The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion
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 functi...
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eLife Sciences Publications Ltd
2016-11-01
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Online Access: | https://elifesciences.org/articles/20062 |
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Article |
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DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
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 |
spellingShingle |
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 The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion eLife Parhyale crustacean genome immunity lignocellulose epigenetics |
author_facet |
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 |
author_sort |
Damian Kao |
title |
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion |
title_short |
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion |
title_full |
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion |
title_fullStr |
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion |
title_full_unstemmed |
The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion |
title_sort |
genome of the crustacean parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion |
publisher |
eLife Sciences Publications Ltd |
series |
eLife |
issn |
2050-084X |
publishDate |
2016-11-01 |
description |
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. |
topic |
Parhyale crustacean genome immunity lignocellulose epigenetics |
url |
https://elifesciences.org/articles/20062 |
work_keys_str_mv |
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doaj-1b8ef24891144568aac813de06a4930a2021-05-05T00:41:37ZengeLife Sciences Publications LtdeLife2050-084X2016-11-01510.7554/eLife.20062The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestionDamian Kao0Alvina G Lai1https://orcid.org/0000-0001-8960-8095Evangelia Stamataki2Silvana Rosic3Nikolaos Konstantinides4Erin Jarvis5Alessia Di Donfrancesco6Natalia Pouchkina-Stancheva7Marie Sémon8Marco Grillo9Heather Bruce10Suyash Kumar11https://orcid.org/0000-0002-5861-4027Igor Siwanowicz12Andy Le13Andrew Lemire14Michael B Eisen15Cassandra Extavour16https://orcid.org/0000-0003-2922-5855William E Browne17Carsten Wolff18https://orcid.org/0000-0002-5926-7338Michalis Averof19https://orcid.org/0000-0002-6803-7251Nipam H Patel20Peter Sarkies21Anastasios Pavlopoulos22Aziz Aboobaker23https://orcid.org/0000-0003-4902-5797Department of Zoology, University of Oxford, Oxford, United KingdomDepartment of Zoology, University of Oxford, Oxford, United KingdomJanelia Research Campus, Howard Hughes Medical Institute, Virginia, United StatesMRC Clinical Sciences Centre, Imperial College London, London, United Kingdom; Clinical Sciences, Imperial College London, London, United KingdomInstitut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, FranceDepartment of Molecular and Cell Biology, University of California, Berkeley, United StatesDepartment of Zoology, University of Oxford, Oxford, United KingdomDepartment of Zoology, University of Oxford, Oxford, United KingdomInstitut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, FranceInstitut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, FranceDepartment of Molecular and Cell Biology, University of California, Berkeley, United StatesJanelia Research Campus, Howard Hughes Medical Institute, Virginia, United StatesJanelia Research Campus, Howard Hughes Medical Institute, Virginia, United StatesJanelia Research Campus, Howard Hughes Medical Institute, Virginia, United StatesJanelia Research Campus, Howard Hughes Medical Institute, Virginia, United StatesMolecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, United StatesDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, United StatesDepartment of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, United StatesVergleichende Zoologie, Institut fur Biologie,Humboldt-Universitat zu Berlin, Berlin, GermanyInstitut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, FranceDepartment of Molecular and Cell Biology, University of California, Berkeley, United StatesMRC Clinical Sciences Centre, Imperial College London, London, United Kingdom; Clinical Sciences, Imperial College London, London, United KingdomJanelia Research Campus, Howard Hughes Medical Institute, Virginia, United StatesDepartment of Zoology, University of Oxford, Oxford, United KingdomThe 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.https://elifesciences.org/articles/20062Parhyalecrustaceangenomeimmunitylignocelluloseepigenetics |