Table_3_A Novel Strategy for Detecting Recent Horizontal Gene Transfer and Its Application to Rhizobium Strains.XLSX

Recent horizontal gene transfer (HGT) is crucial for enabling microbes to rapidly adapt to their novel environments without relying upon rare beneficial mutations that arise spontaneously. For several years now, computational approaches have been developed to detect HGT, but they typically lack the sensitivity and ability to detect recent HGT events. Here we introduce a novel strategy, named RecentHGT. The number of genes undergoing recent HGT between two bacterial genomes was estimated by a new algorithm derived from the expectation-maximization algorithm and is based on the theoretical sequence-similarity distribution of orthologous genes. We tested the proposed strategy by applying it to a set of 10 Rhizobium genomes, and detected several large-scale recent HGT events. We also found that our strategy was more sensitive than other available HGT detection methods. These HGT events were mainly mediated by symbiotic plasmids. Our new strategy can provide clear evidence of recent HGT events and thus it brings us closer to the goal of detecting these potentially adaptive evolution processes in rhizobia as well as pathogens.

近年来，水平基因转移（HGT）对于微生物在不依赖偶然发生的稀有有益突变的情况下，迅速适应其新环境至关重要。数年来，计算方法已被开发出来以检测HGT，但它们通常缺乏对近期HGT事件的高灵敏度和检测能力。本研究中，我们提出了一种名为RecentHGT的创新策略。通过一种源自期望最大化算法的新算法，估计了两个细菌基因组之间正在经历水平基因转移的基因数量，并基于直系同源基因的理论序列相似度分布。我们通过将此策略应用于10个根瘤菌基因组，检测到多个大规模近期HGT事件。此外，我们发现我们的策略比其他可用的HGT检测方法更为敏感。这些HGT事件主要由共生质粒介导。我们的新策略能够提供近期HGT事件的明确证据，从而有助于我们更接近检测根瘤菌以及病原体中这些可能具有适应性进化的过程的目标。