Rearrangements of large genome fragments occur in bacteria between repeat sequences and can impact on growth and gene expression. Homologous recombination resulting in inversion between indirect repeats and excision/translocation between direct repeats enables these structural changes. One form of rearrangement occurs around ribosomal operons, found in multiple copies across many bacteria, but identification of these rearrangements by sequencing requires reads of several thousand bases to span the ribosomal operons. With long-read sequencing aiding the routine generation of complete bacterial assemblies, we have developed socru, a typing method for the order and orientation of genome fragments between ribosomal operons. It allows for a single identifier to convey the order and orientation of genome-level structure and we have successfully applied this typing to 433 of the most common bacterial species. In a focused analysis, we observed the presence of multiple structural genotypes in nine bacterial pathogens, underscoring the importance of routinely assessing this form of variation alongside traditional single-nucleotide polymorphism (SNP) typing.

中文翻译：

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socru：细菌中核糖体操纵子周围基因组水平顺序和方向的键入。

大基因组片段的重排发生在重复序列之间的细菌中，并且可能影响生长和基因表达。同源重组导致间接重复之间的反向转化和直接重复之间的切除/易位使这些结构改变成为可能。一种重排形式发生在核糖体操纵子周围，在许多细菌中有多个拷贝，但是通过测序鉴定这些重排需要读取跨越核糖体操纵子的数千个碱基。通过长时间的测序帮助常规的完整细菌装配的产生，我们开发了socru，一种核糖体操纵子之间基因组片段顺序和方向的打字方法。它允许使用一个标识符来传达基因组水平结构的顺序和方向，并且我们已经成功地将此类型应用于433种最常见的细菌种类。在一项重点分析中，我们观察到九种细菌病原体中存在多种结构基因型，强调了定期评估这种变异形式以及传统单核苷酸多态性（SNP）分型的重要性。