Department of Biology, New York University, New York, United States.
Department of Physics, New York University, New York, United States.
Elife. 2022 Jul 8;11:e78533. doi: 10.7554/eLife.78533.
Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. However, assessing the impact of homologous recombination on accessory genes which are only present in a subset of strains of a given species remains challenging due to their complex phylogenetic relationships. Quantifying homologous recombination for accessory genes (which are important for niche-specific adaptations) in comparison to core genes (which are present in all strains and have essential functions) is critical to understanding how selection acts on variation to shape species diversity and genome structures of bacteria. Here, we apply a computationally efficient, non-phylogenetic approach to measure homologous recombination rates in the core and accessory genome using >100,000 whole genome sequences from and several additional species. By analyzing diverse sets of sequence clusters, we show that core genes often have higher recombination rates than accessory genes, and for some bacterial species the associated effect sizes for these differences are pronounced. In a subset of species, we find that gene frequency and homologous recombination rate are positively correlated. For and several additional species, we find that while the recombination rate is higher for the core genome, the mutational divergence is lower, indicating that divergence-based homologous recombination barriers could contribute to differences in recombination rates between the core and accessory genome. Homologous recombination may therefore play a key role in increasing the efficiency of selection in the most conserved parts of the genome.
重组对于微生物进化至关重要，涉及抗生素耐药性、抗原变异和适应宿主小生境的传播。然而，由于辅助基因与核心基因之间复杂的系统发育关系，评估同源重组对仅存在于特定物种的部分菌株中的辅助基因的影响仍然具有挑战性。与核心基因（存在于所有菌株中并具有必需功能）相比，量化辅助基因（对特定小生境的适应很重要）中的同源重组对于理解选择如何作用于变异以塑造细菌的物种多样性和基因组结构至关重要。在这里，我们应用了一种计算效率高、非系统发育的方法，使用来自 和其他几个物种的超过 100,000 个全基因组序列来测量核心和辅助基因组中的同源重组率。通过分析不同的序列聚类集，我们表明核心基因的重组率通常高于辅助基因，对于一些细菌物种，这些差异的相关效应大小非常显著。在一组亚群物种中，我们发现基因频率和同源重组率呈正相关。对于 和其他几个物种，我们发现虽然核心基因组的重组率较高，但突变分歧较低，这表明基于分歧的同源重组障碍可能导致核心和辅助基因组之间的重组率差异。因此，同源重组可能在增加基因组最保守部分的选择效率方面发挥关键作用。
