Independent losses of the Hypoxia-Inducible Factor (HIF) pathway within Crustacea

Metazoans respond to hypoxic stress via the Hypoxia Inducible Factor (HIF) pathway, a mechanism thought to be extremely conserved due to its importance in monitoring cellular oxygen levels and regulating responses to hypoxia. However, recent work revealed that key members of the HIF pathway have been lost in specific lineages (a tardigrade and a copepod), suggesting alternative mechanisms have evolved but are still undescribed. Using genomic and transcriptomic data from 70 different species across 12 major crustacean groups, we assessed the degree to which the gene HIFa, the master regulator of the HIF pathway, was conserved. Mining of protein domains, followed by phylogenetic analyses of gene families, uncovered group-level losses of HIFa, including one across three orders within Cirripedia, and in three orders within Copepoda. For these groups, additional assessment showed losses of HIF repression machinery (EGLN, VHL). These results suggest the existence of alternative mechanisms for cellular response to low oxygen, and highlight these taxa as models useful for probing these evolutionary outcomes.

Methods
No additional sequencing was performed for this study, as we instead used publically available transcriptomes from both the TSA and SRA. Included in this repository are protein files from the transcriptomes we assemblied de novo (from SRA sources), alignments (in phylip format) and newick files for the phylogenetic trees created. For more specific information regarding the generation and analysis, please see the "Supplemental Methods" associated with this manuscript.