Phylogenetic analyses of the visual opsin genes of the LWS, SWS1, SWS2, RH1 and RH2 clades

<p>Sequence based phylogenetic analyses of the visual opsin genes of the LWS, SWS1, SWS2, RH1 and RH2 clades, with additional analyses including pinopsins, vertebrate ancient (V/A) opsins and Ciona intestinalis opsins. The phylogenetic analyses were made using amino acid sequences predicted from the Ensembl genome browser (http://www.ensembl.org) version 60 (Nov 2010) and the <em>Lepisosteus oculatus</em> (spotted gar) genome assembly LepOcu1 (http://www.ncbi.nlm.nih.gov/genome/assembly/327908/), as well as sequences identified in the NCBI RefSeq database. Database identifiers, location data, genome assembly, and annotation notes for all sequences are included in 'Supplementary Table OPN.xlsx' (Excel spreadsheet).</p> <p><strong>File information:</strong></p> <p>Alignment files are included in FASTA-format: 'align_visual_opsins.fasta' and 'align_visual_opsins_VA_pinops.fasta'. This file format can be opened by most sequence analysis applications as well as text editors. The second alignment file includes additional pinopsin, V/A opsin and Ciona intestinalis opsin sequences, as detailed in 'Supplementary Table OPN.xlsx'. Phylogenetic tree files are included in Phylip/Newick format with the extension '.phb'. This file format can be opened by freely available phylogenetic tree viewers such as FigTree (http://tree.bio.ed.ac.uk/software/figtree/) and TreeView (http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/). The phylogenetic analyses were carried out based on the included alignments using both neighbor joining (NJ) and phylogenetic maximum likelihood (PhyML) methods. Phylogenetic trees are rooted with the human OPN3 amino acid sequence. Corresponding figures for all phylogenetic trees are also included as PDF files.</p> <p>Sequence names/leaf names include species abbreviations (see below) as well as chromosome numbers where known. For the human and zebrafish sequences the full HGNC and ZFIN gene symbols are included. For other species the clade name is indicated in the sequence names/leaf names.</p> <p>The species included in these analyses were (abbreviations and common names in parenthesis): <em>Homo sapiens</em> (Hsa, human), <em>Mus musculus</em> (Mmu, mouse), <em>Monodelphis domestica</em> (Mdo, grey short-tailed opossum), <em>Gallus gallus</em> (Gga, chicken), <em>Anolis carolinensis</em> (Aca, Carolina anole lizard), <em>Xenopus (Silurana) tropicalis</em> (Xtr, Western clawed frog), <em>Latimeria chalumnae</em> (Lch, coelacanth), <em>Lepisosteus oculatus</em> (Loc, spotted gar), <em>Danio rerio</em> (Dre, zebrafish), <em>Oryzias latipes</em> (Ola, medaka), <em>Gasterosteus aculeatus</em> (Gac, three-spined stickleback), <em>Tetraodon nigroviridis</em> (Tni, green spotted pufferfish), <em>Geotria australis</em> (Gau, pouched lamprey) and <em>Ciona intestinalis</em> (Cin, transparent sea squirt).</p> <p><strong>Method details:</strong></p> <p>Alignments were created using the ClustalW algorithm with the following settings: Gonnet weight matrix, gap opening penalty 10.0 and gap extension penalty 0.20. The alignments were edited manually in order to curate short, incomplete or highly divergent amino acid sequence predictions from the genome databases. In this way erroneous automatic exon predictions and exons that had not been predicted could be ratified.</p> <p>Phylogenetic analyses were carried out based on the included alignments. NJ trees were made using standard settings in ClustalX 2.0.12 (http://www.clustal.org/clustal2/), supported by a non-parametric bootstrap analysis with 1000 replicates. PhyML trees were made using the PhyML3.0 algorithm (http://www.atgc-montpellier.fr/phyml/‎) with the following settings: amino acid frequencies (equilibrium frequencies), proportion of invariable sites (with optimised p-invar) and gamma shape parameters were estimated from the alignments, the number of substitution rate categories was set to 8, BIONJ was chosen to create the starting tree, both NNI and SPR tree optimization methods were considered and both tree topology and branch length optimization were chosen. The JTT model of amino acid substitution was chosen using ProtTest 3.0 (https://bitbucket.org/diegodl/prottest3/downloads). PhyML trees are supported by a non-parametric bootstrap analysis with 100 replicates applied through PhyML.</p

