Complete genome sequence of <i>Bradyrhizobium</i> NP1, isolated from forest soil

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ABSTRACT

We report the complete genome sequence of Bradyrhizobium strain NP1. This bacterium was isolated from forest soil that had been subject to chronic warming. The genome of this novel isolated bacteria is presented as a single circular contig of 7,712,921 base pairs with 64.14% GC content.

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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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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan Parks, Michael Imelfort, Connor Skennerton … (2015)

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities.

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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Ryan Wick, Louise Judd, Claire Gorrie … (2017)

The Illumina DNA sequencing platform generates accurate but short reads, which can be used to produce accurate but fragmented genome assemblies. Pacific Biosciences and Oxford Nanopore Technologies DNA sequencing platforms generate long reads that can produce complete genome assemblies, but the sequencing is more expensive and error-prone. There is significant interest in combining data from these complementary sequencing technologies to generate more accurate “hybrid” assemblies. However, few tools exist that truly leverage the benefits of both types of data, namely the accuracy of short reads and the structural resolving power of long reads. Here we present Unicycler, a new tool for assembling bacterial genomes from a combination of short and long reads, which produces assemblies that are accurate, complete and cost-effective. Unicycler builds an initial assembly graph from short reads using the de novo assembler SPAdes and then simplifies the graph using information from short and long reads. Unicycler uses a novel semi-global aligner to align long reads to the assembly graph. Tests on both synthetic and real reads show Unicycler can assemble larger contigs with fewer misassemblies than other hybrid assemblers, even when long-read depth and accuracy are low. Unicycler is open source (GPLv3) and available at github.com/rrwick/Unicycler.

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Author and article information

Contributors

Maureen A. Morrow:

ORCID: https://orcid.org/0000-0001-9571-8805

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, collection): October 2023

Publication date (Electronic, pub): 21 September 2023

Publication date PMC-release: 21 September 2023

Volume: 12

Issue: 10

Electronic Location Identifier: e00585-23

Affiliations

[1 ]Department of Biology, State University of New York at New Paltz; , New Paltz, New York, USA

[2 ]Department of Microbiology, University of Massachusetts; , Amherst, Massachusetts, USA

Wellesley College; , Wellesley, Massachusetts, USA

Author notes

Address correspondence to Maureen A. Morrow, morrowm@ 123456newpaltz.edu

The authors declare no conflict of interest.

Author information

Trevor Fisher https://orcid.org/0009-0001-1982-9201

Francesca Durmazolu https://orcid.org/0009-0004-3914-587X

Kristen M. DeAngelis https://orcid.org/0000-0002-5585-4551

Maureen A. Morrow https://orcid.org/0000-0001-9571-8805

Article

Publisher ID: 00585-23 Publisher ID: MRA.00585-23

DOI: 10.1128/MRA.00585-23

PMC ID: 10586114

PubMed ID: 37732800

SO-VID: 38d1c72c-fc60-471b-9aa3-383cac573bcb

License:

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

History

Date received : 03 July 2023

Date accepted : 14 August 2023

Page count

supplementary-material: 0, authors: 4, Tables: 1, References: 10, Pages: 3, Words: 1357

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cover-date October 2023

Keywords: bradyrhizobium,forest soil

Data availability:

Keywords: bradyrhizobium, forest soil

Complete genome sequence of Bradyrhizobium NP1, isolated from forest soil

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ABSTRACT

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Genome Integrity

Most cited references 10

Trimmomatic: a flexible trimmer for Illumina sequence data

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

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