Figure 1

Species available for comparison in Synorth and their associated species tree. (a) Phylogenetic tree based on data from [14, 50, 70–72]. The red dots indicate the second-round (2R) and third-round (3R) WGD events [72]. The blue dot indicates the genome compaction in the pufferfish lineage beginning 20 to 30 Myr ago [70]. The species shown in the tree are: bichir (Polypterus senegalus), zebrafish (Danio rerio), fugu (Takifugu rubripes), Tetraodon (Tetraodon nigroviridis), stickleback (Gasterosteus aculeatus), medaka (Oryzias latipes), frog (Xenopus tropicalis), chicken (Gallus gallus), mouse (Mus musculus), and human (Homo sapiens). Sources of fish images: Byrappa Venkatesh (fugu), Manfred Schartl (medaka), Wikipedia (zebrafish, tetraodon), Kraft CE et al. [73] (stickleback). (b) Reference and comparison species available in Synorth. Shaded boxes correspond to the reference genomes in Synorth. Connecting lines indicate genome pairs between which GRBs are available to check in the browser. Dashed lines indicate the genome comparison to be offered in the near future. The following genome assemblies underlie the current data sets: human NCBI 36, zebrafish Zv7 (The Wellcome Trust Sanger Institute), fugu v4.0 [74], tetraodon V7 [75], stickleback v1.0 (The Broad Institute), medaka v1.0 [51].