Fig. 1.

Synteny and divergence between the two assembled haplotypes of XYY male of R. hastatulus. Top panel: syntenic genomic position comparison based on whole-genome alignment for the autosomes and the sex chromosomes. Bottom panel: median Ks between syntenic genes in 100 gene windows with a step size of one gene along each chromosome, calculated from individual genes with Ks < 0.2. Autosomal terminology is used to remain consistent with genome assemblies from the XY cytotype. Autosome 3 (A3) from the XY cytotype is a component of the sex chromosomes in the XYY cytotype. The old sex-linked-region (‘Old SLR’) is shared with the XY cytotype; PAR1, a pseudoautosomal region, is shared with XY cytotype; the new sex-linked region (‘New SLR’) was formed from sex chromosome fusions; and PAR2, a recombining region, was formed from the neo-sex chromosome region.