Phylogenetic Maximum Likelihood tree of the GRIN2 gene family

<p>Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements. BMC Evolutionary Biology 2012, 12:231 doi:10.1186/1471-2148-12-231. Please refer to this article if using this figure.</p> <p><strong>Figure 3 Phylogenetic Maximum Likelihood tree of the GRIN2 gene family.</strong> The<br>ionotropic glutamate receptor 2 (GRIN2) gene family is a neighboring family of the <em>SSTR2, -</em><br><em>3</em> and -<em>5</em> chromosomal regions. Phylogenetic methods, monophyletic clusters and leaf names<br>as in Figure 2.</p

Paralogous SSTR-gene bearing chromosome regions in the stickleback and zebrafish genomes

<p>Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements. BMC Evolutionary Biology 2012, 12:231 doi:10.1186/1471-2148-12-231. Please refer to this article if using this figure.</p> <p><strong>Figure 7 Continued from Figure 6.</strong> Paralogous chromosome regions in the stickleback and<br>zebrafish genomes. More rearrangements could be identified in the zebrafish genome than in<br>the stickleback or medaka genomes.</p> <p> </p

Phylogenetic Maximum Likelihood trees of the FNG and FSCN gene families

<p>Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements. BMC Evolutionary Biology 2012, 12:231 doi:10.1186/1471-2148-12-231. Please refer to this article if using this figure.</p> <p><strong>Figure 4 Phylogenetic Maximum Likelihood trees of the FNG and FSCN gene families.</strong> The fringe homolog (FNG) and fascin homolog 1 and 2 (FSCN) gene families are neighboring gene families of the SSTR2, -3 and -5 chromosomal regions. Phylogenetic methods, monophyletic clusters and leaf names as in Figure 2. All neighboring gene family trees for the SSTR2, -3 and -5-bearing regions, including NJ analyses and all branch support values, are shown in Figure S21-S50 (see Additional file 6).</p

Phylogenetic analyses of 47 syntenic gene families in SSTR gene-bearing chromosome regions

