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      Draft Genome Sequence of Streptomyces mexicanus Strain Q0842, Isolated from Human Skin

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          Abstract

          In 2003, Streptomyces mexicanus was reported as a novel xylanolytic bacterial species isolated from soil; a partial genome sequence was determined. In 2019, a strain from the same species was isolated from a hand skin swab sample from a healthy French woman. Genome sequencing revealed an 8,011,832-bp sequence with a GC content of 72.5%.

          ABSTRACT

          In 2003, Streptomyces mexicanus was reported as a novel xylanolytic bacterial species isolated from soil; a partial genome sequence was determined. In 2019, a strain from the same species was isolated from a hand skin swab sample from a healthy French woman. Genome sequencing revealed an 8,011,832-bp sequence with a GC content of 72.5%.

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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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            SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

            Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)
            The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.
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              NCBI prokaryotic genome annotation pipeline

              Tatiana Tatusova, Michael DiCuccio, Azat Badretdin … (2016)
              Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/.
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                Author and article information

                Contributors
                David Rasko: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                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): 29 October 2020
                Publication date Collection: October 2020
                Volume: 9
                Issue: 44
                Electronic Location Identifier: e01527-19
                Affiliations
                [a ]Aix Marseille Université, IRD, AP-HM, MEФI, Marseille, France
                [b ]IHU-Méditerranée Infection, Marseille, France
                University of Maryland School of Medicine
                Author notes
                Address correspondence to Bernard La Scola, bernard.la-scola@ 123456univ-amu.fr .

                Citation Boxberger M, Ben Khedher M, Levasseur A, La Scola B. 2020. Draft genome sequence of Streptomyces mexicanus strain Q0842, isolated from human skin. Microbiol Resour Announc 9:e01527-19. https://doi.org/10.1128/MRA.01527-19.

                Author information
                https://orcid.org/0000-0001-8006-7704
                Article
                Publisher ID: MRA01527-19
                DOI: 10.1128/MRA.01527-19
                PMC ID: 7595954
                PubMed ID: 33122417
                SO-VID: d15bf57e-de03-4e35-8f6c-276570732086
                Copyright © Copyright © 2020 Boxberger 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 : 13 December 2019
                Date accepted : 4 October 2020
                Page count
                Figures: 1, Tables: 0, Equations: 0, References: 11, Pages: 3, Words: 1693
                Funding
                Funded by: Agence Nationale de la Recherche (ANR), https://doi.org/10.13039/501100001665;
                Award ID: ANR-10-IAHU-03
                Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Funded by: EC | European Regional Development Fund (ERDF), https://doi.org/10.13039/501100008530;
                Award ID: PRIMI
                Award Recipient : Award Recipient : Award Recipient : Award Recipient :
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date October 2020

                Data availability:

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