Strains.

Genetic exchange is a cornerstone of evolutionary biology and genomics, driving adaptation and enabling the identification of genetic determinants underlying phenotypic traits. In Escherichia coli, horizontal gene transfer via conjugation and transduction not only promotes diversification and adaptation but has also been instrumental in mapping genetic traits. However, the dynamics and variability of bacterial recombination remain poorly understood, particularly concerning the patterns of recombined DNA fragments. To elucidate these patterns and simultaneously develop a tool for trait mapping, we designed a high-throughput conjugation method to generate recombinant libraries. Recombination profiles were inferred through whole-genome sequencing of individual clones and populations after selection of a marker from the donor strain in the recipient. This analysis revealed an extraordinary range of recombined fragment sizes, spanning less than ten kilobases to over a megabase—a pattern that varied across the three tested strains. Mathematical modelling indicated that this diversity in recombined fragment size enables precise identification of selected loci following genetic crosses. Consistently, population sequencing pinpointed a selected marker at kilobase-scale accuracy, offering a robust tool for identifying subtle genetic determinants that could include point mutations in core genes. These findings challenge the conventional view that conjugation always transfers large fragments, suggesting that even short recombined segments, traditionally attributed to transduction, may originate from conjugation.遗传交换是进化生物学与基因组学的核心基石，既推动适应性演化，也助力解析表型性状背后的遗传决定因子。在大肠杆菌（Escherichia coli）中，通过接合（conjugation）与转导（transduction）介导的水平基因转移，不仅促进了种群多样化与适应性演化，更为遗传性状的定位研究提供了关键技术支撑。然而，细菌重组的动态过程与变异特征仍未得到充分解析，尤其是重组DNA片段的分布模式。为阐明此类重组模式并同步开发性状定位工具，我们设计了一种高通量接合方法以构建重组文库。我们通过对受体菌中经供体菌株标记基因筛选后的单克隆与群体样本开展全基因组测序，推导得到重组特征谱。该分析揭示了跨度极大的重组片段尺寸分布：从不足10千碱基（kilobase，kb）到超过1兆碱基（megabase，Mb），且该模式在3株受试菌株中存在显著差异。数学建模结果表明，重组片段尺寸的多样性可实现遗传杂交后对目标位点的精准定位。与之相符的是，群体测序能够以千碱基级别的精度定位目标标记基因，为解析包括核心基因点突变在内的细微遗传决定因子提供了可靠工具。本研究结果挑战了“接合仅能转移大片段DNA”的传统认知，表明以往归因于转导的短小重组片段，也可能源自接合过程。