Phylogenetic tree of the PhyloFish species. Cladogram showing phylogenetic relationships among ray-finned fish analyzed in the present study. Tree topology was adapted from [2]. For each phylogenetic group, the number of species in the PhyloFish set is indicated between brackets. The teleost specific (TGD) and salmonid-specific (SaGD) whole genome duplication events are indicated in red

Stra8 proposed gene evolution in teleosts following the TGD WGD. Maximum-likelihood phylogeny of Stra8 (a) was performed using the PhyML software [38] implemented in the Phylogeny.fr web platform [39] using default “a la carte” parameters and a bootstrapping procedure (N = 100 bootstraps). The resulting tree was exported and edited in Evolview [40]. Input sequences were retrieved using a tblastn search of the PhyloFish database using as bait the Southern catfish Stra8 protein (AGM53488.1). PhyloFish Stra8 coding sequences (in bold on the tree) were submitted to GenBank with the following accession numbers: Lepisosteus oculatus (KU161162), Osteoglossum bicirhosum (KU161164), Anguilla anguilla (KU161163), Alosa alosa (KU161165), Astyanax mexicanus (KU161166), Apteronotus albifrons (KU161167), Oncorhynchus mykiss (KU161168), Salvelinus fontinalis (KU161169), Coregonus lavaretus (KU161172), Coregonus clupeaformis (KU161171), Salmo trutta (KU161170), Thymallus thymallus (KU161173), Umbra pygmae (KU161174) and Plecoglossus altivelis (KU161175). This dataset was complemented with two additional teleost public sequences of Stra8 in Esox lucius (XP_012986862) and Astyanax mexicanus (XP_007229918.1) and a Stra8 sequence deduced from the Anguilla japonica genome (scaffold 6093). The tree was rooted with tetrapod sequences using the Homo sapiens STRA8 (AAP47163.1) and Alligator mississippiensis Stra8 (XP_006261218.1). b Schematic representation of the deduced evolution of stra8 based on PhyloFish sequences. This analysis suggests that stra8 was completely lost in Acanthomorpha, but also specifically and independently lost in the Cypriniformes lineage. The tree is based on [2]

Tissue expression profiles of stra8 reveal expression predominantly in testes in most PhyloFish species. Relative expression of stra8 was calculated as the percentage of the maximum rpkm (number of reads per kilobase per million reads) value per species. ND: no data (tissue not sequenced in that species)

Phylogeny of Mcam in teleosts following the TGD and SaGD WGDs. Maximum-likelihood phylogeny of Mcam was performed using the PhyML software [38] implemented in the Phylogeny.fr web platform [39] using default “a la carte” parameters and a bootstrapping procedure (N = 100 bootstraps). The resulting tree was exported and edited in Evolview [40]. Input sequences were retrieved using a tblastn search of the PhyloFish database using as bait the zebrafish Mcam protein (XP_005157627.1), in the Mcama branch of the tree. PhyloFish Mcam coding sequences are shown in bold on the tree. The tree was rooted with tetrapod sequences using the Homo sapiens MCAM (AAH56418) and Alligator sinensis Mcam (XP_014373905). A few additional published teleosts Mcam sequences were added in the analysis (normal font). The TGD and SaGD are shown with red stars