DOI: 10.6084/m9.figshare.4531364
title: Evolution of the receptors for growth hormone, prolactin, erythropoietin and thrombopoietin in relation to the vertebrate tetraploidizations [DATASET]

description: Phylogenetic analyses and chromosomal data for the single-chain cytokine class I receptor family (GHR, PRLR, CRFA4, EPOR and TPOR) and 18 neighboring gene families in paralogous chromosome blocks.<br>Supporting data for manuscript GCE-17-19 submitted to <i>General and Comparative Endocrinology</i>.<br><b>Abbreviations:</b><br>CRFA4: Cytokine receptor family member A4<br>EPOR: Erythropoietin receptor<br>GHR: Growth hormone receptorPRLR: Prolactin receptorLBD: Ligand-binding domain<br>MPL: Myoproliferative leukemia proto-oncogene<br>TPOR: Thrombopoietin receptor<br><b>Files:</b><br><b>GHRfam_data.xlxs:</b> Location data, sequence identifiers and prediction/annotation notes for all identified <i>GHR</i>, <i>PRLR</i>, <i>CRFA4</i>, <i>EPOR </i>and <i>TPOR</i> (<i>MPL</i>) sequences. The table also includes species, genome assembly and sequence quality information.<br><b>GHRfam_all_seq.fasta:</b> All curated <i>GHR</i>, <i>PRLR</i>, <i>CRFA4</i>, <i>EPOR</i> and <i>TPOR</i> (<i>MPL</i>) amino acid sequences identified in this study. Partial sequences are indicated by an asterisk (*) in the sequence name. Sequences marked "_edited" have one duplicated ligand-binding domain removed. This applies to all <i>TPOR </i>sequences except anole lizard; chicken and anole lizard <i>PRLR</i>; and cartilaginous fish <i>GHR</i>. The corresponding full-length sequences are marked "_full".<br><br><b>GHRfam_align.fasta:</b> Edited amino acid sequence alignment of <i>GHR, PRLR, CRFA4, EPOR </i>and <i>TPOR </i>(<i>MPL</i>) sequences. Sequence information is shown in '<b>GHRfam_data.xlxs</b>', including species abbreviations used in sequence names. <br><b>GHRfam_PhyML_tree_raw.phb: </b>Phylogenetic Maximum Likelihood (PhyML) tree analysis of the single-chain cytokine class I receptor family. Output file from Seaview v4.6.1 in PHYLIP/Newick format. <br><br><b>GHRfam_PhyML_tree_midpoint.phb: </b>Midpoint-rooted version of the phylogenetic tree above. Midpoint identified in FigTree v1.4.3.<br><br><b>GHRfam_LBD_align.fasta: </b>Amino acid sequence alignment of only ligand-binding domains of <i>GHR, PRLR, CRFA4, EPOR </i>and <i>TPOR </i>(<i>MPL</i>) sequences.<br><br><b>GHRfam_LBD_PhyML_tree_raw.phb:</b> PhyML tree analysis of <i>GHR, PRLR, CRFA4, EPOR </i>and <i>TPOR </i>(<i>MPL</i>) ligand-binding domains. Output file from Seaview v4.6.1 in PHYLIP/Newick format. <br><br><b>GHRfam_LBD_PhyML_tree_midpoint.phb:</b> Midpoint-rooted version of the phylogenetic tree above. Midpoint identified in FigTree v1.4.3.<br><br><b>GHRfam_Bfl_align.fasta: </b>Amino acid sequence alignment including putative <i>Branchiostoma floridae </i>family member. Edited to include only extracellular domains. Extended N-terminal of <i>B. floridae </i>sequence not included. <br><br><b>GHRfam_Bfl_PhyML_tree.phb:</b> PhyML tree analysis of <i>GHR, PRLR, CRFA4, EPOR </i>and <i>TPOR </i>(<i>MPL</i>) extracellular domains, including putative <i>Branchiostoma floridae </i>family member. Output file from Seaview v4.6.1 in PHYLIP/Newick format. <br><br><b>Neighboring_family_data.xlsx: </b>Location data, sequence identifiers and prediction/annotation notes for 18 neighboring gene families in the chromosomal regions of <i>GHR, PRLR, EPOR </i>and <i>TPOR </i>(<i>MPL</i>) genes. Includes explanations of family abbreviations and gene names used in sequence alignment and phylogenetic tree files.<br><br>Amino acid sequence alignments as well as unrooted and rooted PhyML tree files are included for all 18 neighboring gene families. All tree files are in PHYLIP/Newick format.<br>For the FGF3/7/10/22 and ZFR families, two analyses were made for each family owing to the unclear relationships of putative invertebrate family members. <br>Outdated files shared before peer-review are included in the archive file <b>Pre-review-data.zip</b>.