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      Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

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          Abstract

          The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

          Abstract

          A comparative genomics study of anaerobic methanotrophic (ANME) archaea reveals the genetic "parts list" associated with the repeated evolutionary transition between methanogenic and methanotrophic metabolism in the archaeal domain of life.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

            Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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              The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

              SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: Writing – review & editing
                Role: Data curationRole: InvestigationRole: Methodology
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: Data curationRole: Methodology
                Role: Data curationRole: Formal analysisRole: Funding acquisitionRole: MethodologyRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: Writing – review & editing
                Role: Data curationRole: Funding acquisitionRole: Supervision
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Academic Editor
                Journal
                PLoS Biol
                PLoS Biol
                plos
                PLoS Biology
                Public Library of Science (San Francisco, CA USA )
                1544-9173
                1545-7885
                5 January 2022
                January 2022
                5 January 2022
                : 20
                : 1
                : e3001508
                Affiliations
                [1 ] Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, United States of America
                [2 ] Max-Planck Institute for Marine Microbiology, Bremen, Germany
                [3 ] MARUM, Center for Marine Environmental Science, and Department of Geosciences, University of Bremen, Bremen, Germany
                [4 ] Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
                [5 ] Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia, Canada
                [6 ] US Department of Energy Joint Genome Institute, Berkeley, California, United States of America
                [7 ] School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
                [8 ] Department of Microbiology & Immunology, University of British Columbia, British Columbia, Canada
                [9 ] Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada
                [10 ] ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
                [11 ] Life Sciences Institute, University of British Columbia, British Columbia, Canada
                [12 ] Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
                School of Life Sciences and Biotechnology, State Key Laboratory of Ocean Engineering, Shanghai Jiaotong University, CHINA
                Author notes

                S.J.H. is a co-founder of Koonkie Inc., a bioinformatics consulting company that designs and provides scalable algorithmic and data analytics solutions in the cloud.

                [¤a]

                Current address: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America

                [¤b]

                Current address: Department of Chemistry and Biochemistry, Thermal Biology Institute, and Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America

                Author information
                https://orcid.org/0000-0003-0700-9350
                https://orcid.org/0000-0003-1320-4873
                https://orcid.org/0000-0002-2361-5935
                https://orcid.org/0000-0002-5489-3444
                https://orcid.org/0000-0002-4758-7369
                https://orcid.org/0000-0002-9485-5637
                https://orcid.org/0000-0002-4889-6876
                https://orcid.org/0000-0001-8559-9427
                https://orcid.org/0000-0002-6819-373X
                https://orcid.org/0000-0003-2117-4176
                https://orcid.org/0000-0002-5374-6178
                Article
                PBIOLOGY-D-21-02296
                10.1371/journal.pbio.3001508
                9012536
                34986141
                f01798b3-8466-4241-909b-17dfe86b4e4a

                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
                : 27 August 2021
                : 8 December 2021
                Page count
                Figures: 19, Tables: 1, Pages: 71
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100006132, Office of Science;
                Award ID: DE-AC02-05CH11231
                Funded by: funder-id http://dx.doi.org/10.13039/100000001, National Science Foundation;
                Award ID: OCE- 1536702/1536405
                Award Recipient :
                Funded by: Max Planck Society
                Award Recipient :
                Funded by: DFG Leibniz Grant
                Award Recipient :
                Funded by: Joint Genome Institute Director Discretionary Project Award
                Award Recipient :
                The work conducted by the U.S. Department of Energy Joint Genome Institute [ https://jgi.doe.gov/], a Department of Energy Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. Funding for this study was received by the DFG Leibniz grant [ https://www.dfg.de/en/funded_projects/prizewinners/leibniz_prize/index.html] and by the Max Planck Society [ https://www.mpg.de/] to A.B. Genomes of BONCAT-FACS sorted ANME-consortia were generated via a Joint Genome Institute Director Discretionary Project Award to R.H. and V.J.O. [ https://jgi.doe.gov/]. Work with the fosmid libraries was performed under the auspices of the Natural Sciences and Engineering Research Council of Canada, Genome British Columbia, the Canada Foundation for Innovation, Compute/Calcul Canada, and the U.S. Department of Energy Joint Genome Institute supported by the Office of Science of U.S. Department of Energy Contract DE-AC02-05CH11231 to S.H. The National Science Foundation provided support for the Lost City cruise and metagenome sequencing to W.B. (OCE- 1536702/1536405). [ https://www.nsf.gov/]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Genetics
                Genomics
                Biology and Life Sciences
                Organisms
                Archaea
                Methanogens
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Phylogenetic Analysis
                Biology and Life Sciences
                Organisms
                Archaea
                Physical Sciences
                Chemistry
                Chemical Reactions
                Oxidation
                Physical Sciences
                Chemistry
                Chemical Compounds
                Methane
                Biology and Life Sciences
                Biochemistry
                Proteins
                Protein Domains
                Biology and Life Sciences
                Evolutionary Biology
                Evolutionary Systematics
                Phylogenetics
                Biology and Life Sciences
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Computer and Information Sciences
                Data Management
                Taxonomy
                Evolutionary Systematics
                Phylogenetics
                Custom metadata
                vor-update-to-uncorrected-proof
                2022-04-15
                The novel genomes reported in this study are all available in the NCBI database. The accession numbers for these genomes are provided in Table 1. Data products such as protein alignments, phylogenetic tree files, and manual gene annotation lists are provided in the Supporting Information files.

                Life sciences
                Life sciences

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