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.