Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer <i>Adineta vaga</i>

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Abstract

High-quality genome assembly of ancient asexual rotifer reveals homologous chromosomes that frequently recombine.

Abstract

Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g., chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success.

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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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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 gapped-read alignment with Bowtie 2.

Ben Langmead, Steven L Salzberg (2022)

As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

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Author and article information

Contributors

Paul Simion:

ORCID: https://orcid.org/0000-0002-6667-3297

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Jitendra Narayan:

ORCID: https://orcid.org/0000-0002-2065-2861

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Antoine Houtain:

ORCID: https://orcid.org/0000-0002-6489-6868

Alessandro Derzelle: Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Validation

Lyam Baudry:

ORCID: https://orcid.org/0000-0002-9283-674X

Role: Formal analysisRole: MethodologyRole: SoftwareRole: Writing - original draft

Emilien Nicolas: Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - review & editing

Rohan Arora: Role: Investigation

Marie Cariou:

ORCID: https://orcid.org/0000-0002-2544-579X

Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Software

Corinne Cruaud:

ORCID: https://orcid.org/0000-0002-4752-7278

Role: Resources

Florence Rodriguez Gaudray: Role: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: Writing - original draft

Clément Gilbert:

ORCID: https://orcid.org/0000-0002-2131-7467

Role: Formal analysisRole: InvestigationRole: Writing - review & editing

Nadège Guiglielmoni:

ORCID: https://orcid.org/0000-0002-6185-1592

Role: Formal analysisRole: Writing - review & editing

Boris Hespeels: Role: ConceptualizationRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: Validation

Djampa K. L. Kozlowski:

ORCID: https://orcid.org/0000-0003-2173-0937

Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Karine Labadie:

ORCID: https://orcid.org/0000-0001-7467-8509

Role: MethodologyRole: Resources

Antoine Limasset:

ORCID: https://orcid.org/0000-0002-0669-4141

Role: MethodologyRole: Software

Marc Llirós:

ORCID: https://orcid.org/0000-0001-8456-4230

Role: MethodologyRole: ResourcesRole: Writing - review & editing

Martial Marbouty:

ORCID: https://orcid.org/0000-0002-1668-8423

Role: Methodology

Matthieu Terwagne:

ORCID: https://orcid.org/0000-0002-1200-1145

Role: ConceptualizationRole: Writing - original draftRole: Writing - review & editing

Julie Virgo: Role: InvestigationRole: Resources

Richard Cordaux: Role: Data curationRole: SupervisionRole: ValidationRole: Writing - review & editing

Etienne G. J. Danchin:

ORCID: https://orcid.org/0000-0003-4146-5608

Role: ConceptualizationRole: SupervisionRole: Writing - review & editing

Bernard Hallet:

ORCID: https://orcid.org/0000-0001-6707-6382

Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing

Romain Koszul:

ORCID: https://orcid.org/0000-0002-3086-1173

Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: SoftwareRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - review & editing

Thomas Lenormand:

ORCID: https://orcid.org/0000-0001-8930-5393

Role: ConceptualizationRole: Formal analysisRole: MethodologyRole: SupervisionRole: Writing - review & editing

Jean-Francois Flot:

ORCID: https://orcid.org/0000-0003-4091-7916

Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing

Karine Van Doninck:

ORCID: https://orcid.org/0000-0002-4790-8951

Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: ValidationRole: Writing - original draftRole: Writing - review & editing

Journal

Journal ID (nlm-ta): Sci Adv

Journal ID (publisher-id): sciadv

Journal ID (hwp): advances

Title: Science Advances

Publisher: American Association for the Advancement of Science

ISSN (Electronic): 2375-2548

Publication date Collection: October 2021

Publication date (Electronic, pub): 06 October 2021

Volume: 7

Issue: 41

Electronic Location Identifier: eabg4216

Affiliations

[1 ]Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium.

[2 ]Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France.

[3 ]Collège Doctoral, Sorbonne Université, F-75005 Paris, France.

[4 ]Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium.

[5 ]CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France.

[6 ]Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France.

[7 ]Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium.

[8 ]Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, CNRS, IRD, UMR, 91198 Gif-sur-Yvette, France.

[9 ]INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France.

[10 ]Université de Lille, CNRS, UMR 9189 - CRIStAL, 59655 Villeneuve-d’Ascq, France.

[11 ]Institut d’Investigació Biomédica de Girona, Malalties Digestives i Microbiota, 17190 Salt, Spain.

