Comparative chromosomal painting
All painting probes (Lysak et al., 2016; Schranz et al., 2006) each identifying a unique chromosome region confirmed the diploid status of the Megadenia genome. We also compared the M. pygmaeagenome with A. thaliana and C. rubella genome by MCScanX (Wang et al., 2012) using the same method as published previously(M. Kang et al., 2020). The syntenic relationships, order and orientation of the 22 GBs by CCP produced the same schematic diagram of the M. pygmaea genome (Figs. 3, S3 and S4 ).
The complete comparative chromosomal map of M. pygmaea , constructed by CCP, had similarities and notable differences to the structure of ancestral Brassicaceae genomes: ACK, ancPCK and PCK (Fig. 3 ). Three chromosomes of M. pygmaea (Mp1, Mp3 and Mp4) structurally mirrored three ancestral chromosomes (AK1, AK4 and AK7) found in ACK, ancPCK and PCK. Among the three remaining chromosomes, Mp5 was homologous to chromosome AK6/8 (GB association O+P+Wb+R) in ancPCK and PCK. Chromosome Mp6 is homologous to PCK-specific chromosome AK5/8/6 [GBs (M-N), V, X, Q, Wa and (K-L)]. However, it contains a 9.92-Mb Megadenia -specific paracentric inversion on its bottom (long) arm, with breakpoints between GBs V and (K-L) and the (sub)telomere (Fig. 3B ). Chromosome Mp2 was formed by an end-to-end translocation (EET) merging ancestral chromosomes AK2 and AK3 (Fig. 3B ), revealing dysploidy resulting in a reduction from seven to six chromosomes. The presence of the PCK-specific chromosome AK5/8/6 (Mp6) in M. pygmaea suggests descent from a seven chromosome-containing ancestral PCK-like genome.