Evolution of pigment synthesis pathways by gene and genome duplication in fish-5

<p><b>Copyright information:</b></p><p>Taken from "Evolution of pigment synthesis pathways by gene and genome duplication in fish"</p><p>http://www.biomedcentral.com/1471-2148/7/74</p><p>BMC Evolutionary Biology 2007;7():74-74.</p><p>Published online 11 May 2007</p><p>PMCID:PMC1890551.</p><p></p>s. The tree is rooted with Gchfr from nematode. Numbers at the branches denote bootstrap values (maximum likelihood/neighbor joining) above 50%. Gchfr is duplicated in salmon and rainbow trout due to the salmonid-specific tetraploidization

Evolution of pigment synthesis pathways by gene and genome duplication in fish-2

<p><b>Copyright information:</b></p><p>Taken from "Evolution of pigment synthesis pathways by gene and genome duplication in fish"</p><p>http://www.biomedcentral.com/1471-2148/7/74</p><p>BMC Evolutionary Biology 2007;7():74-74.</p><p>Published online 11 May 2007</p><p>PMCID:PMC1890551.</p><p></p>sitions. The repeat region [21] was excluded from the alignment. The tree was rooted with human GPNMB. Numbers at the branches denote bootstrap values (maximum likelihood/neighbor joining) above 50%. (b) Synteny of -containing regions in vertebrate genomes. The human region is syntenic to two paralogons in Tetraodon (Tni), stickleback (Gac), medaka (Ola) and zebrafish (Dre). Numbered bars represent genes contributing to conserved synteny, genes that do not contribute to conserved synteny are not shown. Blue bars indicate genes that are duplicated along with . Dotted lines connect orthologous genes

Evolution of pigment synthesis pathways by gene and genome duplication in fish-6

<p><b>Copyright information:</b></p><p>Taken from "Evolution of pigment synthesis pathways by gene and genome duplication in fish"</p><p>http://www.biomedcentral.com/1471-2148/7/74</p><p>BMC Evolutionary Biology 2007;7():74-74.</p><p>Published online 11 May 2007</p><p>PMCID:PMC1890551.</p><p></p>ions. The tree is rooted with Spr from fruitfly. Numbers at the branches denote bootstrap values (maximum likelihood/neighbor joining) above 50%. Groups are assigned according to synteny. (b) Synteny of regions in vertebrates. The human region is syntenic to two paralogons in Takifugu (Tru), stickleback (Gac) and zebrafish (Dre). was possibly lost in Tetraodon (Tni) and medaka (Ola). Numbered bars represent genes contributing to conserved synteny, genes that do not contribute to conserved synteny are not shown. Blue indicates genes that are duplicated along with . Dotted lines connect orthologous genes

Evolution of pigment synthesis pathways by gene and genome duplication in fish-1

<p><b>Copyright information:</b></p><p>Taken from "Evolution of pigment synthesis pathways by gene and genome duplication in fish"</p><p>http://www.biomedcentral.com/1471-2148/7/74</p><p>BMC Evolutionary Biology 2007;7():74-74.</p><p>Published online 11 May 2007</p><p>PMCID:PMC1890551.</p><p></p>y based on 570 AA positions. The tree is mid-point rooted. Numbers at the branches denote bootstrap values (maximum likelihood/neighbor joining). Bootstrap values above 50 are shown. Tyrp1a and Tyrp1b are assigned according to the analysis of their genomic environment. (b) Synteny of -containing regions in vertebrate genomes. The human region is syntenic to two paralogons in Tetraodon (Tni), stickleback (Gac) and medaka (Ola). was apparently lost in the zebrafish (Dre). (c) Synteny of -containing regions in vertebrate genomes. The human region is syntenic to two paralogons in stickleback, medaka and zebrafish. A pseudogene is found in Tetraodon (asterisk). Numbered bars represent genes contributing to conserved synteny, genes that do not contribute to conserved synteny are not shown. Blue bars indicate genes that are duplicated along with or , respectively. Dotted lines connect orthologous genes. (grey bars), another teleost-specific pigmentation gene duplicate [17] is found 3' of in the four teleost genomes but belongs to a different paralogon (see text)

