Torrance Ellis L, Diop Awa, Bobay Louis-Marie
Department of Biology, University of North Carolina Greensboro, Greensboro, NC 27412, USA.
Systems Biology Dept., Sandia National Laboratories, Livermore, CA 9455, USA.
Nucleic Acids Res. 2025 Feb 8;53(4). doi: 10.1093/nar/gkae1265.
Homologous recombination is a key evolutionary force that varies considerably across bacterial species. However, how the landscape of homologous recombination varies across genes and within individual genomes has only been studied in a few species. Here, we used Approximate Bayesian Computation to estimate the recombination rate along the genomes of 145 bacterial species. Our results show that homologous recombination varies greatly along bacterial genomes and shapes many aspects of genome architecture and evolution. The genomic landscape of recombination presents several key signatures: rates are highest near the origin of replication in most species, patterns of recombination generally appear symmetrical in both replichores (i.e. replicational halves of circular chromosomes) and most species have genomic hotspots of recombination. Furthermore, many closely related species share conserved landscapes of recombination across orthologs indicating that recombination landscapes are conserved over significant evolutionary distances. We show evidence that recombination drives the evolution of GC-content through increasing the effectiveness of selection and not through biased gene conversion, thereby contributing to an ongoing debate. Finally, we demonstrate that the rate of recombination varies across gene function and that many hotspots of recombination are associated with adaptive and mobile regions often encoding genes involved in pathogenicity.
同源重组是一种关键的进化力量，在不同细菌物种间差异很大。然而，同源重组景观如何在基因间以及单个基因组内变化，仅在少数物种中得到研究。在此，我们使用近似贝叶斯计算来估计145种细菌物种基因组的重组率。我们的结果表明，同源重组在细菌基因组中变化很大，并塑造了基因组结构和进化的许多方面。重组的基因组景观呈现出几个关键特征：在大多数物种中，复制起点附近的重组率最高，重组模式在两个复制子（即环状染色体的复制半区）中通常呈对称分布，并且大多数物种具有基因组重组热点。此外，许多密切相关的物种在直系同源基因间共享保守的重组景观，这表明重组景观在显著的进化距离上是保守的。我们有证据表明，重组通过提高选择效率而非偏向性基因转换来驱动GC含量的进化，从而为正在进行的争论提供了依据。最后，我们证明重组率在不同基因功能间存在差异，并且许多重组热点与适应性和移动区域相关，这些区域通常编码与致病性有关的基因。
