In silico Identification of a Molecular Circadian System With Novel Features in the Crustacean Model Organism Parhyale hawaiensis

Abstract

The amphipod Parhyale hawaiensis is a model organism of growing importance in the fields of evolutionary development and regeneration. A small, hardy marine crustacean that breeds year-round with a short generation time, it has simple lab culture requirements and an extensive molecular toolkit including the ability to generate targeted genetic mutant lines. Here we identify canonical core and regulatory clock genes using genomic and transcriptomic resources as a first step in establishing this species as a model in the field of chronobiology. The molecular clock of P. hawaiensis lacks orthologs of the canonical circadian genes cryptochrome 1 and timeless, in common with the mammalian system but in contrast to many arthropods including Drosophila melanogaster. Furthermore the predicted CLOCK peptide is atypical and CRY2 shows an extended 5′ region of unknown function. These results appear to be shared by two other amphipod species.

The circadian clock gene bmal1 is necessary for co-ordinated circatidal rhythms in the marine isopod Eurydice pulchra (Leach)

“…Consequently, the two studies appear to be complementary, and it will be interesting to see in future whether the apparent lack of any robust circatidal effects of Epper and Epcry2 knockdown in Eurydice , is matched by corresponding gene knockouts in Parhyale . It is notable that the amphipod does not have a timeless gene [ 37 ], unlike the isopod in which Eptim encodes the only robust circadian transcript cycle from the suite of canonical clock genes [ 12 ]. Consequently, it is possible that the underlying molecular mechanisms for circadian cycles are different as they are in insects [ 38 ], with the implication that the circatidal clockworks may also show some evolutionary flexibility.…”

The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)

“…[ 19 ]. The data for G. minus [ 36 ] and Parhyale hawaiensis (head transcriptome) [ 60 ], in which opsin diversity has been explored already, were added to the analysis to verify the method. Finally, some transcriptomes were reassembled if only raw data were provided by the authors, namely G. pisinnus [ 61 ], Trinorchestia longiramus [ 62 ], and Gondogeneia antarctica [ 63 ].…”