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

Transposable element insertions in ca. 5.7 Mb of orthologous genomic sequences from the coelacanth species <i>Latimeria chalumnae</i> and <i>L. menadoensis</i>.

<p>TE  =  Transposable Element; LINE  =  Long Interspersed Nuclear Element; SINE  =  Short Interspersed Nuclear Element; LTR  =  Long Terminal Repeat; CR1  =  Chicken Repeat 1; L1  =  LINE 1; L2  =  LINE 2; ERV  =  Endogenous Retrovirus; MITE  =  Miniature Inverted-repeat Transposable Element.</p><p>*The ERV insertion observed in <i>L. menadoensis</i> does not strictly correspond to an insertion polymorphism, the solo LTR observed at the orthologous site in <i>L. chalumnae</i> probably being the result of a recombination between the two LTRs framing the element (see main text).</p><p>**A composite insertion is observed in <i>L. menadoensis</i>, constituted by a Coeg-SINE flanked by two LF-SINEs in direct orientation. Only a “solo” LF-SINE is observed in <i>L. chalumnae</i>, suggesting deletion through homologous recombination between both LF-SINEs.</p><p>These “insertions” mostly comprise insertions <i>sensu stricto</i> but also a few deletions that occurred at the orthologous site in the other species.</p><p>Transposable element insertions in ca. 5.7 Mb of orthologous genomic sequences from the coelacanth species <i>Latimeria chalumnae</i> and <i>L. menadoensis</i>.</p

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

Interspecies Insertion Polymorphism Analysis Reveals Recent Activity of Transposable Elements in Extant Coelacanths

<div><p>Coelacanths are lobe-finned fish represented by two extant species, <i>Latimeria chalumnae</i> in South Africa and Comoros and <i>L. menadoensis</i> in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the <i>L. chalumnae</i> genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both <i>Latimeria</i> species. Comparison of 5.7 Mb (0.2%) of the <i>L. chalumnae</i> genome with orthologous Bacterial Artificial Chromosome clones from <i>L. menadoensis</i> allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both <i>Latimeria</i> species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in <i>Latimeria</i>.</p></div

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)

Structure of coelacanth endogenous retrovirus CoeERV1-1.

<p>(A) Solo-LTR observed in <i>L. chalumnae</i>. (B) Schematic representation of ERV insertion 23 found at the orthologous position in <i>L. menadoensis</i>. (C) Reconstructed structure of CoeERV1-1 in the <i>L. chalumnae</i> genome. TSD  =  Target Site Duplication; LTR  =  Long Terminal Repeats; Gag: ORF encoding protein for the viral capsid; Pol: ORF encoding proteins responsible for synthesis of the viral DNA and integration into host DNA, including protease (Pro), reverse transcriptase (RT), ribonuclease H (RH) and integrase (Int); Env: ORF encoding envelope protein.</p

Structural features of species-specific transposable element insertions in ca. 5.7 Mb of orthologous genomic sequences from the coelacanth species <i>Latimeria chalumnae</i> and <i>L. menadoensis</i>.

<p>ORF  =  Open Reading Frame; L. ch.  =  <i>Latimeria chalumnae</i>; L. me.  =  <i>Latimeria menadoensis</i>; IGR  =  Intergenic Region; RT  =  Reverse Transcriptase; APE  =  Apurinic/Apyrimidic Endonuclease; LTR  =  Long Terminal Repeat; ND  =  Not Detected; TSD  =  Target Site Duplication; *Number of BlastN hits in the analyzed regions, with hit length ≥80% of insertion length and identity ≥80%, criteria that are classically used to define TE families; ** Number of BlastN hits against <i>L. menadoensis</i> testis transcriptome with hit length ≥80 nt and identity ≥95%.</p><p>Structural features of species-specific transposable element insertions in ca. 5.7 Mb of orthologous genomic sequences from the coelacanth species <i>Latimeria chalumnae</i> and <i>L. menadoensis</i>.</p

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