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.
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.phb
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).
afap_20141201_phyml_tree_copy.phb
PhyML tree of the DPYS family
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).
dpys_20141201_phy_phyml_tree_copy.phb
PhyML tree of the JAKMIP family
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.
JAKMIP_20141127-PhyML_tree_phb_copy.phb
PhyML tree of the PPP2R2 family
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).
ppp2r2_20141130_phyml_tree_copy.phb
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).
sh3tc_20141130_phyml_tree_copy.phb
PhyML tree of the STK32 family
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).
stk32_20141201_phy_phyml_tree copy.phb
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).
tbc1d_20141201_phyml_tree_copy.phb
Amino acid sequence alignment of the ABLIM family
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.
ABLIM_20141128.fst
Amino acid sequence alignment of the AFAP family
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.
AFAP_20141201.fst
Amino acid sequence alignment of the DPYS family
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.
DPYS_20141201.fst
Amino acid sequence alignment of the JAKMIP family
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.
JAKMIP_20141127.fst
Amino acid sequence alignment of the PPP2R2 family
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.
PPP2R2_20141130.fst
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.
SH3TC_20141130.fst
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.
STK32_20141201.fst
Amino acid sequence alignment of the TBC1D family
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.
TBC1D_20141201.fst
Supplementary file 2 - Sequence identifiers and locations
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.
Supplementary file 2 - location all gene families.xlsx
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.
Supplementary_file_1.fa
PhyML tree of the PDE6 catalytic subunit family
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.
PDE6_catalytic-PhyML
PhyML tree of the PDE6 catalytic subunit family with extra bird and reptile sequences
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).
pde6_supplementary_birds_reptiles_phyml_tree.phb
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.
PDE6_supplementary_Birds_reptiles.fasta