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...
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| Format: | Article |
| Language: | English |
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BMC
2022-08-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-022-08818-9 |
| _version_ | 1811340064769179648 |
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| author | Chloé Ambroset Aurélie Peticca Agnès Tricot Florence Tardy |
| author_facet | Chloé Ambroset Aurélie Peticca Agnès Tricot Florence Tardy |
| author_sort | Chloé Ambroset |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T18:36:48Z |
| format | Article |
| id | doaj.art-269a01495fc14ddcaeea1c47578938a6 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T18:36:48Z |
| publishDate | 2022-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-269a01495fc14ddcaeea1c47578938a62022-12-22T02:34:51ZengBMCBMC Genomics1471-21642022-08-0123111010.1186/s12864-022-08818-9Genomic features of Mycoplasma bovis subtypes currently circulating in FranceChloé Ambroset0Aurélie Peticca1Agnès Tricot2Florence Tardy3Université de Lyon, VetAgro Sup, Anses laboratoire de Lyon, UMR Mycoplasmoses AnimalesUniversité de Lyon, VetAgro Sup, Anses laboratoire de Lyon, UMR Mycoplasmoses AnimalesUniversité de Lyon, VetAgro Sup, Anses laboratoire de Lyon, UMR Mycoplasmoses AnimalesUniversité de Lyon, Anses Laboratoire de Lyon, VetAgro Sup, UMR Mycoplasmoses AnimalesAbstract 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.https://doi.org/10.1186/s12864-022-08818-9Mycoplasma bovisGenome assemblySubtypeWhole-genome comparisonMobile genetic elements |
| spellingShingle | Chloé Ambroset Aurélie Peticca Agnès Tricot Florence Tardy Genomic features of Mycoplasma bovis subtypes currently circulating in France BMC Genomics Mycoplasma bovis Genome assembly Subtype Whole-genome comparison Mobile genetic elements |
| title | Genomic features of Mycoplasma bovis subtypes currently circulating in France |
| title_full | Genomic features of Mycoplasma bovis subtypes currently circulating in France |
| title_fullStr | Genomic features of Mycoplasma bovis subtypes currently circulating in France |
| title_full_unstemmed | Genomic features of Mycoplasma bovis subtypes currently circulating in France |
| title_short | Genomic features of Mycoplasma bovis subtypes currently circulating in France |
| title_sort | genomic features of mycoplasma bovis subtypes currently circulating in france |
| topic | Mycoplasma bovis Genome assembly Subtype Whole-genome comparison Mobile genetic elements |
| url | https://doi.org/10.1186/s12864-022-08818-9 |
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