Complete Genome Sequence of <i>Desulfomicrobium</i> sp. Strain ZS1 from Zodletone Spring in Oklahoma, USA

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ABSTRACT

Desulfomicrobium sp. strain ZS1 is an obligate anaerobic, sulfate-reducing member of the Desulfobacterota from Zodletone Spring, an anoxic sulfide-rich spring in southwestern Oklahoma. Its complete genome was sequenced using a combination of Illumina and Oxford Nanopore platforms and encodes 3,364 proteins and 81 RNAs on a single chromosome.

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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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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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Assembly of long, error-prone reads using repeat graphs

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin … (2019)

Accurate genome assembly is hampered by repetitive regions. Although long single molecule sequencing reads are better able to resolve genomic repeats than short-read data, most long-read assembly algorithms do not provide the repeat characterization necessary for producing optimal assemblies. Here, we present Flye, a long-read assembly algorithm that generates arbitrary paths in an unknown repeat graph, called disjointigs, and constructs an accurate repeat graph from these error-riddled disjointigs. We benchmark Flye against five state-of-the-art assemblers and show that it generates better or comparable assemblies, while being an order of magnitude faster. Flye nearly doubled the contiguity of the human genome assembly (as measured by the NGA50 assembly quality metric) compared with existing assemblers.

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Author and article information

Contributors

Mircea Podar:

ORCID: https://orcid.org/0000-0003-2776-0205

Vanja Klepac-Ceraj: 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, pub): 13 April 2023

Publication date (Electronic, collection): May 2023

Publication date PMC-release: 13 April 2023

Volume: 12

Issue: 5

Electronic Location Identifier: e00145-23

Affiliations

[a ] Department of Microbiology, University of Tennessee Knoxville, Knoxville, Tennessee, USA

[b ] Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA

[c ] Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA

Wellesley College

Author notes

The authors declare no conflict of interest.

Author information

Noha H. Youssef https://orcid.org/0000-0001-9159-3785

Mircea Podar https://orcid.org/0000-0003-2776-0205

Article

Publisher ID: 00145-23 Publisher ID: mra.00145-23

DOI: 10.1128/mra.00145-23

PMC ID: 10190684

PubMed ID: 37052391

SO-VID: 4c1e7a38-429e-4cd0-9496-f00632f637ab

License:

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

History

Date received : 25 February 2023

Date accepted : 28 March 2023

Page count

Figures: 1, Tables: 0, Equations: 0, References: 15, Pages: 3, Words: 1453

Funding

Funded by: National Science Foundation (NSF), FundRef https://doi.org/10.13039/100000001;

Award ID: 2016371

Award Recipient : Mircea Podar Award Recipient : Sayali A. Mulay

Funded by: National Science Foundation (NSF), FundRef https://doi.org/10.13039/100000001;

Award ID: 2016423

Award Recipient : Mostafa S. Elshahed Award Recipient : Noha H. Youssef Award Recipient : C. Ryan Hahn

Complete Genome Sequence of Desulfomicrobium sp. Strain ZS1 from Zodletone Spring in Oklahoma, USA

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Genome Integrity

Most cited references 15

Trimmomatic: a flexible trimmer for Illumina sequence data

NCBI prokaryotic genome annotation pipeline

Assembly of long, error-prone reads using repeat graphs

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