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bioRxiv · 10.1101/2023.04.13.536562

De novo genome assembly resolving repetitive structures enables genomic analysis of 35 European Mycoplasma bovis strains

Triebel, S.·Sachse, K.·Weber, M.·Heller, M.·Diezel, C.·Hoelzer, M.·Schnee, C.·Marz, M.
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Abstract

Mycoplasma (M.) bovis, the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome of approximately 1 Mbp. Combining data from Illumina and Nanopore technologies, we sequenced and assembled the genomes of 35 European strains and isolate DL422_88 from Cuba. While the high proportion of repetitive structures in M. bovis genomes represents a particular challenge, implementation of our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista) in a hybrid approach enabled contiguous assembly of the genomes and, consequently, improved annotation rates considerably. To put our European strain panel in a global context, we analyzed the new genome sequences together with 175 genome assemblies from public databases. Construction of a phylogenetic tree based on core genes of these 219 strains revealed a clustering pattern according to geographical origin, with European isolates positioned on clades 4 and 5. Genomic data allowing assignment of strains to tissue specificity or certain disease manifestations could not be identified. Seven strains isolated from cattle with systemic circular condition (SCC), still a largely unknown manifestation of M. bovis disease, were located on both clades 4 and 5. Pairwise association analysis revealed 108 genomic elements associated with a particular clade of the phylogenetic tree. Further analyzing these hits, 25 genes are functionally annotated and could be linked to a M. bovis protein, e.g. various proteases and nucleases, as well as ten variable surface lipoproteins (Vsps) and other surface proteins. These clade-specific genes could serve as useful markers in epidemiological and clinical surveys.

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Triebel, S., Sachse, K., Weber, M., Heller, M., Diezel, C., Hoelzer, M., Schnee, C., Marz, M.. 2023-04-13. De novo genome assembly resolving repetitive structures enables genomic analysis of 35 European Mycoplasma bovis strains. https://doi.org/10.1101/2023.04.13.536562

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