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.
The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).
The first completed, circular mitochondrial genome and the first draft chloroplastic genome of Northern Atlantic blue diatom Haslea ostrearia (Naviculaceae, Bacillariophyceae) are described. The mitochondrial genome is composed of 38,696 bases and contains 64 genes, including 31 protein-coding genes (CDS), 2 ribosomal RNA (rRNA) genes and 23 transfer RNA (tRNA) genes. For the chloroplast, the genome is composed of 130,200 bases with 169 genes (131 CDS, 6 rRNA genes, 31 tRNA genes, and 1 transfermessenger RNA (tmRNA) gene). Phylogenetic trees suggest the proximity of all H. ostrearia strains yet available and the possibility to use these genomes as future references.
Background: The pigment produced by Haslea ostrearia, the marennine, is of an important medical and economic interest. Unfortunately this microalgae is complex to grow under axenic conditions, and H. ostrearia probably needs its own bacterial procession to survive. Consequently, this important bacterial presence greatly complicates any study of its ecological, physiological and genomic content. We have therefore tested a first approach of a protocol to control the bacterial concentration without killing the microalgae, by growing four H. ostrearia NCC 532 cultures under two culture conditions: two with and two without antibiotic treatment. We also sought a first bacterial identification method by 16S sequencing adapted to the bacterial community of H. ostrearia. Results: The V3V4 16S region allowed precise identification of bacteria present in H. ostrearia culture. Also, an antibiotic treatment was found necessary to stabilize the bacterial population of the cultures before the DNA extraction. Conclusions: These first results will allow the testing of other antibiotic treatments specific to these bacteria, as well as a wider study of other H. ostreariaisolates to determine the essential bacterial community of this microalga.
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