Genomic features of Mycoplasma bovis subtypes currently circulating in France

Abstract

Background: Mycoplasma (M.) bovis is a major etiological agent of bovine respiratory disease, which is the most economically costly disease of cattle worldwide. Cattle disease surveillance on M. bovis is increasingly using gene-based techniques, such as multilocus sequence typing (MLST), or genome-based techniques such as core genome MLST that both require only partial genomic data. However, accurate up-to-date surveillance also demands complete, circular genomes that can be used as reference to track the evolution of the different lineages. Yet, in France, two of the main subtypes currently circulating still have no representing genome in public databases. Here, to address this gap, we provide and compare three new complete M. bovis genomes obtained from recent clinical isolates that represent major subtypes circulating in France and Europe.

Results: Genomes were obtained using a hybrid assembly strategy (Illumina and Nanopore) with fine-tuning of settings and inputs used in the Unicycler assembly pipeline, such as size selection of reads and quality trimming of the FASTQ files. The main characteristics and synteny of the genomes were compared. The three genomes mainly differed by their content in terms of mobile genetic elements, i.e. integrative conjugative elements (ICE) and insertion sequences (IS), a feature that impacts their structure. For instance, strain L15527, representing subtype3 (st3), harbours an exceptionally high number of ICEs, which results in a bigger-sized genome than all those previously described and could be associated with the propensity of st3 to gain and fix mutations through chromosomal transfer mechanisms. In contrast, strain F9160, of st1, is very close to the PG45 type strain isolated in 1961 in the USA, and harbours a huge number of IS. These features may be associated with an evolution towards a host-restricted state or in a "closed" host or environment reservoir until a recent re-emergence.

Conclusions: Whole-genome comparison of the three French M. bovis subtypes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods.

Keywords: Genome assembly; Mobile genetic elements; Mycoplasma bovis; Subtype; Whole-genome comparison.

Fig. 1

Multiple genome alignment and distribution of mobile genetic elements of the three M. bovis genomes obtained in this study and the PG45^T reference strain. At the bottom of the Mauve alignments, a linear representation of the genomes (done using DNA plotter) shows CDS in light blue, IS in dark blue bars, and ICEs in orange (vICEB_PG45-1) or purple (ICEB_PG45-2) boxes. The alignment process generated a maximum of 16 locally collinear blocks (LCB) representing homologous DNA regions shared between strains without sequence rearrangements. The vertical bars in a LCB denote the conservation level, upward orientation and downward orientation of LCBs relative to the genome, and lines indicate collinear and inverted regions, respectively

Fig. 2

Core-genome and pan- genome representation of the three M. bovis strains. A Distribution of genes shared or not by the three sequenced M. bovis strains (tRNA an rRNA-encoding genes are excluded). Presence of a set of genes in a strain is represented by a black circle. For genes specific to one strain only, there is one black circle only. The horizontal bar chart at the bottom left represents the total number of genes for each strain. B Table showing the number of singletons in total or associated with MGEs. Numbers in brackets represent the percentage of each category as a ratio of total number of singletons