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      Draft Genome Sequences of Five Environmental Bacterial Isolates That Degrade Polyethylene Terephthalate Plastic

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          Abstract

          Here, we report the annotated draft genome sequences of three Pseudomonas spp. and two Bacillus spp. that, as consortia, degrade polyethylene terephthalate plastic. Improved microbial degradation of plastic waste could help reduce the billions of metric tons of these materials that currently exist in our environment.

          ABSTRACT

          Here, we report the annotated draft genome sequences of three Pseudomonas spp. and two Bacillus spp. that, as consortia, degrade polyethylene terephthalate plastic. Improved microbial degradation of plastic waste could help reduce the billions of metric tons of these materials that currently exist in our environment.

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          Most cited references 7

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

            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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              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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                Author and article information

                Contributors
                Role: Editor
                Journal
                Microbiol Resour Announc
                Microbiol Resour Announc
                ga
                mra
                MRA
                Microbiology Resource Announcements
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2576-098X
                20 June 2019
                June 2019
                : 8
                : 25
                Affiliations
                [a ]Department of Biology, Willamette University, Salem, Oregon, USA
                [b ]Department of Biology, Reed College, Portland, Oregon, USA
                Indiana University, Bloomington
                Author notes
                Address correspondence to Rosa León-Zayas, rleonzayas@ 123456willamette.edu .

                Citation León-Zayas R, Roberts C, Vague M, Mellies JL. 2019. Draft genome sequences of five environmental bacterial isolates that degrade polyethylene terephthalate plastic. Microbiol Resour Announc 8:e00237-19. https://doi.org/10.1128/MRA.00237-19.

                Article
                MRA00237-19
                10.1128/MRA.00237-19
                6588364
                31221643
                Copyright © 2019 León-Zayas et al.

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

                Page count
                Figures: 1, Tables: 1, Equations: 0, References: 7, Pages: 3, Words: 1683
                Product
                Funding
                Funded by: M.J. Murdock Charitable Trust (Murdock Trust), https://doi.org/10.13039/100000937;
                Award ID: 2016189:MNL:11/17/2016
                Award Recipient :
                Categories
                Genome Sequences
                Custom metadata
                June 2019

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