eLife (Nov 2016)
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-Stancheva,
- 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,
- Aziz Aboobaker
Affiliations
- Damian Kao
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Alvina G Lai
- ORCiD
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Evangelia Stamataki
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
- Silvana Rosic
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom; Clinical Sciences, Imperial College London, London, United Kingdom
- Nikolaos Konstantinides
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
- Erin Jarvis
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Alessia Di Donfrancesco
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Natalia Pouchkina-Stancheva
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Marie Sémon
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
- Marco Grillo
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
- Heather Bruce
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Suyash Kumar
- ORCiD
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
- Igor Siwanowicz
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
- Andy Le
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
- Andrew Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
- Michael B Eisen
- Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States
- Cassandra Extavour
- ORCiD
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
- William E Browne
- Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, United States
- Carsten Wolff
- ORCiD
- Vergleichende Zoologie, Institut fur Biologie,Humboldt-Universitat zu Berlin, Berlin, Germany
- Michalis Averof
- ORCiD
- Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France
- Nipam H Patel
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Peter Sarkies
- MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom; Clinical Sciences, Imperial College London, London, United Kingdom
- Anastasios Pavlopoulos
- Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States
- Aziz Aboobaker
- ORCiD
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- DOI
- https://doi.org/10.7554/eLife.20062
- Journal volume & issue
-
Vol. 5
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.
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