Graphic representation of the frequencies of newly generated haplotypes along 24 days (corresponding to 432 generations) of evolution inside the mouse gut (see Tables S3 to S6 for numeric data).

<p>Shaded areas are proportional to the relative abundance of each haplotype. Yellow and blue shaded areas represent the two sub-populations of bacteria labeled either with <i>cfp</i> or <i>yfp</i> alleles. The ancestry relations between haplotypes can be inferred by the accumulation of new mutations in a previously existent genotype. Dash lines mark the time points in days (upper axis) or generations (lower axis) where the sampling took place. For the top two populations 1.1 (A) and 1.11 (B), 40 clones were sampled in each time point. For the bottom two populations 1.12 (C) and 1.5 (D) 20 clones were sampled in each time point.</p

The genetic basis of adaptive mutations and the level of parallelism between populations.

<p>Identified mutations in clones isolated from populations 1.1 to 1.14 (evolved <i>in vivo</i> for 24 days), represented along the <i>E. coli</i> chromosome. For simplicity, the genomes are represented linearly and vertically drawn. The type and position of mutations are shown by triangles for insertions and deletions, small vertical bars denote single nucleotide polymorphisms (SNPs), and one duplication in clone number 1.12 is depicted as a horizontal bar. See the symbol legend for other events. The genes <i>dcuB</i>, <i>srlR</i> and <i>focA</i> and one operon (<i>gat</i>) are highlighted. These represent regions of parallel mutation in at least two genomes. The genomic context of these mutations is represented on the right. (reg) after the gene name, means that the regulatory region, rather than the coding region, was affected. Numbers above marked mutations represent the number of times a particular mutation was detected at the same position.</p

Origin of the animal and food isolates.

a<p>the number of MRSA isolates is indicated in brackets.</p>b<p>the origin of one of the 13 food poisoning associated isolates is unknown.</p>c<p>NA : not applicable.</p

Minimum spanning tree of the 251 <i>S. aureus</i> isolates using MLVA-16_Orsay.

<p>Minimum spanning tree of the 251 <i>S. aureus</i> isolates (106 human-associated isolates, 98 animal-associated isolates and 47 isolates from food products among which 13 were related with food-poisoning) using MLVA-16_Orsay. Each circle represents a MLVA genotype. The size of each circle indicates the number of isolates within this MLVA genotype. The different clusters are annotated. The host origin is indicated with a specific color. Isolates involved in food poisoning events are represented by black circles. Human and food isolates are highlighted with two different hatch patterns.</p

Constitution of the different MLVA schemes.

a<p>the VNTR locus name reflects genome localisation (in kb) in strain Mu50 refseq NC_002758.</p>b<p>alternative names given in the literature.</p>c<p>from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033967#pone.0033967-Hardy1" target="_blank">[52]</a>.</p>d<p>from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033967#pone.0033967-Schouls1" target="_blank">[23]</a>.</p>e<p>from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033967#pone.0033967-Gilbert1" target="_blank">[53]</a>.</p>f<p>from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033967#pone.0033967-Sabat1" target="_blank">[54]</a>.</p>g<p>MLVA14_Orsay corresponds to the 14 panel 1-panel 2 loci in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033967#pone.0033967-Pourcel1" target="_blank">[24]</a>.</p>h<p>MLVA10_Orsay corresponds to the 10 panel 1 loci in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033967#pone.0033967-Pourcel1" target="_blank">[24]</a>.</p>i<p>MLVA8_Bilthoven corresponds to the 8 loci used by <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033967#pone.0033967-Schouls1" target="_blank">[23]</a>.</p

VNTRs and associated oligonucleotide primers.

<p>(*HGDI calculated on the 90 isolates from the HARMONY collection).</p>a<p>Multiplex PCR reaction.</p>b<p>Expected amplicon size for strain Mu50 RefSeq NC_002758 (by convention, corresponding number of repeated units for strain Mu50).</p>c<p>Observed allele size range: amplicons length (number of repeated units).</p

Electrophoregrams showing multiplex PCR amplicons resolved by capillary electrophoresis

<p><b>a. PCR1</b> ten dye-colored coamplified VNTR loci. <b>b. PCR2</b> six dye-colored coamplified VNTR loci.</p

ELIXIR Portugal - for BOD17.pdf

We provide an update on the implementation of the ELIXIR infrastructure and in particular <br>in its Portuguese Node (​ http://elixir-portugal.org​ ). ELIXIR is organized into five <br>platforms that support the bioinformatics community across Europe<br>(​ http://elixir-europe.org/platforms​ ): Tools, Data, Compute, Interoperability and Training.<br>Additionally four use cases are currently supported by those platforms (​ http://www.elixir-europe.org/use-cases​ ): Human data, Rare diseases, Marine Metagenomics and Plant Sciences.<br>The Portuguese Node contributes actively to three of ELIXIR’s platforms (Tools, Interoperability and Training) and two of its use cases (Plant Sciences and Marine Metagenomics). The Portuguese Node service delivery plan for 2017, includes six initial services (​ http://elixir-portugal.org/nodeservices​ ): Computing Services, CorkOakDB, YEASTRACT, Plant sRNA Portal, Plant Experimental Assay Ontology (PEAO) and the Gulbenkian Training Programme in BioInformatics. The service delivery plan is to be updated periodically to include those services that are deemed relevant to the BioInformatics community. The Portuguese Node of ELIXIR is deployed on a cloud computing infrastructure provided by the INCD (Infraestrutura Nacional de Computação Distribuída), as well as commercial cloud services providers.<br>One of the active developments is implementing a Breeding API (BrAPI, https://github.com/plantbreeding/API ) endpoint. The BrAPI is a RESTful API that provides a standard programmatic access to data from a plant phenotyping and genotyping databases in  a language agnostic way. BrAPI is an open source project that can be joined by anyone allowing<br>data providers to improve calls that will enhance their data supply. Our endpoint implementation is intended to support access to the Portuguese community’s curated datasets in the woody plants domain.<br>In addition to describing the current development status, we will discuss strategies to incorporate new services and extend the services offered to the Portuguese Bioinformatics community.<br

Source data for samples included in this study.

Listed are institute, specimen code, sample type, Ct value, sequencing platform, percent genome coverage at 10×, and accession numbers. (XLSX)</p