The genome of Pasteuria ramosa reveals a high turnover rate of collagen-like genes

Collagen-like proteins (CLP) are commonly found in many pathogenic bacteria where they serve as adhesins to attach to host tissue. The repetition of the amino-acid pattern (Gly-Xaa-Yaa)n is the major feature of collagen and is essential to the formation of its stable triple helical structure. In the Daphnia magna–Pasteuria ramosa system, a model system for studying antagonistic coevolution, a specific CLP in the virulent parasite P. ramosa plays a pivotal role in host attachment, regulated by matching allele model. Recognizing the crucial role of CLPs in the infection process, we aimed to enhance our understanding of P. ramosa-CLPs by sequencing high-quality genomes of two isolates, using long-read technology. An analysis of a CLP gene tree of representative Bacillota species revealed a clear radiation of these genes in P. ramosa, which was not found in the closely related Pasteuria penetrans. A comparison of the isolates reveals a high synteny, with the exception of a few duplications and inversions, mainly involving CLPs or transposases. Across isolates, we observed a recent burst of transposases as well as duplications of CLP genes. On average, CLP genes are well conserved between isolates, but the presence/absence of individual CLP genes is not fully shared, with 39 and 43 genes in the two isolates. Our findings suggest a rapid radiation of CLP genes combined with a birth and death process of the large P. ramosa-CLP gene family, possibly driven by transposition and coevolution.