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      Comparative genomic analysis between Corynebacterium pseudotuberculosis strains isolated from buffalo

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          Abstract

          Corynebacterium pseudotuberculosis is a Gram-positive, pleomorphic, facultative intracellular pathogen that causes Oedematous Skin Disease (OSD) in buffalo. To better understand the pathogenic mechanisms of OSD, we performed a comparative genomic analysis of 11 strains of C. pseudotuberculosis isolated from different buffalo found to be infected in Egypt during an outbreak that occurred in 2008. Sixteen previously described pathogenicity islands (PiCp) were present in all of the new buffalo strains, but one of them, PiCp12, had an insertion that contained both a corynephage and a diphtheria toxin gene, both of which may play a role in the adaptation of C. pseudotuberculosis to this new host. Synteny analysis showed variations in the site of insertion of the corynephage during the same outbreak. A gene functional comparison showed the presence of a nitrate reductase operon that included genes involved in molybdenum cofactor biosynthesis, which is necessary for a positive nitrate reductase phenotype and is a possible adaptation for intracellular survival. Genomes from the buffalo strains also had fusions in minor pilin genes in the spaA and spaD gene cluster ( spaCX and spaYEF), which could suggest either an adaptation to this particular host, or mutation events in the immediate ancestor before this particular epidemic. A phylogenomic analysis confirmed a clear separation between the Ovis and Equi biovars, but also showed what appears to be a clustering by host species within the Equi strains.

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          The microbial pan-genome.

          A decade after the beginning of the genomic era, the question of how genomics can describe a bacterial species has not been fully addressed. Experimental data have shown that in some species new genes are discovered even after sequencing the genomes of several strains. Mathematical modeling predicts that new genes will be discovered even after sequencing hundreds of genomes per species. Therefore, a bacterial species can be described by its pan-genome, which is composed of a "core genome" containing genes present in all strains, and a "dispensable genome" containing genes present in two or more strains and genes unique to single strains. Given that the number of unique genes is vast, the pan-genome of a bacterial species might be orders of magnitude larger than any single genome.
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            Is Open Access

            Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

            Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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              CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes

              Recent developments in sequencing technologies have given the opportunity to sequence many bacterial genomes with limited cost and labor, compared to previous techniques. However, a limiting step of genome sequencing is the finishing process, needed to infer the relative position of each contig and close sequencing gaps. An additional degree of complexity is given by bacterial species harboring more than one replicon, which are not contemplated by the currently available programs. The availability of a large number of bacterial genomes allows geneticists to use complete genomes (possibly from the same species) as templates for contigs mapping. Here we present CONTIGuator, a software tool for contigs mapping over a reference genome which allows the visualization of a map of contigs, underlining loss and/or gain of genetic elements and permitting to finish multipartite genomes. The functionality of CONTIGuator was tested using four genomes, demonstrating its improved performances compared to currently available programs. Our approach appears efficient, with a clear visualization, allowing the user to perform comparative structural genomics analysis on draft genomes. CONTIGuator is a Python script for Linux environments and can be used on normal desktop machines and can be downloaded from http://contiguator.sourceforge.net.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                26 April 2017
                2017
                : 12
                : 4
                : e0176347
                Affiliations
                [1 ]Departament of General Biology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
                [2 ]Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, United States of America
                [3 ]AQUACEN, National Reference Laboratory for Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
                [4 ]Center of Genomic and System Biology, Federal University of Pará, Belém, Pará, Brazil
                [5 ]Department of Microbiology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
                Defense Threat Reduction Agency, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                • Conceptualization: MVCV HF RR LCG FLP FAD SAKS MS AS ARW VA.

                • Data curation: ARW VA.

                • Formal analysis: MVCV ARW VA.

                • Funding acquisition: VA.

                • Methodology: MVCV HF RR FAD AS ARW VA.

                • Project administration: ARW VA.

                • Resources: HF SAKS MS ARW VA.

                • Supervision: ARW VA.

                • Writing – original draft: MVCV ARW VA.

                • Writing – review & editing: MVCV HF RR LCG FLP FAD SAKS MS AS ARW VA.

                Author information
                http://orcid.org/0000-0002-7017-6437
                Article
                PONE-D-16-43828
                10.1371/journal.pone.0176347
                5406005
                28445543
                e7f9a45a-2911-4aa9-a05d-1fb7c763a6f0

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 21 November 2016
                : 10 April 2017
                Page count
                Figures: 11, Tables: 3, Pages: 24
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100003593, Conselho Nacional de Desenvolvimento Científico e Tecnológico;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100004901, Fundação de Amparo à Pesquisa do Estado de Minas Gerais;
                Funded by: funder-id http://dx.doi.org/10.13039/501100002322, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior;
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: HHSN272201400027C
                Award Recipient :
                This work was supported by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Ministério da Pesca e Agricultura. A.R. Wattam was supported in part by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract no. HHSN272201400027C.
                Categories
                Research Article
                Research and Analysis Methods
                Database and Informatics Methods
                Biological Databases
                Genomic Databases
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genomic Databases
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Genomic Databases
                Biology and Life Sciences
                Computational Biology
                Comparative Genomics
                Biology and Life Sciences
                Genetics
                Genomics
                Comparative Genomics
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Biology and Life Sciences
                Organisms
                Bacteria
                Corynebacteria
                Physical Sciences
                Chemistry
                Chemical Compounds
                Nitrates
                Biology and Life Sciences
                Toxicology
                Toxic Agents
                Toxins
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Toxicology
                Toxic Agents
                Toxins
                Biology and Life Sciences
                Organisms
                Animals
                Vertebrates
                Amniotes
                Mammals
                Equines
                Horses
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genome Annotation
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Genome Annotation
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                All relevant data are within the paper and its Supporting Information files.

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