Synteny analysis
Synteny analyses were performed on two tiers, on whole-genome sequence comparison and at the gene level.
For the whole-genome comparison, the L. sceleratus genome assembly was compared with all available genomes of Tetraodontiformes to date (T. nigroviridis , T. rubripes , T. flavidus andT. bimaculatus ). Furthermore, we performed similar comparisons aligning the genomes of T. nigroviridis and T. rubripes against the other species. For the alignment, we used LAST v1145 (Kielbasa et al., 2011), implementing the sensitive alignment protocol as described for Human-mouse whole-genome project comparison (https://github.com/mcfrith/last-genome-alignments) with e-value cut-off 0.001. On the gene level, we used the one-to-one orthologues outputs of Orthofinder v2.3.12 analysis for comparing the same set of species.
We selected for visualization the 41 largest contigs of the L. sceleratus assembly representing ~91% of the genome (Figure S1), for both whole-genome and gene-based synteny results. In each set of fish, the whole-genome pairwise alignments were plotted by custom python scripts (synteny_plot.py) (Figures S3-S8), while the one-to-one orthologs relationships of all the above-mentioned comparisons, were visualized through Circos (circos_plot.py) (Krzywinski et al., 2009) (Figures S9-S13).