Schistosomiasis in Tone River Area(Kurzfassen)

Amino acid sequence alignment of the ABLIM family which is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The sequences were aligned using ClustalO with standard settings within the Seaview 4.5.3 program

PhyML tree of the AFAP family

Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the AFAP family. AFAP is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml)

Amino acid sequence alignment of the STK32 family

Amino acid sequence alignment of the STK32 family which is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The sequences were aligned using ClustalO with standard settings within the Seaview 4.5.3 program

Transducin Duplicates in the Zebrafish Retina and Pineal Complex : Differential Specialisation after the Teleost Tetraploidisation

Gene duplications provide raw materials that can be selected for functional adaptations by evolutionary mechanisms. We describe here the results of 350 million years of evolution of three functionally related gene families: the alpha, beta and gamma subunits of transducins, the G protein involved in vision. Early vertebrate tetraploidisations resulted in separate transducin heterotrimers: gnat1/gnb1/gngt1 for rods, and gnat2/gnb3/gngt2 for cones. The teleost- specific tetraploidisation generated additional duplicates for gnb1, gnb3 and gngt2. We report here that the duplicates have undergone several types of subfunctionalisation or neofunctionalisation in the zebrafish. We have found that gnb1a and gnb1b are co-expressed at different levels in rods; gnb3a and gnb3b have undergone compartmentalisation restricting gnb3b to the dorsal and medial retina, however, gnb3a expression was detected only at very low levels in both larvae and adult retina; gngt2b expression is restricted to the dorsal and medial retina, whereas gngt2a is expressed ventrally. This dorsoventral distinction could be an adaptation to protect the lower part of the retina from intense light damage. The ontogenetic analysis shows earlier onset of expression in the pineal complex than in the retina, in accordance with its earlier maturation. Additionally, gnb1a but not gnb1b is expressed in the pineal complex, and gnb3b and gngt2b are transiently expressed in the pineal during ontogeny, thus showing partial temporal subfunctionalisation. These retina-pineal distinctions presumably reflect their distinct functional roles in vision and circadian rhythmicity. In summary, this study describes several functional differences between transducin gene duplicates resulting from the teleost-specific tetraploidisation

The vertebrate ancestral repertoire of visual opsins, transducin alpha subunits and oxytocin/vasopressin receptors was established by duplication of their shared genomic region in the two rounds of early vertebrate genome duplications

Background: Vertebrate color vision is dependent on four major color opsin subtypes: RH2 (green opsin), SWS1 (ultraviolet opsin), SWS2 (blue opsin), and LWS (red opsin). Together with the dim-light receptor rhodopsin (RH1), these form the family of vertebrate visual opsins. Vertebrate genomes contain many multi-membered gene families that can largely be explained by the two rounds of whole genome duplication (WGD) in the vertebrate ancestor (2R) followed by a third round in the teleost ancestor (3R). Related chromosome regions resulting from WGD or block duplications are said to form a paralogon. We describe here a paralogon containing the genes for visual opsins, the G-protein alpha subunit families for transducin (GNAT) and adenylyl cyclase inhibition (GNAI), the oxytocin and vasopressin receptors (OT/VP-R), and the L-type voltage-gated calcium channels (CACNA1-L). Results: Sequence-based phylogenies and analyses of conserved synteny show that the above-mentioned gene families, and many neighboring gene families, expanded in the early vertebrate WGDs. This allows us to deduce the following evolutionary scenario: The vertebrate ancestor had a chromosome containing the genes for two visual opsins, one GNAT, one GNAI, two OT/VP-Rs and one CACNA1-L gene. This chromosome was quadrupled in 2R. Subsequent gene losses resulted in a set of five visual opsin genes, three GNAT and GNAI genes, six OT/VP-R genes and four CACNA1-L genes. These regions were duplicated again in 3R resulting in additional teleost genes for some of the families. Major chromosomal rearrangements have taken place in the teleost genomes. By comparison with the corresponding chromosomal regions in the spotted gar, which diverged prior to 3R, we could time these rearrangements to post-3R. Conclusions: We present an extensive analysis of the paralogon housing the visual opsin, GNAT and GNAI, OT/VP-R, and CACNA1-L gene families. The combined data imply that the early vertebrate WGD events contributed to the evolution of vision and the other neuronal and neuroendocrine functions exerted by the proteins encoded by these gene families. In pouched lamprey all five visual opsin genes have previously been identified, suggesting that lampreys diverged from the jawed vertebrates after 2R.De två (2) första författarna delar förstaförfattarskapet.</p

PhyML tree of the SH3TC family

Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the SH3TC family. SH3TC is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml)

Supplementary_file_1 - PDE6 catalytic subunit amino acid sequence alignment

Amino acid alignment of the PDE6 catalytic subunit gene family. The sequences were aligned using ClustalO with standard settings within the Seaview 4.5.3 program

Amino acid sequence alignment of the SH3TC family

Amino acid sequence alignment of the SH3TC family which is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The sequences were aligned using ClustalO with standard settings within the Seaview 4.5.3 program

PhyML tree of the TBC1D family

Phylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the TBC1D family. TBC1D is one of the gene families that was identified as a neighbouring gene family to the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml)

Amino acid sequence alignment of the PDE6 catalytic subunit family with additional Birds reptiles

Amino acid alignment of the PDE6 catalytic subunit gene family with additional birds and reptiles. The sequences were aligned using ClustalW with standard settings within the Jalview 2.7 program