Fig. 3

Impact of hexaploidization on the extant B. rapa genome architecture. a Evolution of the extant B. rapa chromosomes from the ABK1–8 (top) and PCK1–7 (center) protochromosomes. Evolutionary rearrangements in the course of the B. rapa paleohistory are detailed in dashed boxes according to a time scale on the right expressed in millions of years. Dot plots of the gene conservation between PCK (y-axis) and B. rapa (x-axis) are provided with a color code reflecting the ABK1–8 protochromosomes (left) and the LF–MF1–MF2 subgenomes (right), with black arrows indicating the modern centromere positions. Retained ancestral centromeres are illustrated as plain black dots whereas lost ancestral centromeres are shown as gray open circles. The extant B. rapa chromosomes (bottom) are illustrated as a mosaic of colored blocks reflecting the ancestral chromosomes (left) and the subgenomes (right) based on the number of ancestral genes retained as singletons, doublets or triplets (Venn diagram), thus defining the LF, MF1 and MF2 compartments. b The number of ancestral genes (from a PCK chromosome 6 region) within 100-gene windows on the post-hexaploidization extant chromosomes 10, 2, and 3 from B. rapa (top). The microsynteny locus between PCK6 and the extant post-hexaploidization relatives is highlighted in gray. The B. rapa chromosome 10 fragment appears entirely dominant (red) whereas B. rapa chromosomes 2 and 3 show exchanges of dominance/sensitivity (green and blue for MF1 and MF2, respectively). c Substitution rate (Ks, x- axis) distribution curves of gene pairs (number on the y-axis) for all detected pairs (blue), pairs located on LF–MF1 (red), LF–MF2 (green) and MF1–MF2 (purple) compartments. Ks distribution peaks are shown with colored arrows as described in the main text. d Gene ontology (GO) analysis of retained ancestral genes (left) and retained triplicated/duplicated genes (right). GO categories significantly enriched compared with the annotated B. rapa genes are illustrated with a color code at the bottom. e Gene connectivity characterization for singletons, retained pairs and retained triplicates in B. rapa. The color code reflects the nature of the considered genes (singletons, duplicates and triplicates) with regard to their physical location: LF (red), MF (green) and MF2 (blue). The grey bar (right) corresponds to the remaining specific genes from B. rapa not considered in the previous classes