Data from: Novel predators reshape holozoan phylogeny and reveal the presence of a two-component signalling system in the ancestor of animals

Hehenberger E, Tikhonenkov DV, Kolisko M, del Campo J, Esaulov AS, Mylnikov AP, Keeling PJ

Date Published: June 23, 2017

DOI: http://dx.doi.org/10.5061/dryad.26bv4

 

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Title Syssomonas multiformis predicted peptides (culture)
Downloaded 9 times
Description Peptides predicted from Trinity assembly using TransDecoder (including a blastp similarity search against the Swiss-prot Database). NOTE: although raw reads were subjected to several cleaning steps, this file still contains a number of prey peptides (Spumella sp.)
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Title Syssomonas multiformis predicted peptides (sorted)
Downloaded 6 times
Description Peptides predicted from Trinity assembly using TransDecoder (including a blastp similarity search against the Swiss-prot Database).
Download Colp-12_sorted_predicted_peptides.fasta (6.067 Mb)
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Title Pigoraptor vietnamica predicted peptides
Downloaded 7 times
Description Peptides predicted from Trinity assembly using TransDecoder (including a blastp similarity search against the Swiss-prot Database). NOTE: bacterial contamination present
Download Opistho-1_predicted_peptides.fa (11.46 Mb)
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Title Pigoraptor chileana predicted peptides
Downloaded 7 times
Description Peptides predicted from Trinity assembly using TransDecoder (including a blastp similarity search against the Swiss-prot Database).
Download Opistho-2_predicted_peptides.fa (10.93 Mb)
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Title Single gene alignments (trimmed) for phylogenomic analysis
Downloaded 8 times
Description Trimmed alignments for 255 genes and 38 taxa as used for the phylogenomic analysis (see Figure 2A and Table S1 of the manuscript) in fasta format.
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Title Phylogenomic reconstruction without novel taxa
Downloaded 16 times
Description Phylogenomic tree based on 255 concatenated proteins inferred by IQ-TREE under the LG+C40+F+G4 model. Novel species have been removed from the 255-gene data set. Node supports are ultrafast bootstrap (UF) values obtained from IQ-TREE. Black dots on branches correspond to >95% UF.
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Title Src protein tyrosine kinase phylogeny
Downloaded 14 times
Description Best of 50 ML trees as inferred by RAxML under the LG+ Γ model (see STAR methods). Purple, pink, orange, blue, light blue and brown texts indicate C. owczarzaki, M. vibrans, Pigoraptor (strains Opistho-1 and Opistho-2), S. multiformis (strain Colp-12), C. limacisporum and H. sapiens, respectively. The query sequence is indicated in red. A shaded rectangle indicates the protein in question in filastereans and Pluriformea. An asterisk indicates annotated human proteins belonging to the Src family. Other protein tyrosine kinases (Tec, Abl2 and Csk) are indicated and were identified by the annotated C. owczarzaki homolog present in the respective clade. Node supports are nonparametric ML bootstrap values obtained from 1000 ML replicates using the LG+Γ model implemented in RAxML, numbers at nodes represent bootstrap supports of greater than 50%. The scale bar represents the estimated number of amino acid substitutions per site.
Download Src_Opistho_2@35310_RAxML_50Trees_1000BS.pdf (364.0 Kb)
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Title Csk and FAK protein tyrosine kinase phylogenies
Downloaded 14 times
Description (A) and (B) Best of 50 ML trees as inferred by RAxML under the LG+ Γ model (see STAR methods). Purple, pink, orange, blue, light blue and brown texts indicate C. owczarzaki, M. vibrans, Pigoraptor (strains Opistho-1 and Opistho-2), S. multiformis (strain Colp-12), C. limacisporum and H. sapiens, respectively. The query sequence is indicated in red. A shaded rectangle indicates the protein in question in filastereans and Pluriformea, if present. An asterisk indicates human proteins annotated as Csk (A) and FAK (B), respectively. Other protein tyrosine kinases are indicated and were identified by the annotated C. owczarzaki homolog(s) present in the respective clade if not otherwise indicated. Clades in (B) are collapsed to increase clarity. Node supports are nonparametric ML bootstrap values obtained from 1000 ML replicates using the LG+ Γ model implemented in RAxML, numbers at nodes represent bootstrap supports of greater than 50%. The scale bar represents the estimated number of amino acid substitutions per site.
