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The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion

Damian Kao, Alvina G. Lai, Evangelia Stamataki, Silvana Rosic, Nikolaos Konstantinides, Erin Jarvis, Alessia Di Donfrancesco, Natalia Pouchkina-Stantcheva, Marie Sémon, Marco Grillo, Heather Bruce, Suyash Kumar, Igor Siwanowicz, Andy Le, Andrew Lemire, Michael B. Eisen, Cassandra Extavour, William E. Browne, Carsten Wolff, Michalis Averof, Nipam H. Patel, Peter Sarkies, Anastasios Pavlopoulos, A. Aziz Aboobaker
doi: https://doi.org/10.1101/065789
Damian Kao
1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
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Alvina G. Lai
1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
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Evangelia Stamataki
2Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
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Silvana Rosic
3MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN
4Institute for Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN
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Nikolaos Konstantinides
5Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and École Normale Supérieure de Lyon, Lyon, France
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Erin Jarvis
6University of California, Berkeley, Dept. of Molecular and Cell Biology, 519A LSA 3200 Berkeley, CA 94720-3200
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Alessia Di Donfrancesco
1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
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Natalia Pouchkina-Stantcheva
1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
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Marie Sémon
5Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and École Normale Supérieure de Lyon, Lyon, France
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Marco Grillo
5Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and École Normale Supérieure de Lyon, Lyon, France
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Heather Bruce
6University of California, Berkeley, Dept. of Molecular and Cell Biology, 519A LSA 3200 Berkeley, CA 94720-3200
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Suyash Kumar
2Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
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Igor Siwanowicz
2Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
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Andy Le
2Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
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Andrew Lemire
2Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
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Michael B. Eisen
7Howard Hughes Medical Institute, University of California, Berkeley, Department Of Molecular and Cell Biology
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Cassandra Extavour
8Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, BioLabs Building 4109-4111 Cambridge, MA 02138
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William E. Browne
9Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, MRC-163, P.O. Box 37012, Washington, DC 20013-7012 USA
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Carsten Wolff
10Humboldt-Universität zu Berlin, Institut für Biologie, Vergleichende Zoologie, Philippstr. 13, Haus 2, 10115 Berlin, Germany
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Michalis Averof
5Institut de Génomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and École Normale Supérieure de Lyon, Lyon, France
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Nipam H. Patel
6University of California, Berkeley, Dept. of Molecular and Cell Biology, 519A LSA 3200 Berkeley, CA 94720-3200
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Peter Sarkies
3MRC Clinical Sciences Centre, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN
4Institute for Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN
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Anastasios Pavlopoulos
2Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
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A. Aziz Aboobaker
1Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
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ABSTRACT

The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion (“wood eating”), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source.

Footnotes

  • Competing interests The authors declare no competing interests

  • Funding AAA and co-workers are funded by the Biotechnology and Biological Sciences Reserarch Council (BBSRC grant number BB/K007564/1), the Medical Research Council (MRC grant number MR/M000133/1), the John Fell Fund Oxford University Press (OUP) and the Elizabeth Hannah Jenkinson Fund. AGL receives funding from the Human Frontier Science Program postdoctoral fellowship and the Elizabeth Hannah Jenkinson Research Fund. NHP and co-workers are funded by NSF grant IOS-1257379. AP and co-workers are funded by the Howard Hughes Medical Institute. PS and co-workers are funded by the Medical Research council (MRC MC-A652-5PZ80) and an Imperial College Research Fellowship too PS. MA and colleagues received funding from the Agence Nationale de la Recherche (France), grant ANR-12-CHEX-0001-01. The funding bodies had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 13, 2016.
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The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion
Damian Kao, Alvina G. Lai, Evangelia Stamataki, Silvana Rosic, Nikolaos Konstantinides, Erin Jarvis, Alessia Di Donfrancesco, Natalia Pouchkina-Stantcheva, Marie Sémon, Marco Grillo, Heather Bruce, Suyash Kumar, Igor Siwanowicz, Andy Le, Andrew Lemire, Michael B. Eisen, Cassandra Extavour, William E. Browne, Carsten Wolff, Michalis Averof, Nipam H. Patel, Peter Sarkies, Anastasios Pavlopoulos, A. Aziz Aboobaker
bioRxiv 065789; doi: https://doi.org/10.1101/065789
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The genome of the crustacean Parhyale hawaiensis: a model for animal development, regeneration, immunity and lignocellulose digestion
Damian Kao, Alvina G. Lai, Evangelia Stamataki, Silvana Rosic, Nikolaos Konstantinides, Erin Jarvis, Alessia Di Donfrancesco, Natalia Pouchkina-Stantcheva, Marie Sémon, Marco Grillo, Heather Bruce, Suyash Kumar, Igor Siwanowicz, Andy Le, Andrew Lemire, Michael B. Eisen, Cassandra Extavour, William E. Browne, Carsten Wolff, Michalis Averof, Nipam H. Patel, Peter Sarkies, Anastasios Pavlopoulos, A. Aziz Aboobaker
bioRxiv 065789; doi: https://doi.org/10.1101/065789

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