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      Immune-suppression by OsHV-1 viral infection causes fatal bacteraemia in Pacific oysters

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          Abstract

          Infectious diseases are mostly explored using reductionist approaches despite repeated evidence showing them to be strongly influenced by numerous interacting host and environmental factors. Many diseases with a complex aetiology therefore remain misunderstood. By developing a holistic approach to tackle the complexity of interactions, we decipher the complex intra-host interactions underlying Pacific oyster mortality syndrome affecting juveniles of Crassostrea gigas, the main oyster species exploited worldwide. Using experimental infections reproducing the natural route of infection and combining thorough molecular analyses of oyster families with contrasted susceptibilities, we demonstrate that the disease is caused by multiple infection with an initial and necessary step of infection of oyster haemocytes by the Ostreid herpesvirus OsHV-1 µVar. Viral replication leads to the host entering an immune-compromised state, evolving towards subsequent bacteraemia by opportunistic bacteria. We propose the application of our integrative approach to decipher other multifactorial diseases that affect non-model species worldwide.

          Abstract

          Pacific oyster mortality syndrome is a poorly understood cause of mortality in commercially important oyster species. Here, the authors use multiple infection experiments to show that the syndrome is caused by sequential infection by herpesvirus and opportunistic bacteria.

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          Most cited references 51

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          FLASH: fast length adjustment of short reads to improve genome assemblies.

          Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end libraries with a fragment size shorter than twice the read length provides an opportunity to generate much longer reads by overlapping and merging read pairs before assembling a genome. We present FLASH, a fast computational tool to extend the length of short reads by overlapping paired-end reads from fragment libraries that are sufficiently short. We tested the correctness of the tool on one million simulated read pairs, and we then applied it as a pre-processor for genome assemblies of Illumina reads from the bacterium Staphylococcus aureus and human chromosome 14. FLASH correctly extended and merged reads >99% of the time on simulated reads with an error rate of <1%. With adequately set parameters, FLASH correctly merged reads over 90% of the time even when the reads contained up to 5% errors. When FLASH was used to extend reads prior to assembly, the resulting assemblies had substantially greater N50 lengths for both contigs and scaffolds. The FLASH system is implemented in C and is freely available as open-source code at http://www.cbcb.umd.edu/software/flash. t.magoc@gmail.com.
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            Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

            Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
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              Manipulation of FASTQ data with Galaxy

              Summary: Here, we describe a tool suite that functions on all of the commonly known FASTQ format variants and provides a pipeline for manipulating next generation sequencing data taken from a sequencing machine all the way through the quality filtering steps. Availability and Implementation: This open-source toolset was implemented in Python and has been integrated into the online data analysis platform Galaxy (public web access: http://usegalaxy.org; download: http://getgalaxy.org). Two short movies that highlight the functionality of tools described in this manuscript as well as results from testing components of this tool suite against a set of previously published files are available at http://usegalaxy.org/u/dan/p/fastq Contact: james.taylor@emory.edu; anton@bx.psu.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                ygueguen@ifremer.fr
                mitta@univ-perp.fr
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                11 October 2018
                11 October 2018
                2018
                : 9
                Affiliations
                [1 ]ISNI 0000 0001 2097 0141, GRID grid.121334.6, IHPE, , Université de Montpellier, CNRS, Ifremer, Université de Perpignan Via Domitia, ; Place E. Bataillon, 34095 Montpellier, France
                [2 ]LEMAR UMR 6539, UBO/CNRS/IRD/Ifremer, 11 presqu’île du vivier, 29840 Argenton-en-Landunvez, France
                [3 ]ISNI 0000 0004 0641 9240, GRID grid.4825.b, Laboratoire de Génétique et Pathologie des Mollusques Marins, , Ifremer, ; Avenue du Mus de Loup, 17930 La Tremblade, France
                [4 ]ISNI 0000 0001 2097 0141, GRID grid.121334.6, Marine Biodiversity, Exploitation and Conservation (MARBEC), , Université de Montpellier, CNRS, IRD, Ifremer, Place E. Bataillon, ; 34095 Montpellier, France
                [5 ]CRCM, Comité de la Conchyliculture de Méditerranée, Quai Baptiste Guitard, 34140 Mèze, France
                [6 ]LEMAR UMR6539, CNRS/UBO/IRD/Ifremer, ZI pointe du diable, CS 10070, F-29280 Plouzané, France
                [7 ]ISNI 0000 0004 0641 9240, GRID grid.4825.b, Sorbonne Universités, UPMC Paris 06, CNRS, UMR 8227, LBI2M, , Ifremer, ; Station Biologique de Roscoff, CS 90074, F-29680 Roscoff, France
                Article
                6659
                10.1038/s41467-018-06659-3
                6182001
                30310074
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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