The widespread crucifer species C ardamine flexuosa is an allotetraploid with a conserved subgenomic structure

Summary The origin of C ardamine flexuosa ( W avy B ittercress) has been a conundrum for more than six decades. Here we identify its parental species, analyse its genome structure in comparison to parental genomes and describe intergenomic structural variations in C . flexuosa . Genomic in situ hybridization ( GISH ) and comparative chromosome painting ( CCP ) uncovered the parental genomes and the chromosome composition of C . flexuosa and its presumed diploid progenitors. Cardamine flexuosa is an allotetraploid (2 n  = 4 x  = 32), originating from two diploid species, C ardamine amara and C ardamine hirsuta (2 n  = 2 x  = 16). The two parental species display almost perfectly conserved chromosomal collinearity for seven out of the eight chromosomes. A 13 Mb pericentric inversion distinguishes chromosome CA 1 from CH 1. A comparative cytomolecular map was established for C . flexuosa by CCP / GISH . Whereas conserved chromosome collinearity between the C . amara and C . hirsuta subgenomes might have promoted intergenomic rearrangements through homeologous recombination, only one reciprocal translocation between two homeologues has occurred since the origin of C . flexuosa . The genome of C . flexuosa demonstrates that allopolyploids can maintain remarkably stable subgenomes over 10 4 –10 5  yr throughout a wide distribution range. By contrast, the r RNA genes underwent genome‐specific elimination towards a diploid‐like number of loci.