Complete Genome and Partial Megaplasmid Sequences of Mycobacterium pseudoshottsii Strain NJB1907-Z4, Isolated from an Aquarium-Reared Japanese Sardine (Sardinops melanostictus) in Japan

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ABSTRACT

Mycobacterium pseudoshottsii, a slow-growing nontuberculous mycobacterium, has been isolated from wild and cultured fish. We report here the complete genome and partial megaplasmid sequences of a strain isolated from an aquarium-reared Japanese sardine ( Sardinops melanostictus) in Japan, M. pseudoshottsii NJB1907-Z4.

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Most cited references 17

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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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fastp: an ultra-fast all-in-one FASTQ preprocessor

Shifu Chen, Yanqing Zhou, Yaru Chen … (2018)

Abstract Motivation Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2–5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.

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Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

Bruce Walker, Thomas Abeel, Terrance Shea … (2014)

Advances in modern sequencing technologies allow us to generate sufficient data to analyze hundreds of bacterial genomes from a single machine in a single day. This potential for sequencing massive numbers of genomes calls for fully automated methods to produce high-quality assemblies and variant calls. We introduce Pilon, a fully automated, all-in-one tool for correcting draft assemblies and calling sequence variants of multiple sizes, including very large insertions and deletions. Pilon works with many types of sequence data, but is particularly strong when supplied with paired end data from two Illumina libraries with small e.g., 180 bp and large e.g., 3–5 Kb inserts. Pilon significantly improves draft genome assemblies by correcting bases, fixing mis-assemblies and filling gaps. For both haploid and diploid genomes, Pilon produces more contiguous genomes with fewer errors, enabling identification of more biologically relevant genes. Furthermore, Pilon identifies small variants with high accuracy as compared to state-of-the-art tools and is unique in its ability to accurately identify large sequence variants including duplications and resolve large insertions. Pilon is being used to improve the assemblies of thousands of new genomes and to identify variants from thousands of clinically relevant bacterial strains. Pilon is freely available as open source software.

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Author and article information

Contributors

Takeshi Komine:

ORCID: https://orcid.org/0000-0002-5962-8295

Frank J. Stewart: 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): 9 November 2022

Publication date (Electronic, collection): December 2022

Publication date PMC-release: 9 November 2022

Volume: 11

Issue: 12

Electronic Location Identifier: e00785-22

Affiliations

[a ] Laboratory of Aquatic Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan

[b ] Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashi-Murayama, Tokyo, Japan

Montana State University

Author notes

The authors declare no conflict of interest.

Author information

Takeshi Komine https://orcid.org/0000-0002-5962-8295

Hanako Fukano https://orcid.org/0000-0003-2143-1160

Mitsunori Yoshida https://orcid.org/0000-0003-4061-6910

Article

Publisher ID: 00785-22 Publisher ID: mra.00785-22

DOI: 10.1128/mra.00785-22

PMC ID: 9753711

PubMed ID: 36350130

SO-VID: 820d531d-bbef-4c95-b999-d97940afc02a

License:

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

History

Date received : 31 July 2022

Date accepted : 28 October 2022

Page count

Figures: 1, Tables: 0, Equations: 0, References: 17, Pages: 3, Words: 1429

Funding

Funded by: Japan Agency for Medical Research and Development (AMED), FundRef https://doi.org/10.13039/100009619;

Award ID: JP20fk0108064

Award ID: JP20fk0108075

Award ID: JP21jm0510004

Award ID: JP22fk0108093

Award ID: JP22fk0108129

Award ID: JP22fk0108608

Award ID: JP22gm1610003

Award ID: JP22wm0125007

Award ID: JP22wm0225004

Award ID: JP22wm0225022

Award ID: JP22wm0325003

Award ID: JP22wm0325054

Award Recipient : Yoshihiko Hoshino

Funded by: Japan Agency for Medical Research and Development (AMED), FundRef https://doi.org/10.13039/100009619;

Award ID: 22wm0225022j0001

Award Recipient : Mitsunori Yoshida

Funded by: Japan Agency for Medical Research and Development (AMED), FundRef https://doi.org/10.13039/100009619;

Award ID: JP22wm0325054

Award Recipient : Hanako Fukano

Funded by: MEXT | Japan Society for the Promotion of Science (JSPS), FundRef https://doi.org/10.13039/501100001691;

Award ID: JP19KK0217

Award Recipient : Yoshihiko Hoshino

Funded by: MEXT | Japan Society for the Promotion of Science (JSPS), FundRef https://doi.org/10.13039/501100001691;

Award ID: JP18K15966

Award ID: JP22K16382

Award Recipient : Hanako Fukano

Funded by: MEXT | Japan Society for the Promotion of Science (JSPS), FundRef https://doi.org/10.13039/501100001691;

Award ID: JP20H02282

Award Recipient : Yoshihiko Hoshino

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cover-date December 2022

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Retrospective identification of pathogenic mycobacterial species in fish: Mycobacterium pseudoshottsii YM-3, isolated from a yellowtail fish in 1986 in Kochi, Japan
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Complete Genome and Partial Megaplasmid Sequences of Mycobacterium pseudoshottsii Strain NJB1907-Z4, Isolated from an Aquarium-Reared Japanese Sardine (Sardinops melanostictus) in Japan

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ABSTRACT

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Genome Integrity

Most cited references 17

The Sequence Alignment/Map format and SAMtools

fastp: an ultra-fast all-in-one FASTQ preprocessor

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

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