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Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot JF, Van Doninck K. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Sci Adv 2021; 7:eabg4216. [PMID: 34613768 PMCID: PMC8494291 DOI: 10.1126/sciadv.abg4216] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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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Affiliation(s)
- Paul Simion
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Jitendra Narayan
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Antoine Houtain
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Alessandro Derzelle
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Lyam Baudry
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
- Collège Doctoral, Sorbonne Université, F-75005 Paris, France
| | - Emilien Nicolas
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Rohan Arora
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Marie Cariou
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- 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
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | | | - Clément Gilbert
- Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, CNRS, IRD, UMR, 91198 Gif-sur-Yvette, France
| | - Nadège Guiglielmoni
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
| | - Boris Hespeels
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Djampa K. L. Kozlowski
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Karine Labadie
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Antoine Limasset
- Université de Lille, CNRS, UMR 9189 - CRIStAL, 59655 Villeneuve-d’Ascq, France
| | - Marc Llirós
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Institut d’Investigació Biomédica de Girona, Malalties Digestives i Microbiota, 17190 Salt, Spain
| | - Martial Marbouty
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Matthieu Terwagne
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Julie Virgo
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
| | - Richard Cordaux
- Ecologie et Biologie des interactions, Université de Poitiers, UMR CNRS 7267, 5 rue Albert Turpain, 86073 Poitiers, France
| | - Etienne G. J. Danchin
- INRAE, Université Côte-d’Azur, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis 06903, France
| | - Bernard Hallet
- LIBST, Université Catholique de Louvain (UCLouvain), Croix du Sud 4/5, Louvain-la-Neuve 1348, Belgium
| | - Romain Koszul
- Institut Pasteur, Unité Régulation Spatiale des Génomes, UMR 3525, CNRS, Paris F-75015, France
| | - Thomas Lenormand
- CEFE, Univ Montpellier, CNRS, Univ Paul Valéry Montpellier 3, EPHE, IRD, Montpellier, France
| | - Jean-Francois Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
| | - Karine Van Doninck
- Research Unit in Environmental and Evolutionary Biology, Université de Namur, Namur 5000, Belgium
- Molecular Biology and Evolution, Université libre de Bruxelles (ULB), Brussels 1050, Belgium
- Corresponding author. (K.V.D.); (J.-F.F.); (P.S.)
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Kozlowski DKL, Hassanaly‐Goulamhoussen R, Da Rocha M, Koutsovoulos GD, Bailly‐Bechet M, Danchin EGJ. Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. Evol Appl 2021; 14:1844-1866. [PMID: 34295368 PMCID: PMC8288018 DOI: 10.1111/eva.13246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022] Open
Abstract
Despite reproducing without sexual recombination, Meloidogyne incognita is an adaptive and versatile phytoparasitic nematode. This species displays a global distribution, can parasitize a large range of plants, and can overcome plant resistance in a few generations. The mechanisms underlying this adaptability remain poorly known. At the whole-genome level, only a few single nucleotide variations have been observed across different geographical isolates with distinct ranges of compatible hosts. Exploring other factors possibly involved in genomic plasticity is thus important. Transposable elements (TEs), by their repetitive nature and mobility, can passively and actively impact the genome dynamics. This is particularly expected in polyploid hybrid genomes such as the one of M. incognita. Here, we have annotated the TE content of M. incognita, analyzed the statistical properties of this TE landscape, and used whole-genome pool-seq data to estimate the mobility of these TEs across twelve geographical isolates, presenting variations in ranges of compatible host plants. DNA transposons are more abundant than retrotransposons, and the high similarity of TE copies to their consensus sequences suggests they have been at least recently active. We have identified loci in the genome where the frequencies of presence of a TE showed substantial variations across the different isolates. Overall, variations in TE frequencies across isolates followed their phylogenetic divergence, suggesting TEs participate in the species diversification. Compared with the M. incognita reference genome, we detected isolate and lineage-specific de novo insertion of some TEs, including within genic regions or in the upstream regulatory regions. We validated by PCR the insertion of some of these TEs inside genic regions, confirming TE movements have possible functional impacts. Overall, we show DNA transposons can drive genomic plasticity in M. incognita and their role in genome evolution of other parthenogenetic animal deserves further investigation.
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Koutsovoulos GD, Poullet M, Elashry A, Kozlowski DKL, Sallet E, Da Rocha M, Perfus-Barbeoch L, Martin-Jimenez C, Frey JE, Ahrens CH, Kiewnick S, Danchin EGJ. Author Correction: Genome assembly and annotation of Meloidogyne enterolobii, an emerging parthenogenetic root-knot nematode. Sci Data 2020; 7:413. [PMID: 33214557 PMCID: PMC7677529 DOI: 10.1038/s41597-020-00747-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A Correction to this paper has been published: https://doi.org/10.1038/s41597-020-00747-0.
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Affiliation(s)
| | - Marine Poullet
- Université Côte d'Azur, IN RAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | | | - Djampa K L Kozlowski
- Université Côte d'Azur, IN RAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - Erika Sallet
- Laboratoire des Interactions Plantes-Microorganismes, INRAE, CNRS, 31326, Castanet-Tolosan, France
| | - Martine Da Rocha
- Université Côte d'Azur, IN RAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | | | | | - Juerg Ernst Frey
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil, Switzerland
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, Wädenswil, Switzerland.,Swiss Institute of Bioinformatics, Bioinformatics, Wädenswil, Switzerland
| | - Sebastian Kiewnick
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants Federal Research Centre for cultivated Plants, Messeweg 11/12, 38104, Braunschweig, Germany.
| | - Etienne G J Danchin
- Université Côte d'Azur, IN RAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France.
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