Data from: Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity

Lagman D, Franzen IE, Eggert J, Larhammar D, Abalo XM

Date Published: June 2, 2016

DOI: http://dx.doi.org/10.5061/dryad.k2f04

 

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Title PhyML tree of the ABLIM family.
Downloaded 2 times
Description 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.
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Title PhyML tree of the AFAP family
Downloaded 1 time
Description 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).
Download afap_20141201_phyml_tree_copy.phb (1.3 Kb)
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Title PhyML tree of the DPYS family
Downloaded 1 time
Description Phylogenetic 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).
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Title PhyML tree of the JAKMIP family
Description Phylogenetic 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.
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Title PhyML tree of the PPP2R2 family
Downloaded 1 time
Description Phylogenetic 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).
Download ppp2r2_20141130_phyml_tree_copy.phb (1.56 Kb)
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Title PhyML tree of the SH3TC family
Downloaded 1 time
Description 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).
Download sh3tc_20141130_phyml_tree_copy.phb (615 bytes)
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Title PhyML tree of the STK32 family
Description Phylogenetic 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).
Download stk32_20141201_phy_phyml_tree copy.phb (960 bytes)
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Title PhyML tree of the TBC1D family
Downloaded 1 time
Description 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).
Download tbc1d_20141201_phyml_tree_copy.phb (793 bytes)
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Title Amino acid sequence alignment of the ABLIM family
Downloaded 1 time
Description 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.
Download ABLIM_20141128.fst (41.58 Kb)
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Title Amino acid sequence alignment of the AFAP family
Downloaded 1 time
Description Amino 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.
Download AFAP_20141201.fst (44.27 Kb)
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Title Amino acid sequence alignment of the DPYS family
Downloaded 2 times
Description Amino 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.
Download DPYS_20141201.fst (51.96 Kb)
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Title Amino acid sequence alignment of the JAKMIP family
Downloaded 2 times
Description Amino 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.
Download JAKMIP_20141127.fst (25.19 Kb)
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Title Amino acid sequence alignment of the PPP2R2 family
Downloaded 1 time
Description Amino 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.
Download PPP2R2_20141130.fst (29.13 Kb)
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Title Amino acid sequence alignment of the SH3TC family
Downloaded 1 time
Description 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.
Download SH3TC_20141130.fst (30.00 Kb)
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Title Amino acid sequence alignment of the STK32 family
Downloaded 2 times
Description 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.
Download STK32_20141201.fst (13.52 Kb)
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Title Amino acid sequence alignment of the TBC1D family
Downloaded 3 times
Description Amino 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.
Download TBC1D_20141201.fst (25.23 Kb)
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Title Supplementary file 2 - Sequence identifiers and locations
Downloaded 6 times
Description Excel 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.
Download Supplementary file 2 - location all gene f....xlsx (60.20 Kb)
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Title Supplementary_file_1 - PDE6 catalytic subunit amino acid sequence alignment
Downloaded 4 times
Description 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.
Download Supplementary_file_1.fa (54.75 Kb)
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Title PhyML tree of the PDE6 catalytic subunit family
Downloaded 2 times
Description Phylogenetic 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.
Download PDE6_catalytic-PhyML (1.486 Kb)
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Title PhyML tree of the PDE6 catalytic subunit family with extra bird and reptile sequences
Downloaded 1 time
Description Phylogenetic 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).
Download pde6_supplementary_birds_reptiles_phyml_tree.phb (1.73 Kb)
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Title Amino acid sequence alignment of the PDE6 catalytic subunit family with additional Birds reptiles
Downloaded 1 time
Description 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.
Download PDE6_supplementary_Birds_reptiles.fasta (68.02 Kb)
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When using this data, please cite the original publication:

Lagman D, Franzen IE, Eggert J, Larhammar D, Abalo XM (2016) Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity. BMC Evolutionary Biology 16: 124. http://dx.doi.org/10.1186/s12862-016-0695-z

Additionally, please cite the Dryad data package:

Lagman D, Franzen IE, Eggert J, Larhammar D, Abalo XM (2016) Data from: Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.k2f04
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