Van Etten Julia, Stephens Timothy G, Bhattacharya Debashish
Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA.
Environ Microbiol. 2025 Feb;27(2):e70048. doi: 10.1111/1462-2920.70048.
Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.
水平基因转移（HGT）是所有生命领域基因组新颖性的重要驱动因素。尽管在许多研究中都对HGT进行了调查，但重点一直放在引人注目的蛋白质编码DNA转移上，这些转移往往被证明在受体生物体中具有适应性，因此在谱系中能长期固定下来。这些结果构成了HGT的一个子类，并不能代表详尽的（编码和非编码）DNA转移及其对生态的影响。揭示详尽的HGT可以为群落中基因组的连通性以及这些转移可能如何发生提供关键见解。在本研究中，我们使用词频逆文档频率（TF-IDF）技术，该技术已成功用于挖掘真实和模拟的高质量原核生物基因组中的DNA转移，以在极端微生物群落中搜索详尽的HGT。我们建立了一个用于验证使用此方法识别出的转移的流程。我们发现大多数DNA转移发生在域内，并且涉及非编码DNA。预测的蛋白质编码HGT中相对较高比例似乎编码转座酶活性、限制修饰系统成分和生物膜形成功能。我们的研究证明了TF-IDF方法在HGT检测中的实用性，并为近期DNA转移的机制提供了见解。
