Evolution of the receptors for growth hormone, prolactin, erythropoietin and thrombopoietin in relation to the vertebrate tetraploidizations [DATASET]

Version 2 2017-07-03, 11:23

Version 1 2017-06-24, 08:37

dataset

posted on 2017-07-03, 11:23 authored by Daniel Ocampo DazaDaniel Ocampo Daza, Dan LarhammarDan Larhammar

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.

Supporting data for manuscript GCE-17-19 submitted to General and Comparative Endocrinology.

Abbreviations:

CRFA4: Cytokine receptor family member A4

EPOR: Erythropoietin receptor

GHR: Growth hormone receptor

PRLR: Prolactin receptor

LBD: Ligand-binding domain

MPL: Myoproliferative leukemia proto-oncogene

TPOR: Thrombopoietin receptor

Files:

GHRfam_data.xlxs: Location data, sequence identifiers and prediction/annotation notes for all identified GHR, PRLR, CRFA4, EPOR and TPOR (MPL) sequences. The table also includes species, genome assembly and sequence quality information.

GHRfam_all_seq.fasta: All curated GHR, PRLR, CRFA4, EPOR and TPOR (MPL) 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 TPOR sequences except anole lizard; chicken and anole lizard PRLR; and cartilaginous fish GHR. The corresponding full-length sequences are marked "_full".

GHRfam_align.fasta: Edited amino acid sequence alignment of GHR, PRLR, CRFA4, EPOR and TPOR (MPL) sequences. Sequence information is shown in 'GHRfam_data.xlxs', including species abbreviations used in sequence names.

GHRfam_PhyML_tree_raw.phb: 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.

GHRfam_PhyML_tree_midpoint.phb: Midpoint-rooted version of the phylogenetic tree above. Midpoint identified in FigTree v1.4.3.

GHRfam_LBD_align.fasta: Amino acid sequence alignment of only ligand-binding domains of GHR, PRLR, CRFA4, EPOR and TPOR (MPL) sequences.

GHRfam_LBD_PhyML_tree_raw.phb: PhyML tree analysis of GHR, PRLR, CRFA4, EPOR and TPOR (MPL) ligand-binding domains. Output file from Seaview v4.6.1 in PHYLIP/Newick format.

GHRfam_LBD_PhyML_tree_midpoint.phb: Midpoint-rooted version of the phylogenetic tree above. Midpoint identified in FigTree v1.4.3.

GHRfam_Bfl_align.fasta: Amino acid sequence alignment including putative Branchiostoma floridae family member. Edited to include only extracellular domains. Extended N-terminal of B. floridae sequence not included.

GHRfam_Bfl_PhyML_tree.phb: PhyML tree analysis of GHR, PRLR, CRFA4, EPOR and TPOR (MPL) extracellular domains, including putative Branchiostoma floridae family member. Output file from Seaview v4.6.1 in PHYLIP/Newick format.

Neighboring_family_data.xlsx: Location data, sequence identifiers and prediction/annotation notes for 18 neighboring gene families in the chromosomal regions of GHR, PRLR, EPOR and TPOR (MPL) genes. Includes explanations of family abbreviations and gene names used in sequence alignment and phylogenetic tree files.

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.

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.

Outdated files shared before peer-review are included in the archive file Pre-review-data.zip.