[12 ]Ecologie et Biologie des interactions, Université de Poitiers, UMR CNRS 7267, 5 rue Albert Turpain, 86073 Poitiers, France.

[13 ]LIBST, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, Louvain-la-Neuve 1348, Belgium.

[14 ]CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France.

[15 ]Interuniversity Institute of Bioinformatics in Brussels - ( IB) ², Brussels 1050, Belgium.

Author notes

[* ]Corresponding author. Email: karine.vandoninck@ 123456unamur.be (K.V.D.); jflot@ 123456ulb.ac.be (J.-F.F.); polo.simion@ 123456gmail.com (P.S.)

[†]

These authors contributed equally to this work.

Author information

Paul Simion https://orcid.org/0000-0002-6667-3297

Jitendra Narayan https://orcid.org/0000-0002-2065-2861

Antoine Houtain https://orcid.org/0000-0002-6489-6868

Lyam Baudry https://orcid.org/0000-0002-9283-674X

Marie Cariou https://orcid.org/0000-0002-2544-579X

Corinne Cruaud https://orcid.org/0000-0002-4752-7278

Clément Gilbert https://orcid.org/0000-0002-2131-7467

Nadège Guiglielmoni https://orcid.org/0000-0002-6185-1592

Djampa K. L. Kozlowski https://orcid.org/0000-0003-2173-0937

Karine Labadie https://orcid.org/0000-0001-7467-8509

Antoine Limasset https://orcid.org/0000-0002-0669-4141

Marc Llirós https://orcid.org/0000-0001-8456-4230

Martial Marbouty https://orcid.org/0000-0002-1668-8423

Matthieu Terwagne https://orcid.org/0000-0002-1200-1145

Etienne G. J. Danchin https://orcid.org/0000-0003-4146-5608

Bernard Hallet https://orcid.org/0000-0001-6707-6382

Romain Koszul https://orcid.org/0000-0002-3086-1173

Thomas Lenormand https://orcid.org/0000-0001-8930-5393

Jean-Francois Flot https://orcid.org/0000-0003-4091-7916

Karine Van Doninck https://orcid.org/0000-0002-4790-8951

Article

Publisher ID: abg4216

DOI: 10.1126/sciadv.abg4216

PMC ID: 8494291

PubMed ID: 34613768

SO-VID: ed83d8ab-8bcb-4553-8568-95378a8daeda

Copyright © Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

History

Date received : 05 January 2021

Date accepted : 13 August 2021

Funding

Funded by: doi http://dx.doi.org/10.13039/100010663, H2020 European Research Council;

Award ID: 260822

Funded by: doi http://dx.doi.org/10.13039/100010665, H2020 Marie Skłodowska-Curie Actions;

Award ID: 764840

Funded by: doi http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: 725998

Funded by: doi http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: 725998

Funded by: doi http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: 260822

Funded by: doi http://dx.doi.org/10.13039/501100000781, European Research Council;

Award ID: JPI-EC-AMR STARCS ANR-16-JPEC-0003-05

Funded by: doi http://dx.doi.org/10.13039/501100000844, European Space Agency;

Award ID: ILSRA-2014-0106

Funded by: doi http://dx.doi.org/10.13039/501100011924, European Society of Anaesthesiology;

Award ID: ILSRA-2014-0106 P

Funded by: doi http://dx.doi.org/10.13039/501100019687, Amaldi Research Center;

Award ID: 764840

Funded by: French Government Investissement Avenir program FRANCE GENOMIQUE;

Award ID: ANR-10-INBS-09

Funded by: doi http://dx.doi.org/10.13039/501100017653, Fonds Spéciaux de Recherche;

Funded by: doi http://dx.doi.org/10.13039/501100011031, Alimentary Health;

Funded by: doi http://dx.doi.org/10.13039/501100002661, Fonds De La Recherche Scientifique - FNRS;

Funded by: FSR UNamur;

Funded by: Action de Recherche Concertée;

Funded by: doi http://dx.doi.org/10.13039/501100002661, Fonds De La Recherche Scientifique - FNRS;

Funded by: Action de Recherche Concertée;

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Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

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Abstract

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Genome Integrity

Most cited references 89

Trimmomatic: a flexible trimmer for Illumina sequence data

The Sequence Alignment/Map format and SAMtools

Fast gapped-read alignment with Bowtie 2.

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Contributors

Journal

Affiliations

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Article

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Funding

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Cited by 13

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