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

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.

The evolution of selector gene function: Expression dynamics and regulatory interactions of tiptop/teashirt across Arthropoda

“…Orthology was inferred using multiple sequence alignment of peptide sequences with MUSCLE v. 3.8.31 (Edgar, 2004). Additional sequence data included were selected to represent major lineages of Mandibulata, namely, from the amphipod crustacean Parhyale hawaiensis (Kao et al, 2016). Phylogenetic inference under maximum likelihood was conducted with RAxML v. 8.0 (Stamatakis, 2014) under an LG model (Le, Dang, & Gascuel, 2012) and correction for a discrete gamma distribution, with 500 independent starts and 500 bootstrap replicates (Stamatakis, Hoover, & Rougemont, 2008).…”

Reconstruction of cell lineages and behaviors underlying arthropod limb outgrowth with multi-view light-sheet imaging and tracking

“…We demonstrated here that in the multi-view mode it is particularly suited for imaging embryos of the crustacean amphipod Parhyale hawaiensis for several days. Parhyale has been already established as an attractive new model organism for developmental genetic and functional genomic studies supported by many experimental techniques, including transgenesis, CRISPR/Casmediated knock-out and knock-in approaches, genomic resources and other experimental tools (Kao et al, 2016;Martin et al, 2016;Pavlopoulos and Averof, 2005;Pavlopoulos et al, 2009;Stamataki and Pavlopoulos, 2016). By extending here the Parhyale toolkit with multi-view LSFM and the MaMuT reconstructions, it is now feasible to study gene expression and function in the context of single-cell resolution fate maps and cell pedigrees.…”

“…Again, these cells displayed some of the highest proliferation rates quantified during limb outgrowth, suggesting a Dpp-dependent control of Parhyale limb growth. Thanks to the stereotyped and highly ordered Parhyale body plan, we anticipate that the LSFM imaging and tracking approaches described here, together with the recent application of CRSIPR/Cas-based methodologies for genome editing (Kao et al, 2016) will provide excellent material to further explore how morphogens like Dpp regulate form and function at cellular resolution.…”

“…Third, Parhyale eggs have the appropriate size and optical properties for microscopic live imaging of constituent cells with very high spatial and temporal resolution; embryos are about 500 µm long, transparent with low autofluorescence and light scattering. Finally, an increasing number of functional genetic approaches, embryological treatments, genomic and transcriptomic resources allow diverse experimental manipulations of Parhyale embryos (Kao et al, 2016).…”

The draft genome of the invasive walking stick,Medauroidea extradendata, reveals extensive lineage-specific gene family expansions of cell wall degrading enzymes in Phasmatodea

“…78.8% of genes in the Arthropod DB were complete, 17.4% were 245 present but fragmented and only 3.8% were missing. For comparative purposes, two large 246 arthropod genomes recently published (Parhyale, a crustacean, and Locust) have values of 78.5% 247 and 41.4% for completeness, 10.4% and 31.5% for fragmented, and 11.1% and 27.1% for 248 missing (Wang et al 2014;Kao et al 2016). Essentially, these 3 large genomes are 10 times the 249 size of most holometabolous insect genomes (which are about 300MB) and have very high levels 250 of repetitive DNA(Kidwell 2002).…”