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.

Keywords: amphipod; circadian; clock; crustacean; genetics; hyalella; parhyale; talitrus.

Figure 1

Schematics of predicted P. hawaiensis core clock peptides aligned with examples from other species. (A) BMAL1/CYCLE, (B) CLOCK, (C) CRYPTOCHROME and (D) PERIOD. Ph, Parhayle hawaiensis; Dm, Drosophila melanogaster; Es, Euphausia superba; Tal, Talitrus saltator; Ha, Hyalella azteca; QQQ, polyglutamine domain (defined as a run of 10 or more amino acids in which 60% or more are glutamine).^apeptide is predicted on the basis of BLAST alignments and read mapping.^bpeptide is a construct of multiple separate de novo assembled contigs. Both Tal-CRY2 and Tal-CLK have been previously reported in a shorter form (O'Grady et al., 2016).

Figure 2

Optimal neighbor-joining trees depicting the evolutionary relationships of (A) CRYPTOCHROME and (B) TIMELESS/TIMEOUT peptides.