<p>Sequence based phylogenetic analyses of 47 gene families identified in an analysis of conserved synteny around somatostatin receptor gene-bearing chromosome regions. For each gene family amino acid sequences were predicted from the Ensembl genome browser (http://www.ensembl.org) and used to create sequence alignments and phylogenetic trees. Gene families were defined based on Ensembl protein family predictions. Database identifiers, location data, genome assembly information and annotation notes for all identified protein families and sequences are included in 'Supplemental Table 2.xlsx' and 'Supplemental Table 3.xlsx' (Excel spreadsheets). </p> <p>File information: </p> <p>Gene families are identified by unique abbreviations based on approved HUGO Gene Nomenclature Committe (HGNC) gene symbols, or known aliases from the NCBI Entrez Gene database. For each gene family an alignment file '...align.fasta', a neighbor joining tree '...NJ_rooted.phb' and a phylogenetic maximum likelihood tree '...PhyML_rooted.phb' are included. </p> <p>Alignments are included in FASTA format with the extension '.fasta'. This file format can be opened by most sequence analysis applications as well as text editors. Alignments were created using the ClustalWS sequence alignment program with standard settings (Gonnet weight matrix, gap opening penalty 10.0 and gap extension penalty 0.20) through the JABAWS 2 tool in Jalview 2.7 (http://www.jalview.org/).</p> <p>Phylogenetic tree files are included in Phylip/Newick format with the extension '.phb'. This file format can be opened by freely available phylogenetic tree viewers such as FigTree (http://tree.bio.ed.ac.uk/software/figtree/) and TreeView (http://darwin.zoology.gla.ac.uk/~rpage/treeviewx/). The phylogenetic analyses were carried out based on the included alignments using bootstrap-supported neighbor joining (NJ) as well as phylogenetic maximum likelihood (PhyML) methods. Phylogenetic trees are rooted with identified <em>Drosophila melanogaster </em>(fruit fly) sequences, or with identified <em>Ciona intestinalis</em> or <em>Ciona savignyi</em> (tunicates), <em>Branchiostoma floridae </em>(Florida lancelet, amphioxus), or <em>Caenorhabditis elegans</em> (nematode) sequences if no fruit fly sequence could be found. </p> The NJ trees are supported by non-parametric bootstrap analyses with 1000 replicates, applied through ClustalX 2.0 (http://www.clustal.org/clustal2/) with standard settings. The PhyML trees are supported by non-parametric bootstrap analyses with 100 replicates made using the PhyML 3.0 algorithm (http://www.atgc-montpellier.fr/phyml/) with the following settings: amino acid frequencies (equilibrium frequencies), proportion of invariable sites (with optimised p-invar) and gamma-shape parameters were estimated from the datasets; the number of substitution rate categories was set to 8; BIONJ was chosen to create the starting tree and the nearest neighbor interchange (NNI) tree improvement method was used to estimate the best topology; both tree topology and branch length optimization were chosen. The LG model of amino acid substitution, which is standard for PhyML 3.0, was chosen.   Species abbreviations are applied as follows:   <em>Homo sapiens</em> (Hsa, human), <em>Mus musculus</em> (Mmu, mouse), <em>Canis familiaris</em> (Cfa, dog), <em>Monodelphis domestica</em> (Mdo, grey short-tailed opossum), <em>Macropus eugenii</em> (Meu, tammar wallaby), <em>Ornitorhynchus anatinus</em> (Oan, platypus), <em>Gallus gallus</em> (Gga, chicken), <em>Taeniopygia guttata</em> (Tgu, zebra finch), <em>Meleagris gallopavo</em> (Mga, turkey), <em>Anolis carolinensis</em> (Aca, Carolina anole lizard), <em>Silurana (Xenopus) tropicalis</em> (Xtr, Western clawed frog), <em>Danio rerio</em> (Dre, zebrafish), <em>Oryzias latipes</em> (Ola, medaka), <em>Gasterosteus aculeatus</em> (Gac, three-spined stickleback), <em>Tetraodon nigroviridis</em> (Tni, green spotted pufferfish), <em>Takifugu rubripes</em> (Tru, fugu), <em>Ciona intestinalis</em> (Cin, tunicate), <em>Ciona savignyi</em> (Csa, tunicate), <em>Branchiostoma floridae</em> (Bfl, amphioxus), <em>Caenorhabditis elegans</em> (Cel, nematode) and <em>Drosophila melanogaster</em> (Dme, fruit fly).   The following gene families are included in this file set:   ABHD12: Abhydrolase domain containing 12 CFL: Cofilin and destrin (actin depolymerizing factor) FLRT: Fibronectin leucine rich transmembrane protein FOXA: Forkhead box A ISM: Isthmin homolog JAG: Jagged NIN: Ninein (GSK3B interacting protein) NKX2: NK2 homeobox 1 and 4 PAX: Paired box 1 and 9 PYG: Glycogen phosphorylase; brain, liver and muscle variants RALGAPA: Ral GTPase activating protein, alpha subunit RIN: Ras and Rab interactor SEC23: Sec23 homologs A and B SLC24A: Solute carrier family 24 members 3 and 4 SNX: Sorting nexin 5, 6 and 32 SPTLC: Serine palmitoyltransferase, long chain base subunit 2 and 3 VSX: Visual system homeobox   ADAP: ArfGAP with dual PH domains ATP2A: ATPase, Ca++ transporting, cardiac muscle, fast twitch C1QTNF: C1q and tumor necrosis factor related protein CABP: Calcium binding protein 1, 3, 4 and 5 CACNA1: Calcium channel, voltage dependent, T type alpha subunit CREBBP: CREB binding protein CYTH: Cytohesin FAM20: Family with sequence similarity 20 FNG: Fringe homolog FSCN: Fascin homolog 1 and 2, actin-bundling protein GLPR: Glucagon, glucagon-like and gastric inhibitory polypeptide receptors GGA: Golgi-associated, gamma adapting ear containing, ARF-binding protein GRIN2: Glutamate receptor, ionotropic, N-methyl D-aspartate 2 KCNJ: Potassium inwardly-rectifying channel, subfamily J member 2, 4, 12 and 14 KCTD: Potassium channel tetramerisation domain containing 2, 5 and 17 METRN: Meteorin, glial cell differentiation regulator NDE: nudE nuclear distribution gene E homolog RAB11FIP: RAB11 family interacting protein 3 and 4 (class II) RADIL: Ras association and DIL domains/Ras interacting protein RHBDF: Rhomboid 5 homolog RHOT: Ras homolog gene family, member T1 and T2 RPH3A: Rabphilin 3A homolog/double C2-like domains, alpha SDK: Sidekick cell adhesion molecule SOX: Sex-determining region Y-box 8, 9 and 10 TEX2: Testis expressed 2 TNRC6: Trinucleotide repeat containing 6 TOM1: Target of myb1 TTYH: Tweety homolog USP: Ubiquitin specific peptidase 31 and 43 WFIKKN: WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain contanin

