A sequence-tagged genetic map for the brown alga Ectocarpus siliculosus provides large-scale assembly of the genome sequence

Authors

  • Svenja Heesch,

    1. UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
    2. CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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  • Ga Youn Cho,

    1. UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
    2. CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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  • Akira F. Peters,

    1. Bezhin Rosko, 28 route de Perharidy, 29680 Roscoff, France
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  • Gildas Le Corguillé,

    1. Analyses and Bioinformatics for Marine Sciences (ABiMS) Platform, Computer and Genomics Resource Centre, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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  • Cyril Falentin,

    1. INRA, Agrocampus Ouest, Université de Rennes 1, UMR 118 APBV (Plant Genetics and Biotechnologies), BP35327, 35653 Le Rheu Cedex, France
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  • Gilles Boutet,

    1. INRA, Plateforme Séquençage-Génotypage Biogenouest, UMR 118 INRA-AGROcampus Ouest-Université Rennes 1, 35653 Le Rheu, France
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  • Solène Coëdel,

    1. INRA, Plateforme Séquençage-Génotypage Biogenouest, UMR 118 INRA-AGROcampus Ouest-Université Rennes 1, 35653 Le Rheu, France
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  • Claire Jubin,

    1. CEA, DSV, Institut de Génomique, Génoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France
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  • Gaelle Samson,

    1. CEA, DSV, Institut de Génomique, Génoscope, 2 rue Gaston Crémieux, CP5706, 91057 Evry, France
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  • Erwan Corre,

    1. Analyses and Bioinformatics for Marine Sciences (ABiMS) Platform, Computer and Genomics Resource Centre, FR 2424, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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  • Susana M. Coelho,

    1. UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
    2. CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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  • J. Mark Cock

    1. UPMC Univ. Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
    2. CNRS, UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
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Author for correspondence:
J. Mark Cock
Tel +33 (0)2 98 29 23 60
Email: cock@sb-roscoff.fr

Summary

  • Ectocarpus siliculosus has been proposed as a genetic and genomic model for the brown algae and the 214 Mbp genome of this organism has been sequenced. The aim of this project was to obtain a chromosome-scale view of the genome by constructing a genetic map using microsatellite markers that were designed based on the sequence supercontigs.
  • To map genetic markers, a segregating F2 population was generated from a cross between the sequenced strain (Ec 32) and a compatible strain from northern Chile. Amplified fragment length polymorphism (AFLP) analysis indicated a significant degree of polymorphism (41%) between the genomes of these two parental strains. Of 1,152 microsatellite markers that were selected for analysis based on their location on long supercontigs, their potential as markers and their predicted ability to amplify a single genomic locus, 407 were found to be polymorphic.
  • A genetic map was constructed using 406 markers, resulting in 34 linkage groups. The 406 markers anchor 325 of the longest supercontigs on to the map, representing 70.1% of the genome sequence.
  • The Ectocarpus genetic map described here not only provides a large-scale assembly of the genome sequence, but also represents an important tool for future genetic analysis using this organism.

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