Université de Lyon, VetAgro Sup, Anses laboratoire de Lyon, UMR Mycoplasmoses Animales, 69280, Marcy l'Etoile, France.
Present Address: Université du Mans, Laboratoire Biologie Des Organismes, Stress, Santé, Environnement (BiOSSE), Avenue Olivier Messiaen, 72085, LE MANS Cedex 09, France.
BMC Genomics. 2022 Aug 19;23(1):603. doi: 10.1186/s12864-022-08818-9.
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.
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.
Whole-genome comparison of the three French M. bovis subtypes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods.
牛支原体（M. bovis）是牛呼吸道疾病的主要病原体，是全球范围内对牛最具经济成本的疾病。牛支原体疾病监测越来越多地使用基于基因的技术，如多位点序列分型（MLST），或基于基因组的技术，如核心基因组 MLST，这两种技术都只需要部分基因组数据。然而，准确的最新监测还需要完整的环状基因组，这些基因组可用作跟踪不同谱系进化的参考。然而，在法国，目前流行的两个主要亚型仍然没有在公共数据库中代表基因组。在这里，为了解决这一差距，我们提供并比较了三种从最近的临床分离株中获得的新的完整的 M. bovis 基因组，这些分离株代表了法国和欧洲流行的主要亚型。
使用混合组装策略（Illumina 和 Nanopore）获得基因组，并对 Unicycler 组装管道中的设置和输入进行微调，例如读取大小选择和 FASTQ 文件的质量修剪。比较了基因组的主要特征和基因排列。三个基因组主要在移动遗传元件（即整合性共轭元件（ICE）和插入序列（IS））的含量方面存在差异，这一特征影响了它们的结构。例如，代表 3 型（st3）的 L15527 菌株含有异常高数量的 ICE，这导致其基因组比之前描述的所有基因组都要大，并且可能与 st3 通过染色体转移机制获得和固定突变的倾向有关。相比之下，代表 1 型（st1）的 F9160 菌株非常接近 1961 年在美国分离的 PG45 型菌株，并且含有大量的 IS。这些特征可能与向宿主受限状态或“封闭”宿主或环境储库的进化有关，直到最近才重新出现。
对三种法国 M. bovis 亚型的全基因组比较为未来结合流行病学、系统发育数据和系统发育动力学方法的研究提供了有价值的资源。
