Brezner Shelly, Garushyants Sofya K, Wolf Yuri I, Koonin Eugene V, Snir Sagi
Department. of Evolutionary Biology, University of Haifa, Haifa, Israel.
Computational Biology Branch, Division of Intramural Research, National Library of Medicine, National Institutes of Health, Bethesda, Md 20894, USA.
bioRxiv. 2025 Apr 8:2025.04.03.647019. doi: 10.1101/2025.04.03.647019.
Evolution of bacterial and archaeal genomes is highly dynamic including extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene order is not highly conserved even among closely related organisms. We sought to quantify the contributions of different genome dynamics processes to the evolution of the gene order relying on the recently developed "jump" model of gene translocation. The jump model has been completely solved analytically and provides the exact distribution of syntenic gene block lengths (SBL) in compared genomes based on gene translocations alone. Comparing the SBL distribution predicted by the jump model with the distributions empirically observed for multiple groups of closely related bacterial and archaeal genomes, we obtained robust estimates of the genome rearrangement to gene flux (gain and loss) ratio. In most groups of bacteria and archaea, this ratio was found to be on the order of 0.1 indicating that the loss of synteny in the evolution of bacteria and archaea is driven primarily by gene gain and loss rather than by gene translocation.
细菌和古菌基因组的进化具有高度动态性，包括通过水平基因转移广泛获得基因、基因丢失以及不同类型的基因组重排，如倒位和易位，因此即使在亲缘关系密切的生物体之间，基因顺序也不是高度保守的。我们试图依靠最近开发的基因易位“跳跃”模型，量化不同基因组动态过程对基因顺序进化的贡献。跳跃模型已通过解析完全求解，并仅基于基因易位提供了比较基因组中同线基因块长度（SBL）的精确分布。将跳跃模型预测的SBL分布与多组亲缘关系密切的细菌和古菌基因组的经验观察分布进行比较，我们获得了基因组重排与基因通量（获得和丢失）比率的可靠估计。在大多数细菌和古菌类群中，该比率约为0.1，这表明细菌和古菌进化过程中同线性的丧失主要是由基因的获得和丢失驱动的，而不是由基因易位驱动的。
