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      Aureococcus anophagefferens strain CCMP1851: draft genome of a second Kratosvirus quantuckense-susceptible host strain for an emerging host–giant virus model system

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          ABSTRACT

          Here, we report the draft genome of Aureococcus anophagefferens strain CCMP1851, which is susceptible to the virus Kratosvirus quantuckense. CCMP1851 complements an available genome for a virus-resistant strain (CCMP1850) isolated from the same bloom. Future studies can now use this genome to examine genetic hints of virus resistance and susceptibility.

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)
          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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            Prokka: rapid prokaryotic genome annotation.

            T Seemann (2014)
            The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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              IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

              Bui Minh, Heiko Schmidt, Olga Chernomor … (2020)
              Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
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                Author and article information

                Contributors
                Steven W. Wilhelm:
                ORCID: https://orcid.org/0000-0001-6283-8077
                André O. Hudson: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (publisher-id): mra
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic, collection): June 2024
                Publication date (Electronic, pub): 03 May 2024
                Publication date PMC-release: 03 May 2024
                Volume: 13
                Issue: 6
                Electronic Location Identifier: e00292-24
                Affiliations
                [1 ]Department of Microbiology, University of Tennessee; , Knoxville, Tennessee, USA
                Rochester Institute of Technology; , Rochester, New York, USA
                Author notes
                Address correspondence to Steven W. Wilhelm, wilhelm@ 123456utk.edu

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0002-8668-4989
                https://orcid.org/0000-0002-7194-6819
                https://orcid.org/0000-0001-6283-8077
                Article
                Publisher ID: 00292-24 Publisher ID: mra.00292-24
                DOI: 10.1128/mra.00292-24
                PMC ID: 11237714
                PubMed ID: 38700347
                SO-VID: 35b7c769-3171-4126-947a-e0561a461a37
                Copyright © Copyright © 2024 Chase et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 22 March 2024
                Date accepted : 22 April 2024
                Page count
                supplementary-material: 0, authors: 4, Figures: 1, Tables: 1, References: 23, Pages: 3, Words: 1734
                Funding
                Funded by: Simons Foundation (SF);
                Award ID: 735077
                Award Recipient :
                Funded by: National Science Foundation (NSF);
                Award ID: 1922958
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Compound subject: ecology, Ecology
                Custom metadata
                cover-date June 2024

                Keywords: harmful algal blooms,nucleocytoviricota,brown tides,giant viruses,pelagophyceae
                Data availability:
                Keywords: harmful algal blooms, nucleocytoviricota, brown tides, giant viruses, pelagophyceae

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