Evolution of gene order in prokaryotes is driven primarily by gene gain and loss

• 成果类型: Article
• 署名作者: Brezner, Shelly; Garushyants, Sofya K.; Wolf, Yuri I.; Koonin, Eugene V.; Snir, Sagi
• 署名单位: University of Haifa; National Institutes of Health (NIH) - USA; NIH National Library of Medicine (NLM); Division of Intramural Research (DIR)
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-8722
• DOI: 10.1073/pnas.2502752122
• 发表日期: 2025-06-17
• 关键词: selfish operons; ORGANIZATION; CONSERVATION; bacterial; archaeal; genomes

摘要

Evolution of bacterial and archaeal genomes is highly dynamic, including extensive gene gain via horizontal gene transfer (HGT) 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 in prokaryote genomes, relying on the recently developed, simple, stochastic model of genome rearrangement through single gene translocations (jump model). The jump model was completely solved analytically in our previous work 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. Significance Evolution of bacterial and archaeal genomes is a highly dynamic process that includes extensive gene gain via horizontal gene transfer (HGT) and gene loss as well as different types of genome rearrangements, so that gene order is not highly conserved even among closely related organisms. We developed a theoretical framework to quantify the contributions of different genome dynamics processes to the evolution of the gene order. In most groups of bacteria and archaea, the genome rearrangement to gene flux (combined gain and loss) was found to be on the order of 0.1. Thus, the loss of genomic synteny in the evolution of bacteria and archaea appears to be driven primarily by gene gain and loss rather than by gene translocation.