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      Identification of a novel archaea virus, detected in hydrocarbon polluted Hungarian and Canadian samples

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          Abstract

          Metagenomics is a helpful tool for the analysis of unculturable organisms and viruses. Viruses that target bacteria and archaea play important roles in the microbial diversity of various ecosystems. Here we show that Methanosarcina virus MV (MetMV), the second Methanosarcina sp. virus with a completely determined genome, is characteristic of hydrocarbon pollution in environmental (soil and water) samples. It was highly abundant in Hungarian hydrocarbon polluted samples and its genome was also present in the NCBI SRA database containing reads from hydrocarbon polluted samples collected in Canada, indicating the stability of its niche and the marker feature of this virus. MetMV, as the only currently identified marker virus for pollution in environmental samples, could contribute to the understanding of the complicated network of prokaryotes and their viruses driving the decomposition of environmental pollutants.

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          Most cited references23

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          The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

          Background In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element) are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. Description We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. Conclusion It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the dictionary creator. CRISPRdb is accessible at
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            SAMBLASTER: fast duplicate marking and structural variant read extraction

            Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times. Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results. Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster. Contact: imh4y@virginia.edu
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              Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli.

              The role of historical contingency in evolution has been much debated, but rarely tested. Twelve initially identical populations of Escherichia coli were founded in 1988 to investigate this issue. They have since evolved in a glucose-limited medium that also contains citrate, which E. coli cannot use as a carbon source under oxic conditions. No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population. We tested these hypotheses in experiments that "replayed" evolution from different points in that population's history. We observed no Cit+ mutants among 8.4 x 10(12) ancestral cells, nor among 9 x 10(12) cells from 60 clones sampled in the first 15,000 generations. However, we observed a significantly greater tendency for later clones to evolve Cit+, indicating that some potentiating mutation arose by 20,000 generations. This potentiating change increased the mutation rate to Cit+ but did not cause generalized hypermutability. Thus, the evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.
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                Author and article information

                Contributors
                Role: Data curationRole: InvestigationRole: SoftwareRole: Visualization
                Role: InvestigationRole: Resources
                Role: Investigation
                Role: InvestigationRole: Resources
                Role: Investigation
                Role: ConceptualizationRole: Funding acquisitionRole: Resources
                Role: Investigation
                Role: ConceptualizationRole: MethodologyRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                17 April 2020
                2020
                : 15
                : 4
                : e0231864
                Affiliations
                [1 ] Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Pécs, Hungary
                [2 ] Biocentrum Ltd., Gyongyosoroszi, Hungary
                [3 ] Institute of Medical Microbiology and Immunology, University of Pécs, Pécs, Hungary
                [4 ] Department of Biotechnology, University of Szeged, Szeged, Hungary
                [5 ] Institute of Biophysics, Biological Research Center, Szeged, Hungary
                University of Trento, ITALY
                Author notes

                Competing Interests: J. Molnár, Á. L. Kovács, I. K. Nagy and T. Kovács are employees of Enviroinvest Corp., B. Magyar is employee of Biocentrum Ltd. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

                Author information
                http://orcid.org/0000-0002-9399-7406
                http://orcid.org/0000-0001-6647-8136
                Article
                PONE-D-19-31815
                10.1371/journal.pone.0231864
                7164591
                32302368
                4ae8f32d-4c5b-40e6-83ef-774040bdd3e7
                © 2020 Molnár et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 18 November 2019
                : 2 April 2020
                Page count
                Figures: 1, Tables: 2, Pages: 10
                Funding
                This work was funded by the Norway Grants (project: HU09-0044-A1-2013) and by the Hungarian Government (project: KFI-16-1-2016-0150246 and 2019-1.1.1-PIACIKFI- 2019-00184). Enviroinvest Corp. and Biocentrum Ltd provided support in the form of salaries for authors J.M., Á.L.K., I.K.N., T.K., B.M., but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.
                Categories
                Research Article
                Biology and Life Sciences
                Genetics
                Genomics
                Microbial Genomics
                Viral Genomics
                Biology and Life Sciences
                Microbiology
                Microbial Genomics
                Viral Genomics
                Biology and Life Sciences
                Microbiology
                Virology
                Viral Genomics
                Biology and Life Sciences
                Genetics
                Genomics
                Metagenomics
                Research and Analysis Methods
                Database and Informatics Methods
                Biological Databases
                Sequence Databases
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Databases
                Physical Sciences
                Chemistry
                Chemical Compounds
                Hydrocarbons
                Ecology and Environmental Sciences
                Pollution
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Genomic Libraries
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Genomic Libraries
                Biology and Life Sciences
                Organisms
                Archaea
                Custom metadata
                The complete genome sequence of MetMV has been submitted to GenBank and assigned accession number MK170447. It has been released now. Metagenomes were uploaded to the European Bioinformatics Institute (EBI). Accession numbers are: SAMEA4368876, SAMEA4368878, SAMEA4368881, SAMEA4373315, SAMEA4373317, SAMEA4373321, SAMEA4373324, SAMEA4373325, SAMEA4373328, SAMEA4373332, SAMEA4373334 and SAMEA4373336.

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