Download Csk_Opistho_2@90386_RAxML_50Trees_1000BS.pdf (285.7 Kb)
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Title Receptor protein tyrosine phosphatase phylogeny
Downloaded 13 times
Description Best of 50 ML trees as inferred by RAxML under the LG+ Γ model (see STAR methods). Purple, pink, orange, blue, light blue and brown texts indicate C. owczarzaki, M. vibrans, Pigoraptor, S. multiformis, C. limacisporum and H. sapiens, respectively. The query sequence is indicated in red. The Pigoraptor (strains Opistho-1 and Opistho-2) and S. multiformis (strain Colp-12) sequences cluster with an annotated C. owczarzaki receptor protein tyrosine phosphatase also containing Fibronectin-3 domains (XP_004365141); note the Opistho-1 and the Colp-12 homolog are truncated. Other protein tyrosine kinases (receptor and non-receptor) are indicated and were identified by the annotated H. sapiens homologs present in the respective clade. Selected clades are collapsed to increase clarity. Node supports are nonparametric ML bootstrap values obtained from 1000 ML replicates using the LG+ Γ model implemented in RAxML, numbers at nodes represent bootstrap supports of greater than 50%. The scale bar represents the estimated number of amino acid substitutions per site.
Download RecepTyrPhos_Opistho-2@91678_RAxML_50Tree...BS.pdf (246.8 Kb)
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Title Receptor protein tyrosine kinase phylogeny
Downloaded 16 times
Description Best of 50 ML trees as inferred by RAxML under the LG+ Γ model (see STAR methods). Purple, orange, blue, and brown texts indicate C. owczarzaki, Pigoraptor (strains Opistho-1 and Opistho-2), S. multiformis (strain Colp-12) and H. sapiens, respectively. The query sequence is indicated in red and with a grey box. An asterisk next to the Opistho-1/-2 and Colp-12 transcript(s) indicates the presence of a transmembrane domain plus a catalytic tyrosine kinase domain. The presence of Fibronectin-3 (FN3) and signal peptides indicating N-terminal complete proteins (SP) or of catalytic tyrosine kinase domains only (TyrKc only) is also indicated. Selected clades are collapsed to increase clarity; annotated H. sapiens homologs in all clades are indicated. Node supports are nonparametric ML bootstrap values obtained from 1000 ML replicates using the LG+ Γ model implemented in RAxML, numbers at nodes represent bootstrap supports of greater than 50%. The scale bar represents the estimated number of amino acid substitutions per site. TIE, tyrosine kinase with immunoglobulin like and EGF like domains; INSR, insulin receptor; INSRR, insulin receptor related receptor; IGF1R, insulin like growth factor 1 receptor; ERBB3, erb-b2 receptor tyrosine kinase 3; EPHB1, EPH receptor B1.
Download RecepTyrK_Opistho-2@52696_RAxML_50Trees_1..._2.pdf (352.5 Kb)
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Title Phylogenetic trees in newick format
Downloaded 8 times
Description All phylogenetic trees shown as Main Figure or Supplemental Figures in the manuscript are collected in this file as unrooted trees in newick format. Descriptions for the single trees can be found within the file.
Download Phylogenetic_trees_newick_format.docx (172.2 Kb)
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When using this data, please cite the original publication:

Hehenberger E, Tikhonenkov DV, Kolisko M, del Campo J, Esaulov AS, Mylnikov AP, Keeling PJ (2017) Novel Predators Reshape Holozoan Phylogeny and Reveal the Presence of a Two-Component Signaling System in the Ancestor of Animals. Current Biology 27(13): 2043-2050.e6. http://dx.doi.org/10.1016/j.cub.2017.06.006

Additionally, please cite the Dryad data package:

Hehenberger E, Tikhonenkov DV, Kolisko M, del Campo J, Esaulov AS, Mylnikov AP, Keeling PJ (2017) Data from: Novel predators reshape holozoan phylogeny and reveal the presence of a two-component signalling system in the ancestor of animals. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.26bv4
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