Phylogenetic Maximum Likelihood trees of the PYG and RIN gene families

<p>Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements. BMC Evolutionary Biology 2012, 12:231 doi:10.1186/1471-2148-12-231. Please refer to this article if using this figure.</p> <p><strong>Figure 2 Phylogenetic Maximum Likelihood trees of the PYG and RIN gene families.</strong><br>The glycogen phosphorylase (PYG) and Ras and Rab interactor (RIN) gene families are<br>neighboring families of the SSTR1, -4 and -6 chromosomal regions. Monophyletic subtype<br>clusters including both tetrapod and teleost sequences are indicated by bars to the right.<br>Chromosomal or genomic scaffold assignments of the family members are indicated next to<br>species names. Lowercase a and b are used to distinguish sequences located on the same<br>chromosomes. Branch support values (bootstrap replicates) for deep divergences are shown at<br>the nodes. The trees were rooted with the identified fruit fly sequences. All neighboring gene<br>family trees for the SSTR1, -4 and -6-bearing regions, including NJ analyses and all branch<br>support values, are shown in Figures S4-S20 (see Additional file 5).</p

Phylogenetic Maximum Likelihood tree of the somatostatin receptor gene family

<p>Published in: Ocampo Daza D, Sundström G, Bergqvist CA, Larhammar D. <em>The evolution of vertebrate somatostatin receptors and their gene regions involves extensive chromosomal rearrangements.</em> BMC Evolutionary Biology 2012, 12:231 doi:10.1186/1471-2148-12-231. Please refer to this article if using this figure.</p> <p><strong>Figure 1 Phylogenetic Maximum Likelihood tree of the somatostatin receptor gene</strong><br><strong>family.</strong> The topology is supported by a non-parametric bootstrap test with 100 replicates as<br>well as an SH-like approximate likelihood ratio test (aLRT). The tree is rooted with the<br>human kisspeptin receptor 1 sequence (not shown). Branch support (bootstrap replicates) for<br>deep divergences is shown at the nodes. All branch support values are shown in Figure S1<br>(bootstrap replicates) and Figure S2 (aLRT) (see Additional file 2). The phylogenetic tree<br>shows six well-supported subtype clusters, with the somatostatin receptor subtypes <em>SSTR2, -3</em><br>and <em>-5</em> forming one ancestral branch and the <em>SSTR1, -4</em> and <em>-6</em> receptor subtypes forming one<br>ancestral branch. This phylogenetic analysis supports the emergence of all six subtypes early<br>in vertebrate evolution, with the subsequent loss of <em>SSTR4</em> in ray-finned fishes, before the<br>divergence of the spotted gar and teleost lineages, and of <em>SSTR6</em> in the tetrapod lineage. All<br>six subtypes could be identified in the coelacanth genome. A seventh <em>SSTR2</em>-like sequence,<br>called <em>SSTRX</em> in the tree, could also be identified on the same genomic scaffold in the<br>coelacanth genome (see Additional file 1, Supplemental note 1). There are well-supported<br>teleost-specific duplicate branches of <em>SSTR2, -3</em> and <em>-5</em>, although all could not be identified in<br>all teleost genomes. These duplicates have been named <em>a</em> and <em>b</em> based on the phylogenetic<br>analysis. There is a third <em>SSTR3</em> sequence in the green puffer, called <em>SSTR3c</em> in the tree.</p> <p> </p

Supplementary data archive for the Delhomme et al., 2015 manuscript.

This archive contains supplementary data for the Delhomme et al, 2015 manuscript. It contains two directories annotation and fasta. The annotation directory contains the metadata resulting from several analysis conducted on the transcriptome assembly. The fasta directory contains the transcriptome assembly and several different subsets of it. The description of the methods used to generate: 1) the different fasta sets that can be found in the fasta directory 2) the metadata summarized in the annotation tsv file can be found in the manuscript method section

Comparison of canFam2.0 and canFam3.1.

<p>Comparison of canFam2.0 and canFam3.1.</p

Distance trees of expression profiles.

<p>We constructed neighbor-joining trees based on the correlation between expression values (FPKM>1.0) between samples, with 1 minus Spearman's rho defining the distance. Colors denote library construction methods (poly-A: blue, DSN: red). We divided transcribed loci into (a) protein coding genes with RNA-Seq support, either annotated by EnsEMBL in dog or EnsEMBL in the human orthologous regions. Replicates cluster together, so do the library constructions methods poly-A and DSN, as well as related tissues, such as heart and muscle; (b) antisense transcripts, that overlap at least one exon of a protein coding gene, as defined in (a). With the exception of testis, poly-A and DSN separate the samples, with both the poly-A and DSN sub-trees maintaining closer relationships between the related tissues heart and muscle; (c) spliced intergenic loci, excluding sequences that have coding potential. Similar to protein coding genes, the poly-A and DSN group by tissue first, with the exception of kidney DSN; and (d) intergenic and uncharacterized single-exon transcript loci. In this set, DSN and poly-A are, similar to antisense loci, the most dominant factor when grouping samples.</p