Dong X , Fredman D , Lenhard B .

	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].
	Figure 2. Synorth pipeline and three data views. (a) The Synorth data/analysis pipeline. (b) The Synorth genome locus browser: (A) navigation bar; (B) search field; (C) external link to other browsers (Ancora, UCSC Genome Browser, Ensembl and Vista) for the same region; (D) GRB genomic coordinates - the coordinates are the union of all synteny regions overlapping with the query gene - if no overlapping synteny region is found, no region will be shown; (E) reference species track; (F) track(s) of compared species - in each track, the species name and the sub-tracks for all synteny regions are shown; (G) browser legend; (H) chromosome color key for the compared species. For more details, see the description in the Help page of the Synorth website [20]. (c) Synorth table browser (d) Synorth tree browser.
	Figure 3. Scenario code illustration and statistics. (a) Definition of scenario code. (b) Descriptive statistics of scenario codes for all bystander-target pairs in 215 curated GRBs.
	Figure 4. Using Synorth to show GRB duplication, maintenance and breakage. (a) FOXD3 locus, (b) TBX2 locus and (c) LHX1 locus. See the text for description.
	Figure 5. PAX2 example. Using Synorth to trace the GRB changes between teleost fish and to detect possible errors in genome assembly or missed annotation. See detailed interpretation in the text.

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