10.5061/DRYAD.8CZ8W9GKQ
Graham, Allie
0000-0001-7404-168X
Oregon State University
Barreto, Felipe
0000-0002-7949-7747
Oregon State University
Independent losses of the Hypoxia-Inducible Factor (HIF) pathway within
Crustacea
Dryad
dataset
2020
crustacean
HIF-pathway
VHL
EGLN
National Science Foundation
https://ror.org/021nxhr62
PRFB 1812103
2020-01-08T00:00:00Z
2020-01-08T00:00:00Z
en
https://doi.org/10.1093/molbev/msaa008
241425372 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.
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)"...]