Data from: Core genes evolve rapidly in the long-term evolution experiment with Escherichia coli

Bacteria can evolve rapidly under positive selection owing to their vast numbers, allowing their genes to diversify by adapting to different environments. We asked whether the same genes that evolve rapidly in the long-term evolution experiment with Escherichia coli (LTEE) have also diversified extensively in nature. To make this comparison, we identified ~2000 core genes shared among 60 E. coli strains. During the LTEE, core genes accumulated significantly more nonsynonymous mutations than flexible (i.e., noncore) genes. Furthermore, core genes under positive selection in the LTEE are more conserved in nature than the average core gene. In some cases, adaptive mutations appear to modify protein functions, rather than merely knocking them out. The LTEE conditions are novel for E. coli, at least in relation to its evolutionary history in nature. The constancy and simplicity of the environment likely favor the complete loss of some unused functions and the fine-tuning of others.

细菌凭借其庞大的种群规模，可在正选择压力下快速演化，使其基因通过适应不同环境实现多样化。我们旨在探究：在大肠杆菌（Escherichia coli）长期演化实验（LTEE）中快速演化的基因，是否同样在自然环境中发生了广泛的多样化。为完成此项对比分析，我们从60株大肠杆菌菌株中鉴定出约2000个共享核心基因（core genes）。在LTEE实验过程中，核心基因所累积的非同义突变（nonsynonymous mutations）数量显著高于弹性基因（即非核心基因，flexible/noncore genes）。此外，在LTEE实验中受到正选择压力的核心基因，其在自然环境中的保守性也高于普通核心基因。在部分案例中，适应性突变似乎会修饰蛋白质功能，而非仅仅使其功能失活。LTEE实验的培养条件对于大肠杆菌而言属于全新环境，至少相较于其在自然界中的演化历程而言是如此。该环境的恒定性与简洁性，可能会促使大肠杆菌完全丧失部分闲置功能，并对其余功能进行精细调控。