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

Citation

Graham, Allie; Barreto, Felipe (2020), Independent losses of the Hypoxia-Inducible Factor (HIF) pathway within Crustacea, Dryad, Dataset, https://doi.org/10.5061/dryad.8cz8w9gkq

Abstract

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.

Usage Notes

NOTE: As stated in the methods, the alignments and newick tree files may have residual PAS-only containing protein sequenes and some host/fish sequences. We deleted them in post, which is why they are not present in the final phylogenetic tree image [Supplementa Methods: "In the event that a sequences made it into the final tree and was revealed during post-processing to be a member of a PAS-only containing gene family, these were pruned from the final phylogenetic tree (though are still present in the deposited final alignment and newick file)"...]

Funding

National Science Foundation, Award: PRFB 1812103