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7 results for “multilocus sequence typing”
Supplemental material of "An annotated whole-genome multilocus sequence typing schema for scalable high resolution typing of Streptococcus pyogenes"
<p>This supplemental material includes the genome assemblies, associated metadata and analysis results for five datasets used to define a publicly available annotated wgMLST schema for <em>S. pyogenes</em> and to evaluate its suitability for high resolution typing. A brief description for each file in the dataset is available in the included README file. Raw sequencing data and sample metadata for the 265 isolates included in Dataset1 have been deposited in the European Nucleotide Archive (ENA) under Project <a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB49967?show=reads">PRJEB49967</a>.</p> <p>The wgMLST schema was created with <a href="https://github.com/B-UMMI/chewBBACA">chewBBACA</a> and is publicly available at <a href="https://chewbbaca.online/species/1/schemas/1">chewie-NS</a>, where a more detailed description of schema creation, annotation and curation can be found.</p>
New methods for the genotyping of Legionella pneumophila - Establishment, validation and implementation of a DNA-based microarray and a core genome multilocus sequence typing
<p>This data presented here are part a doctoral thesis with the focus on new genotyping methods for the human pathogen <em>Legionella pneumophila</em>. The data are partially published in articles. </p> <p>The thesis can be downloaded: update of the URL is coming soon</p>
Data from: Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny
The endosymbiotic bacterium Wolbachia enhances its spread via vertical transmission by generating reproductive effects in its hosts, most notably cytoplasmic incompatibility (CI). Additionally, frequent interspecific horizontal transfer is evident from a lack of phylogenetic congruence between Wolbachia and its hosts. The mechanisms of this lateral transfer are largely unclear. To identify potential pathways of Wolbachia movements, we performed multilocus sequence typing of Wolbachia strains from bees (Anthophila). Using a host phylogeny and ecological data, we tested various models of horizontal endosymbiont transmission. In general, Wolbachia strains seem to be randomly distributed among bee hosts. Kleptoparasite-host associations among bees as well as other ecological links could not be supported as sole basis for the spread of Wolbachia. However, cophylogenetic analyses and divergence time estimations suggest that Wolbachia may persist within a host lineage over considerable timescales and that strictly vertical transmission and subsequent random loss of infections across lineages may have had a greater impact on Wolbachia strain distribution than previously estimated. Although general conclusions about Wolbachia movements among arthropod hosts cannot be made, we present a framework by which precise assumptions about shared evolutionary histories of Wolbachia and a host taxon can be modelled and tested.
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, ex-neotype, or reference strain).
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain). in Six new species of Cladosporium associated with decayed leaves of native bamboo (Bambusoideae) in a fragment of Brazilian Atlantic Forest
FIGURE. (Continued) Multilocus phylogenetic tree inferred from Bayesian analysis based on the combined TEF1-α and ACT sequences. Bayesian posterior probabilities are indicated next to the nodes. The tree was rooted with Cladosporium herbarum CBS 121621. The species in this study are indicated in bold. Types of species are indicated after the culture collection number (T = ex-type, ex-epitype, exneotype, or reference strain).
Data from: Tracing horizontal Wolbachia movements among bees (Anthophila): a combined approach using multilocus sequence typing data and host phylogeny
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Data from: Development and validation of a core genome multilocus sequence typing (cgMLST) scheme for Klebsiella oxytoca
<p>The dataset hereby shared contains the genomes used to create and validate a newly proposed schema for <i>Klebsiella oxytoca.</i> </p><p>As reference dataset, all publicly available <i>K. oxytoca</i> draft and complete genomes (199) were downloaded from RefSeq in NCBI database in September 2021. All assemblies were filtered by quality and identification methods in order to remove highly fragmented genomes (more than 200 contigs) and genomes that did not correspond to <i>K. oxytoca sensu stricto</i>. A series of assemblies, including complete and draft genomes, were removed because they (i) did not correspond to <i>K. oxytoca</i> species based on MLST or rMLST, and because they (ii) produced ANI values lower than 96% against <i>K. oxytoca</i>. Apart from some genomes that had no correspondence to<i> K. oxytoca,</i> several others were discarded because they did not correspond to <i>K. oxytoca </i>species sensu stricto, but other closely related species included in the <i>K. oxytoca </i>species complex, such as <i>K. michiganensis</i> or <i>K. grimontii.</i> Additional identification of blaOXY gene variants supported this observation. Finally, genomes that had not been assigned an assigned ST were also removed, since they would not contribute to the schema validation. Therefore, the final dataset consisted in 16 high-quality complete genomes of <i>K. oxytoca sensu stricto. </i></p><p> </p>
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