Fig. 2

Distribution of repeats in the light of ancestral karyotype history. a Brassicaceae synteny. Schematic representation in circles of the A. thaliana, A. lyrata, C. rubella and T. parvula chromosomes according to a color code (illustrated on the right) highlighting the ancestral chromosome origins (ABK1–8, inner part of circle). Conserved genes between circles are linked with gray connecting lines. Functional and non-functional paleo-centromeres are illustrated as black ellipses and gray ellipses, respectively, on the chromosomes. Translocations and reciprocal translocations are illustrated as plain and dashed black double arrows, respectively. b Synteny between A. thaliana, A. lyrata, C. rubella and T. parvula regarding ABK1 (yellow) and ABK2 (red) protochromosomes where conserved genes are linked with gray connecting lines between extant chromosomes. The repeat density (deep/regular repeatome) is provided for C. rubella chromosomes 1 and 2 (top). c Deep repeatome (as percentage of TE coverage within 100-kb physical windows), regular repeatome (as percentage TE of coverage within 100-kb physical windows), recombination (Rho per kilobase), and deletion (as percentage of coverage within 100-kb physical windows) patterns on A. thaliana chromosome 1 (derived from the fusion of ABK1 and ABK 2, top) are shown as light blue, gray, green and dark blue curves, respectively. Colored arrows are as discussed in the text. d Microsynteny between A. thaliana, C. rubella and T. parvula at two inversion/translocation break points where conserved genes are linked with black connecting lines. Ancestral genes (from ABK1 and ABK2 protochromosomes) retained in extant species are shown as yellow boxes (deriving from ABK1) and red boxes (deriving from ABK2) and non-protogenes are shown as gray boxes. Local gene duplications are illustrated with red arrows. e Two scenarios of A. thaliana chromosome 1 evolution from ABK1 (yellow bars) and ABK2 (red bars). Empty circles and full circles correspond to telomeres and centromeres respectively; arrows indicate inversions and double arrows translocations