Evolution of pigment synthesis pathways by gene and genome duplication in fish-8

<p><b>Copyright information:</b></p><p>Taken from "Evolution of pigment synthesis pathways by gene and genome duplication in fish"</p><p>http://www.biomedcentral.com/1471-2148/7/74</p><p>BMC Evolutionary Biology 2007;7():74-74.</p><p>Published online 11 May 2007</p><p>PMCID:PMC1890551.</p><p></p>tions. The tree is rooted with Dhpr from urochordates. Numbers at the branches denote bootstrap values (maximum likelihood/neighbor joining) above 50%. (b) Synteny of regions in vertebrates. The human region is syntenic to two paralogons in Tetradon (Tni), stickleback (Gac), medaka (Ola) and zebrafish (Dre). was apparently lost in Tetraodon (Tni), stickleback (Gac) and medaka (Ola) and further duplicated in zebrafish, so that two duplicates, and , are found on chromosome 1. Numbered bars represent genes contributing to conserved synteny, genes that do not contribute to conserved synteny are not shown. Blue bars indicate genes that are also duplicated. Dotted lines connect orthologous genes

Evolution of pigment synthesis pathways by gene and genome duplication in fish-3

<p><b>Copyright information:</b></p><p>Taken from "Evolution of pigment synthesis pathways by gene and genome duplication in fish"</p><p>http://www.biomedcentral.com/1471-2148/7/74</p><p>BMC Evolutionary Biology 2007;7():74-74.</p><p>Published online 11 May 2007</p><p>PMCID:PMC1890551.</p><p></p>iopterin from GTP (top line), the Hbiopterin regeneration pathway (grey) and the synthesis of yellow pteridine pigments. The formation of orange drosopterin has not been elucidated yet in vertebrates. In , the clot enzyme is involved [53], which corresponds to the vertebrate Txnl5 protein. Asterisks indicate hypothetical reactions and question marks unidentified enzymes. Red indicates duplications during the fish-specific genome duplication, blue other types of duplication

Evolution of pigment synthesis pathways by gene and genome duplication in fish-0

<p><b>Copyright information:</b></p><p>Taken from "Evolution of pigment synthesis pathways by gene and genome duplication in fish"</p><p>http://www.biomedcentral.com/1471-2148/7/74</p><p>BMC Evolutionary Biology 2007;7():74-74.</p><p>Published online 11 May 2007</p><p>PMCID:PMC1890551.</p><p></p>his requires members of the Tyrosinase family (TYR, DCT, TYRP1) and probably Silver (SILV). Three melanosomal transporters (OCA2, AIM1 and SLC24A5) are crucial for proper melanin synthesis. Red indicates duplications during the fish-specific genome duplication

Evolution of pigment synthesis pathways by gene and genome duplication in fish-7

<p><b>Copyright information:</b></p><p>Taken from "Evolution of pigment synthesis pathways by gene and genome duplication in fish"</p><p>http://www.biomedcentral.com/1471-2148/7/74</p><p>BMC Evolutionary Biology 2007;7():74-74.</p><p>Published online 11 May 2007</p><p>PMCID:PMC1890551.</p><p></p>e tree is rooted with Pcbd from sea urchin. Numbers at the branches denote bootstrap values (maximum likelihood/neighbor joining) above 50%. Pcbd was duplicated in vertebrates (Pcbd1 and Pcbd2). In Takifugu, two are observed in scaffolds 53 and 178. The latter (red) is a retro-pseudogene. (b) Exon-intron structure of Pcbd1. Pcbd1 from human and Takifugu scaffold 53 consists of four exons indicated by 4 blocks. Takifugu scaffold 178 contains a "processed" pseudogene with a single exon (bottom row) and a premature stop codon (arrowhead)

CrossQuery syntax examples.

<p>CrossQuery syntax examples.</p

The general interface of CrossQuery employs a top-tab navigation to jump between the possible actions (yellow box labelled "Navigation").

<p>The here shown "SETUP" tab allows to edit the query-settings ("Input" box). The box highlighted on the bottom ("Control") features three buttons that will run the given query on the server or allow loading and saving queries for later use.</p