title: The genome of the crustaceanParhyale hawaiensis,a model for animal development, regeneration, immunity and lignocellulose digestion.
abstract: The amphipod crustaceanParhyale hawaiensisis 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.Parhyaleis a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes ofParhyaleas an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find thatParhyaleand 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 ofParhyaleas an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source.
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Damian
authors.initials: D
authors.lastname: Kao
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Alvina G
authors.identifier: http://orcid.org/0000-0001-8960-8095
authors.initials: AG
authors.lastname: Lai
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States.
authors.forename: Evangelia
authors.initials: E
authors.lastname: Stamataki
authors.affiliation: MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.|Clinical Sciences, Imperial College London, London, United Kingdom.
authors.forename: Silvana
authors.initials: S
authors.lastname: Rosic
authors.affiliation: Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France.
authors.forename: Nikolaos
authors.initials: N
authors.lastname: Konstantinides
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, United States.
authors.forename: Erin
authors.initials: E
authors.lastname: Jarvis
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Alessia
authors.initials: A
authors.lastname: Di Donfrancesco
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Natalia
authors.initials: N
authors.lastname: Pouchkina-Stancheva
authors.affiliation: Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France.
authors.forename: Marie
authors.initials: M
authors.lastname: Sémon
authors.affiliation: Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France.
authors.forename: Marco
authors.initials: M
authors.lastname: Grillo
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, United States.
authors.forename: Heather
authors.initials: H
authors.lastname: Bruce
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States.
authors.forename: Suyash
authors.identifier: http://orcid.org/0000-0002-5861-4027
authors.initials: S
authors.lastname: Kumar
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States.
authors.forename: Igor
authors.initials: I
authors.lastname: Siwanowicz
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States.
authors.forename: Andy
authors.initials: A
authors.lastname: Le
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States.
authors.forename: Andrew
authors.initials: A
authors.lastname: Lemire
authors.affiliation: Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, United States.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Eisen
authors.affiliation: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.
authors.forename: Cassandra
authors.identifier: http://orcid.org/0000-0003-2922-5855
authors.initials: C
authors.lastname: Extavour
authors.affiliation: Department of Invertebrate Zoology, Smithsonian National Museum of Natural History, Washington, United States.
authors.forename: William E
authors.initials: WE
authors.lastname: Browne
authors.affiliation: Vergleichende Zoologie, Institut fur Biologie,Humboldt-Universitat zu Berlin, Berlin, Germany.
authors.forename: Carsten
authors.identifier: http://orcid.org/0000-0002-5926-7338
authors.initials: C
authors.lastname: Wolff
authors.affiliation: Institut de Gé nomique Fonctionnelle de Lyon, Centre National de la Recherche Scientifique (CNRS) and É cole Normale Supé rieure de Lyon, Lyon, France.
authors.forename: Michalis
authors.identifier: http://orcid.org/0000-0002-6803-7251
authors.initials: M
authors.lastname: Averof
authors.affiliation: Department of Molecular and Cell Biology, University of California, Berkeley, United States.
authors.forename: Nipam H
authors.initials: NH
authors.lastname: Patel
authors.affiliation: MRC Clinical Sciences Centre, Imperial College London, London, United Kingdom.|Clinical Sciences, Imperial College London, London, United Kingdom.
authors.forename: Peter
authors.initials: P
authors.lastname: Sarkies
authors.affiliation: Janelia Research Campus, Howard Hughes Medical Institute, Virginia, United States.
authors.forename: Anastasios
authors.initials: A
authors.lastname: Pavlopoulos
authors.affiliation: Department of Zoology, University of Oxford, Oxford, United Kingdom.
authors.forename: Aziz
authors.identifier: http://orcid.org/0000-0003-4902-5797
authors.initials: A
authors.lastname: Aboobaker
mesh_terms: D033304:Amphipoda / Q000145:classification / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D000818:Animals; D017756:Aquaculture; D060829:Arthropod Proteins / Q000235:genetics* / Q000276:immunology; D005260:Female; D018507:Gene Expression Regulation, Developmental; D063990:Gene Ontology; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D007113:Immunity, Innate; D059785:Karyotype; D008018:Life Cycle Stages / Q000235:genetics* / Q000276:immunology; D008031:Lignin / Q000378:metabolism*; D008297:Male; D053858:Metabolic Networks and Pathways / Q000235:genetics* / Q000276:immunology; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D022661:RNA, Untranslated / Q000235:genetics / Q000276:immunology; D012038:Regeneration; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000276:immunology
chemical_list: D060829:Arthropod Proteins; D022661:RNA, Untranslated; D014157:Transcription Factors; C036909:lignocellulose; D008031:Lignin
keywords: Parhyale; crustacean; developmental biology; epigenetics; evolutionary biology; genome; genomics; immunity; lignocellulose; stem cells