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

Elife. 2016 Nov 16;5:e20062. doi: 10.7554/eLife.20062.

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.

Keywords: Parhyale; crustacean; developmental biology; epigenetics; evolutionary biology; genome; genomics; immunity; lignocellulose; stem cells.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amphipoda / classification
  • Amphipoda / genetics*
  • Amphipoda / growth & development
  • Amphipoda / metabolism
  • Animals
  • Aquaculture
  • Arthropod Proteins / genetics*
  • Arthropod Proteins / immunology
  • Female
  • Gene Expression Regulation, Developmental
  • Gene Ontology
  • Genome*
  • High-Throughput Nucleotide Sequencing
  • Immunity, Innate
  • Karyotype
  • Life Cycle Stages / genetics*
  • Life Cycle Stages / immunology
  • Lignin / metabolism*
  • Male
  • Metabolic Networks and Pathways / genetics*
  • Metabolic Networks and Pathways / immunology
  • Molecular Sequence Annotation
  • Phylogeny
  • RNA, Untranslated / genetics
  • RNA, Untranslated / immunology
  • Regeneration
  • Signal Transduction
  • Transcription Factors / genetics
  • Transcription Factors / immunology

Substances

  • Arthropod Proteins
  • RNA, Untranslated
  • Transcription Factors
  • lignocellulose
  • Lignin