Department of Biology, McMaster University, Hamilton, Ontario, Canada.
Genome Biol Evol. 2021 Jan 7;13(1). doi: 10.1093/gbe/evaa260.
Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, whereas substitution rates usually increase with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and the distance from the origin of replication is significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), whereas others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS, and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.
越来越多的证据支持这样一种观点，即基因组的不同区域具有独特的分子变化速率。这种变异在细菌基因组中尤为明显，先前的研究报告称，基因表达和必需性往往随着与复制起点距离的增加而降低，而取代率通常随着距离的增加而增加。基因组重排，如重排，在细菌中经常发生，允许遗传物质的引入和重组，在基因组中形成分子特征的梯度。在这里，我们通过将替换映射到大肠杆菌、枯草芽孢杆菌、链霉菌和苜蓿中华根瘤菌的基因组上来探索这些现象的相互作用，量化了基因组中每个位置发生了多少替换。之前的工作表明，取代率随着与起点的距离显著增加。使用更大的样本量，并通过祖先重建来解释基因组重排，我们的分析表明，替换数与复制起点距离之间的相关性虽然显著，但很小，且方向不一致。一些复制子呈现出显著的下降趋势（大肠杆菌和苜蓿中华根瘤菌的染色体），而其他复制子则呈现出相反的显著趋势（枯草芽孢杆菌、链霉菌、苜蓿中华根瘤菌中的 pSymA 和 pSymB）。在所有基因中都检查了 dN、dS 和 ω，并且这些值与距离起点之间没有显著的相关性。这项研究强调了基因组重排和位置对某些细菌中分子趋势的影响，说明了在分子进化分析中考虑空间趋势的重要性。假设分子趋势仅朝一个方向发展可能会有问题。
