Arnold Brian J, Huang I-Ting, Hanage William P
Department of Computer Science, Princeton University, Princeton, NJ, USA.
Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA.
Nat Rev Microbiol. 2022 Apr;20(4):206-218. doi: 10.1038/s41579-021-00650-4. Epub 2021 Nov 12.
Horizontal gene transfer (HGT) is arguably the most conspicuous feature of bacterial evolution. Evidence for HGT is found in most bacterial genomes. Although HGT can considerably alter bacterial genomes, not all transfer events may be biologically significant and may instead represent the outcome of an incessant evolutionary process that only occasionally has a beneficial purpose. When adaptive transfers occur, HGT and positive selection may result in specific, detectable signatures in genomes, such as gene-specific sweeps or increased transfer rates for genes that are ecologically relevant. In this Review, we first discuss the various mechanisms whereby HGT occurs, how the genetic signatures shape patterns of genomic variation and the distinct bioinformatic algorithms developed to detect these patterns. We then discuss the evolutionary theory behind HGT and positive selection in bacteria, and discuss the approaches developed over the past decade to detect transferred DNA that may be involved in adaptation to new environments.
水平基因转移（HGT）可以说是细菌进化最显著的特征。在大多数细菌基因组中都能找到HGT的证据。尽管HGT能极大地改变细菌基因组，但并非所有的转移事件都具有生物学意义，相反，它们可能代表了一个持续进化过程的结果，而这个过程只是偶尔具有有益的目的。当发生适应性转移时，HGT和正选择可能会在基因组中产生特定的、可检测到的特征，例如基因特异性的选择性清除或与生态相关基因的转移率增加。在这篇综述中，我们首先讨论HGT发生的各种机制、遗传特征如何塑造基因组变异模式以及为检测这些模式而开发的不同生物信息学算法。然后，我们讨论细菌中HGT和正选择背后的进化理论，并讨论在过去十年中为检测可能参与适应新环境的转移DNA而开发的方法。
