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Nature:探索大肠杆菌基因组演化的速度和模式

来源:未知 编辑:admin 发布时间:2017-08-14

在韩、美、法三国科学家组成的研究小组长达20年实验中,研究人员在实验室中培养了一批大肠杆菌,它们在近20年时间里一直以葡萄糖为一种限制性营养物。这项实验为研究基因组演化的速度和模式提供了一个机会。

大肠杆菌克隆的基因组分别在2,000代、5,000代、10,000代、15,000代、20,000代和 40,000代后被取样。适应性的发展加速极快,但基因组演化在20,000代几乎是不变的。这样的一致性被认为是中性演化的特点,但来自几个方面的证据都表明,这些突变大部分都是有益的。这个种群后来突变速度加快,并且积累了数百个另外的、以中性为特征的突变。显然,基因组演化和适应性演化之间的耦合是一个复杂的问题。

原始出处:

Nature 461, 1243-1247 (29 October 2009) | doi:10.1038/nature08480

Genome evolution and adaptation in a long-term experiment with Escherichia coli

Jeffrey E. Barrick1,7, Dong Su Yu2,3,7, Sung Ho Yoon2, Haeyoung Jeong2, Tae Kwang Oh2,4, DominIQue Schneider5, Richard E. Lenski1 & Jihyun F. Kim2,6

1 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
2 Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong, Daejeon 305-806, Korea
3 Department of Computer Science and Engineering, Chungnam National University, Yuseong, Daejeon 305-764, Korea
4 21C Frontier Microbial Genomics and Applications Center, Yuseong, Daejeon 305-806, Korea
5 Institut Jean Roget, Laboratoire Adaptation et Pathogénie des Microorganismes, CNRS UMR 5163, Université Joseph Fourier, Grenoble 1, BP 170, F-38042 Grenoble cedex 9, France
6 Functional Genomics Program, School of Science, University of Science and Technology, Yuseong, Daejeon 305-333, Korea
7 These authors contributed equally to this work.
Correspondence to: Richard E. Lenski1Jihyun F. Kim2,6 Correspondence and requests for materials should be addressed to R.E.L. or J.F.K.

The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.

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