(a) Double-conserved synteny between the trout and medaka genomes. Each medaka chromosome (represented as a horizontal black line) is mostly syntenic with two different chromosomes in the trout genome (syntenic trout regions represented on either side by different colours according to their chromosomal location), a pattern typically associated with whole-genome duplication. Pairs of paralogous trout genes that are inserted in a double-conserved synteny block compared to a non-salmonid fish genome are consistent with an origin at the Ss4R event (ohnologues), while genes that are inserted in a double-conserved synteny block but have no paralogue are singletons that have lost their duplicate copy since the Ss4R event. Only genes anchored to a trout chromosome are represented. (b) Successive rounds of duplication in the trout genome. The double-conserved synteny pattern between trout and non-salmonid fish delineates large chromosomal regions in the trout genome that are Ss4R duplicates of each other (outer circle, joined by grey links), descended from the same ancestral region. These ancestral pre-duplication regions could be grouped into 31 ancestral chromosomes (inner circle) based on the organization of their orthologous counterparts in non-salmonid genomes. The ancestral pre-duplication karyotype itself is an ancient tetraploid following the Ts3R event: Ts3R-duplicated regions in the pre-duplication karyotype are highlighted by grey links within the inner circle. On the right is detailed the evolutionary history of one ancestral genomic region that gave rise to paralogous regions in chromosomes 6/11 and 5/12/Sex through the Ts3R and Ss4R successive WGD events. (c) Chromosomal organization of the modern rainbow trout genome. Colours as in (b); duplicated regions are joined by grey links. Most modern trout chromosomes result from a fusion between two Ss4R-duplicated blocks descending from different ancestral chromosomes. The order of the duplicated blocks within each modern chromosome does not necessarily reflect the actual organization of the chromosome, as gene orders may have been reshuffled by intra-chromosomal rearrangements (see (d)). (d) Modern organization of the Ss4R-duplicated regions in the trout genome. Colours are as in (b,c).