A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus

Authors

  • Lorena Rivarola-Duarte,

    1. Department of Bioanalytical Ecotoxicology, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
    2. Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
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    • Joint first authors.
  • Christian Otto,

    1. Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
    2. LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
    3. Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany
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    • Joint first authors.
  • Frank Jühling,

    1. Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
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  • Stephan Schreiber,

    1. Young Investigators Group Bioinformatics and Transcriptomics, Department Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
    2. RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Leipzig, Germany
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  • Daria Bedulina,

    1. Irkutsk State University, Irkutsk, Russia
    2. Baikal Research Centre, Irkutsk, Russia
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  • Lena Jakob,

    1. Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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  • Anton Gurkov,

    1. Irkutsk State University, Irkutsk, Russia
    2. Baikal Research Centre, Irkutsk, Russia
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  • Denis Axenov-Gribanov,

    1. Irkutsk State University, Irkutsk, Russia
    2. Baikal Research Centre, Irkutsk, Russia
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  • Abdullah H. Sahyoun,

    1. Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany
    2. Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon
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  • Magnus Lucassen,

    1. Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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  • Jörg Hackermüller,

    1. Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
    2. Young Investigators Group Bioinformatics and Transcriptomics, Department Proteomics, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
    3. RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Leipzig, Germany
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  • Steve Hoffmann,

    1. Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
    2. LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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  • Franz Sartoris,

    1. Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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  • Hans-Otto Pörtner,

    Corresponding author
    1. Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
    • Correspondence to: Hans-Otto Pörtner, Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany.

      E-mail: hans.poertner@awi.de

      Correspondence to: Maxim Timofeyev, Irkutsk State University, Karl Marx 1, 664003 Irkutsk, Russia.

      E-mail: m.a.timofeyev@gmail.com

      Correspondence to: Till Luckenbach, Department of Bioanalytical Ecotoxicology, UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany.

      E-mail: till.luckenbach@ufz.de

      Correspondence to: Peter F. Stadler, Bioinformatics Group, Department of Computer Science, Härtelstraße 16-18, D-04107 Leipzig, Germany.

      E-mail: studla@bioinf.uni-leipzig.de

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  • Maxim Timofeyev,

    Corresponding author
    1. Irkutsk State University, Irkutsk, Russia
    2. Baikal Research Centre, Irkutsk, Russia
    • Correspondence to: Hans-Otto Pörtner, Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany.

      E-mail: hans.poertner@awi.de

      Correspondence to: Maxim Timofeyev, Irkutsk State University, Karl Marx 1, 664003 Irkutsk, Russia.

      E-mail: m.a.timofeyev@gmail.com

      Correspondence to: Till Luckenbach, Department of Bioanalytical Ecotoxicology, UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany.

      E-mail: till.luckenbach@ufz.de

      Correspondence to: Peter F. Stadler, Bioinformatics Group, Department of Computer Science, Härtelstraße 16-18, D-04107 Leipzig, Germany.

      E-mail: studla@bioinf.uni-leipzig.de

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  • Till Luckenbach,

    Corresponding author
    1. Department of Bioanalytical Ecotoxicology, UFZ—Helmholtz Centre for Environmental Research, Leipzig, Germany
    • Correspondence to: Hans-Otto Pörtner, Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany.

      E-mail: hans.poertner@awi.de

      Correspondence to: Maxim Timofeyev, Irkutsk State University, Karl Marx 1, 664003 Irkutsk, Russia.

      E-mail: m.a.timofeyev@gmail.com

      Correspondence to: Till Luckenbach, Department of Bioanalytical Ecotoxicology, UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany.

      E-mail: till.luckenbach@ufz.de

      Correspondence to: Peter F. Stadler, Bioinformatics Group, Department of Computer Science, Härtelstraße 16-18, D-04107 Leipzig, Germany.

      E-mail: studla@bioinf.uni-leipzig.de

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  • Peter F. Stadler

    Corresponding author
    1. Interdisciplinary Center for Bioinformatics, University Leipzig, Leipzig, Germany
    2. LIFE, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
    3. Bioinformatics Group, Department of Computer Science, University Leipzig, Leipzig, Germany
    4. RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Leipzig, Germany
    5. Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
    6. Department of Theoretical Chemistry, University of Vienna, Wien, Austria
    7. Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
    8. Santa Fe Institute, New Mexico
    • Correspondence to: Hans-Otto Pörtner, Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D-27570 Bremerhaven, Germany.

      E-mail: hans.poertner@awi.de

      Correspondence to: Maxim Timofeyev, Irkutsk State University, Karl Marx 1, 664003 Irkutsk, Russia.

      E-mail: m.a.timofeyev@gmail.com

      Correspondence to: Till Luckenbach, Department of Bioanalytical Ecotoxicology, UFZ—Helmholtz Centre for Environmental Research, Permoserstraße 15, D-04318 Leipzig, Germany.

      E-mail: till.luckenbach@ufz.de

      Correspondence to: Peter F. Stadler, Bioinformatics Group, Department of Computer Science, Härtelstraße 16-18, D-04107 Leipzig, Germany.

      E-mail: studla@bioinf.uni-leipzig.de

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  • Conflicts of interest: None.

ABSTRACT

Eulimnogammarus verrucosus is an amphipod endemic to the unique ecosystem of Lake Baikal and serves as an emerging model in ecotoxicological studies. We report here on a survey sequencing of its genome as a first step to establish sequence resources for this species. From a single lane of paired-end sequencing data, we estimated the genome size as nearly 10 Gb and we obtained an overview of the repeat content. At least two-thirds of the genome are non-unique DNA, and a third of the genomic DNA is composed of just five families of repetitive elements, including low-complexity sequences. Attempts to use off-the-shelf assembly tools failed on the available low-coverage data both before and after removal of highly repetitive components. Using a seed-based approach we nevertheless assembled short contigs covering 33 pre-microRNAs and the homeodomain-containing exon of nine Hox genes. The absence of clear evidence for paralogs implies that a genome duplication did not contribute to the large genome size. We furthermore report the assembly of the mitochondrial genome using a new, guided “crystallization” procedure. The initial results presented here set the stage for a more complete sequencing and analysis of this large genome. J. Exp. Zool. (Mol. Dev. Evol.) 322B: 177–189, 2014. © 2014 Wiley Periodicals, Inc.

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