsberg, William
通讯作者：
Konigsberg, William
影响因子：
14.9
作者：
Sharp PM;Bailes E;Grocock RJ;Peden JF;Sockett RE
通讯作者：
Sockett RE
DOI：
10.1073/pnas.88.16.7160
发表时间：
1991-08-01
影响因子：
11.1
作者：
DRAKE, JW
通讯作者：
DRAKE, JW