Bacterial populations that originate from a single bacterium are not strictly clonal and often contain subgroups with distinct phenotypes¹. Bacteria can generate heterogeneity through phase variation—a preprogrammed, reversible mechanism that alters gene expression levels across a population¹. One well-studied type of phase variation involves enzyme-mediated inversion of specific regions of genomic DNA². Frequently, these DNA inversions flip the orientation of promoters, turning transcription of adjacent coding regions on or off². Through this mechanism, inversion can affect fitness, survival or group dynamics^3,4. Here, we describe the development of PhaVa, a computational tool that identifies DNA inversions using long-read datasets. We also identify 372 ‘intragenic invertons’, a novel class of DNA inversions found entirely within genes, in genomes of bacterial and archaeal isolates. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We validate ten intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, and experimentally characterize an intragenic inverton in the thiamine biosynthesis gene thiC.

源自单个细菌的细菌种群不是严格克隆的，通常包含具有不同表型的亚群¹。细菌可以通过相变产生异质性，相变是一种预先编程的可逆机制，可改变整个群体的基因表达水平¹。一种经过充分研究的相变类型涉及酶介导的基因组 DNA 特定区域的倒置²。通常，这些 DNA 倒置会翻转启动子的方向，打开或关闭相邻编码区的转录²。通过这种机制，倒置可以影响适应性、生存或群体动态^3,4。在这里，我们描述了 PhaVa 的开发，这是一种使用长读长数据集识别 DNA 倒置的计算工具。我们还在细菌和古细菌分离株的基因组中鉴定了 372 个“基因内反转”，这是一类完全在基因内发现的新型 DNA 倒置。基因内反转子允许基因通过在编码区内翻转 DNA 序列来编码两个或多个版本的蛋白质，从而在不增加基因组大小的情况下增加编码能力。我们验证了肠道共生拟杆菌 thetaiotaomicron 中的 10 个基因内反转子，并实验表征了硫胺素生物合成基因 thiC 中的基因内反转子。