Chromosomal gene order defines several structural classes of Staphylococcus epidermidis genomes

The original methodology for describing the pangenome of a prokaryotic species is based on modeling genomes as unordered sets of genes. More recent findings have underlined the importance of considering the ordering of genes along the genetic material as well, when making comparisons among genomes. To further investigate the benefits of gene order when describing genomes of a given species, we applied two distance metrics on a dataset of 84 genomes of Staphylococcus epidermidis. The first metric, GeLev, depends on the order of genes and is a derivative of the Levenshtein distance. The second, the Jaccard distance, depends on gene sets only. The application of these distances reveals information about the global structure of the genomes, and allows clustering of the genomes into classes. The main biological result is that, while genomes within the same class are structurally similar, genomes of different classes have an additional characteristic. Between genomes in different classes we can discover instances where a large segment of the first genome appears in reverse order in the second. This feature suggests that genome rearrangements in S. epidermidis happen on a large scale, while micro-rearrangements of single or a small number of genes are rare. Thus, this paper describes a straight-forward method to classify genomes into structural classes with the same order of genes and makes it possible to visualize reversed segments in pairs of genomes. The method can be readily applied to other species.