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

BMC Genomics

Research

Martin Hölzer¹  Michael Weber²  Christiane Schnee²  Martin Heller²  Celia Diezel³  Sandra Triebel⁴  Konrad Sachse⁴  Manja Marz⁵ 

[1] Genome Competence Center (MF1), Method Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany;Institute of Molecular Pathogenesis, Friedrich-Loeffler Institute, Jena, Germany;Leibniz Institute of Photonic Technology (IPHT), Jena, Germany;RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany;RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany;FLI Leibniz Institute for Age Research, Jena, Germany;European Virus Bioinformatics Center, Jena, Germany;

关键词: Mycoplasmopsis bovis;    de novo;    Oxford Nanopore Technologies;    Illumina;   

DOI  :  10.1186/s12864-023-09618-5

 received in 2023-04-17, accepted in 2023-08-23,  发布年份 2023

来源: Springer

【 摘 要 】

Mycoplasmopsis (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 represent 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.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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