Draft genome sequences of representative Paenibacillus polymyxa, Bacillus cereus, Fictibacillus sp., and Brevibacillus agri strains isolated from Amazonian dark earth

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ABSTRACT

Here, we report 10 distinct bacterial genomes from Amazonian dark earths, including six identified as Paenibacillus polymyxa, while the remaining four were unique representatives of Paenibacillus vini, Bacillus cereus, Brevibacillus agri, and Fictibacillus sp., respectively. Each strain exhibited antagonistic activity against Fusarium oxysporum, underscoring their potential as sustainable agriculture resources.

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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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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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QUAST: quality assessment tool for genome assemblies.

Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi … (2013)

Limitations of genome sequencing techniques have led to dozens of assembly algorithms, none of which is perfect. A number of methods for comparing assemblers have been developed, but none is yet a recognized benchmark. Further, most existing methods for comparing assemblies are only applicable to new assemblies of finished genomes; the problem of evaluating assemblies of previously unsequenced species has not been adequately considered. Here, we present QUAST-a quality assessment tool for evaluating and comparing genome assemblies. This tool improves on leading assembly comparison software with new ideas and quality metrics. QUAST can evaluate assemblies both with a reference genome, as well as without a reference. QUAST produces many reports, summary tables and plots to help scientists in their research and in their publications. In this study, we used QUAST to compare several genome assemblers on three datasets. QUAST tables and plots for all of them are available in the Supplementary Material, and interactive versions of these reports are on the QUAST website. http://bioinf.spbau.ru/quast . Supplementary data are available at Bioinformatics online.

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Author and article information

Contributors

Thierry Alexandre Pellegrinetti: Role: ConceptualizationRole: Data curationRole: Formal analysisRole: MethodologyRole: Writing – original draftRole: Writing – review and editing

Izadora De Cássia Mesquita da Cunha: Role: InvestigationRole: Methodology

Miriam Gonçalves de Chaves: Role: InvestigationRole: Methodology

Anderson Santos de Freitas: Role: Formal analysis

Ana Vitória Reina da Silva: Role: Investigation

Siu Mui Tsai:

ORCID: https://orcid.org/0000-0002-3733-6312

Role: Funding acquisitionRole: Supervision

Lucas William Mendes:

ORCID: https://orcid.org/0000-0003-0980-7006

Simon Roux: 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): November 2023

Publication date (Electronic, pub): 09 October 2023

Publication date PMC-release: 09 October 2023

Volume: 12

Issue: 11

Electronic Location Identifier: e00574-23

Affiliations

[1 ] Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo; , Piracicaba, Brazil

[2 ] Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo; , Piracicaba, Brazil

DOE Joint Genome Institute; , Berkeley, California, USA

Author notes

Address correspondence to Lucas William Mendes, lwmendes@ 123456cena.usp.br

The authors declare no conflict of interest.

Author information

Siu Mui Tsai https://orcid.org/0000-0002-3733-6312

Lucas William Mendes https://orcid.org/0000-0003-0980-7006

Article

Publisher ID: 00574-23 Publisher ID: MRA.00574-23

DOI: 10.1128/MRA.00574-23

PMC ID: 10652921

PubMed ID: 37811974

SO-VID: 9c8cf9d7-cf93-4e87-a45c-565603becd09

License:

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

History

Date received : 07 July 2023

Date accepted : 26 July 2023

Page count

supplementary-material: 0, authors: 7, Tables: 1, References: 13, Pages: 4, Words: 1707

Funding

Funded by: Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP);

Award ID: 2014/03217-3, 2015/00251-9

Award Recipient : Lucas William Mendes

Funded by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES);

Award ID: 88887.185941/2018-00

Award Recipient : Lucas William Mendes

Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq);

Award ID: 408191/2018-0, 307670/2021-0

Award Recipient : Lucas William Mendes

Funded by: PRPI-USP;

Award ID: 22.1.08498.01.0

Award Recipient : Thierry Alexandre Pellegrinetti

Custom metadata

cover-date November 2023

Keywords: plant-microbe interaction,rhizosphere-inhabiting microbes,fusarium,terra preta

Data availability:

Keywords: plant-microbe interaction, rhizosphere-inhabiting microbes, fusarium, terra preta

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The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype
Authors: Izadora de Cássia Mesquita da Cunha, Ana Vitória Reina da Silva, Eduardo Henrique Marcandalli Boleta …

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Draft genome sequences of representative Paenibacillus polymyxa, Bacillus cereus, Fictibacillus sp., and Brevibacillus agri strains isolated from Amazonian dark earth

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ABSTRACT

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Genome Integrity

Most cited references 12

The Sequence Alignment/Map format and SAMtools

Fast and accurate short read alignment with Burrows–Wheeler transform

QUAST: quality assessment tool for genome assemblies.

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