Figure 1. Phylogenetic analysis of GSDM proteins.
Time-calibrated maximum clade credibility coalescent Bayesian phylogenetic tree of all protein sequences in selected superphyla by hidden Markov model identification method. Tree was visualized using iTOL v6 (Letunic and Bork, 2021).
Figure 1—source data 1. Tree in .tre format.
elife-92362-fig1-data1.zip (301.1KB, zip)
Figure 1—source data 2. Alignment file of all sequences in nexus format.
elife-92362-fig1-data2.zip (466.7KB, zip)
Figure 1—figure supplement 1. Tree identical to Figure 1 with individual nodes labeled.
Figure 1—figure supplement 1—source data 1. Text file with all sequences with seqID and ID used in nexus alignment file.
elife-92362-fig1-figsupp1-data1.zip (13.6KB, zip)
Figure 1—figure supplement 2. Tree identical to Figure 1 with individual nodes labeled and posterior probabilities displayed at the midpoint of each node.
Figure 1—figure supplement 3. Maximum likelihood tree generated using the same sequences in Figure 1 Bayesian tree.
Figure 1—figure supplement 3—source data 1. Maximum likelihood tree in Newick format.
elife-92362-fig1-figsupp3-data1.zip (35.5KB, zip)
Figure 1—figure supplement 3—source data 2. Maximum likelihood tree with bootstrap values.
elife-92362-fig1-figsupp3-data2.pdf (50.5KB, pdf)
Figure 1—figure supplement 3—source data 3. Maximum likelihood tree with node tips labeled.
elife-92362-fig1-figsupp3-data3.pdf (67.3KB, pdf)
Figure 1—figure supplement 3—source data 4. Maximum likelihood tree with node tips labeled and bootstrap values.
elife-92362-fig1-figsupp3-data4.pdf (54KB, pdf)
Figure 1—figure supplement 4. Visualization of the locus where GSDMA is found in the clades of animals that encode this gasdermin.
In tetrapods, the genes found in this region are identical, though ORMDL3 and LRRC3C are in opposing positions in some animals. Note that Microcaecilia unicolor (Tiny Cayenne caecilian) is an amphibian despite appearing morphologically similar to a snake. Duplications of GSDMA are indicated by numbers below GSDMA. Though not annotated as CSF3 in Anolis carolinensis (Carolina anole), the protein encoded by this sequence aligns with granulocyte colony-stimulating factor (encoded by CSF3) in mammals by BLASTp. It is colored and labeled as CSF3 here for ease of appreciating synteny. In fish that encode GSDMEc, like Callorhinchus milii (elephant shark), GSDMEc is found in a similar locus near LRRC3Ca and MED24. Gene labels are not to scale.