DOI: 10.5061/dryad.k2f04
title: Data from: Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity

description: Background: Phosphodiesterase 6 (PDE6) is a protein complex that
 hydrolyses cGMP and acts as the effector of the vertebrate
 phototransduction cascade. The PDE6 holoenzyme consists of catalytic and
 inhibitory subunits belonging to two unrelated gene families. Rods and
 cones express distinct genes from both families: PDE6A and PDE6B code for
 the catalytic and PDE6G the inhibitory subunits in rods while PDE6C codes
 for the catalytic and PDE6H the inhibitory subunits in cones. We performed
 phylogenetic and comparative synteny analyses for both gene families in
 genomes from a broad range of animals. Furthermore, gene expression was
 investigated in zebrafish. Results: We found that both gene families
 expanded from one to three members in the two rounds of genome doubling
 (2R) that occurred at the base of vertebrate evolution. The PDE6
 inhibitory subunit gene family appears to be unique to vertebrates and
 expanded further after the teleost-specific genome doubling (3R). We also
 describe a new family member that originated in 2R and has been lost in
 amniotes, which we have named pde6i. Zebrafish has retained two additional
 copies of the PDE6 inhibitory subunit genes after 3R that are highly
 conserved, have high amino acid sequence identity, are coexpressed in the
 same photoreceptor type as their amniote orthologs and, interestingly,
 show strikingly different daily oscillation in gene expression levels.
 Conclusions: Together, these data suggest specialisation related to the
 adaptation to different light intensities during the day-night cycle, most
 likely maintaining the regulatory function of the PDE inhibitory subunits
 in the phototransduction cascade.
description: PhyML tree of the ABLIM
 family.Phylogenetic maximum
 likelihood tree using the JTT amino acid substitution model and 100
 bootstrap replicates of the ABLIM family. ABLIM 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
 implementation in the Seaview 4.5.3 program.ABLIM_20141128-PhyML_tree_phb_copy.phbPhyML tree of the AFAP familyPhylogenetic 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).afap_20141201_phyml_tree_copy.phbPhyML tree of the DPYS familyPhylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the DPYS family. DPYS 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).dpys_20141201_phy_phyml_tree_copy.phbPhyML tree of the JAKMIP familyPhylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the JAKMIP family. JAKMIP 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 implementation in the Seaview 4.5.3 program.JAKMIP_20141127-PhyML_tree_phb_copy.phbPhyML tree of the PPP2R2 familyPhylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the PPP2R2 family. PPP2R2 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).ppp2r2_20141130_phyml_tree_copy.phbPhyML tree of the SH3TC familyPhylogenetic 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).sh3tc_20141130_phyml_tree_copy.phbPhyML tree of the STK32 familyPhylogenetic maximum likelihood tree using the JTT amino acid substitution model and 100 bootstrap replicates of the STK32 family. STK32 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).stk32_20141201_phy_phyml_tree copy.phbPhyML tree of the TBC1D familyPhylogenetic 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).tbc1d_20141201_phyml_tree_copy.phbAmino acid sequence alignment of the ABLIM familyAmino 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.ABLIM_20141128.fstAmino acid sequence alignment of the AFAP familyAmino acid sequence alignment of the AFAP 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.AFAP_20141201.fstAmino acid sequence alignment of the DPYS familyAmino acid sequence alignment of the DPYS 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.DPYS_20141201.fstAmino acid sequence alignment of the JAKMIP familyAmino acid sequence alignment of the JAKMIP 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.JAKMIP_20141127.fstAmino acid sequence alignment of the PPP2R2 familyAmino acid sequence alignment of the PPP2R2 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.PPP2R2_20141130.fstAmino acid sequence alignment of the SH3TC familyAmino 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.SH3TC_20141130.fstAmino acid sequence alignment of the STK32 familyAmino 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.STK32_20141201.fstAmino acid sequence alignment of the TBC1D familyAmino acid sequence alignment of the TBC1D 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.TBC1D_20141201.fstSupplementary file 2 - Sequence identifiers and locationsExcel file containing all sequence identifiers, genomic locations and sequence names used in the tree and alignment files for the sequences included in the phylogenetic analyses. Each family has its own sheet within the file.Supplementary file 2 - location all gene families.xlsxSupplementary_file_1 - PDE6 catalytic subunit amino acid sequence alignmentAmino 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.Supplementary_file_1.faPhyML tree of the PDE6 catalytic subunit familyPhylogenetic maximum likelihood tree using the WAG amino acid substitution model and 100 bootstrap replicates of the PDE6 catalytic subunit gene family. The tree was made using the PhyML implementation in the Seaview 4.5.3 program.PDE6_catalytic-PhyMLPhyML tree of the PDE6 catalytic subunit family with extra bird and reptile sequencesPhylogenetic maximum likelihood tree using the WAG amino acid substitution model and 100 bootstrap replicates of the PDE6 catalytic subunit gene family. The tree was made using the PhyML web server (http://www.atgc-montpellier.fr/phyml).pde6_supplementary_birds_reptiles_phyml_tree.phbAmino acid sequence alignment of the PDE6 catalytic subunit family with additional Birds reptilesAmino 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.PDE6_supplementary_Birds_reptiles.fasta