Fig. 1

Methodological principles for ancestral genome reconstruction. The four-step strategy is as follows. Step 1: identification of conserved or duplicated genes (putative protogenes (pPGs)); here, genes are illustrated as rectangles and connected with red lines when conserved between all the investigated species or blue lines when conserved in a subset of these species. Species-specific genes, which are not present in the inferred ancestor, are shown as black rectangles. Step 2: identification of synteny in groups of conserved adjacent genes (synteny blocks (SBs)), which are highlighted by grey dashed rectangles. Step 3: reconstruction of contiguous ancestral regions (CARs; highlighted by grey dashed rectangles) containing genes that are conserved in all of the investigated species (referenced as core-pPGs). Step 4: ancestral genome reconstruction delivering protochromosomes (highlighted by grey dashed rectangles) and reordered protogenes (oPGs) [23]