Allotetraploid origin of O. kokonorica
We concluded that O. kokonorica was an allotetraploid (2n = 4x =
40) based on: (1) k-mer analysis, in which two peaks were present, with
the smaller peak at the doubled multiplicity of the major peak, and the
result estimated by Smudgeplot (Figure S1); (2) the high degree of
collinearity among the 20 assembled pseudochromosomes (Figure 1B; Figure
S5); and (3) the results of genome synteny and K s (synonymous
substitutions per synonymous site) values between O. kokonoricaand C. songorica described below (Figure 1C).
To investigate the structure of the O. kokonorica subgenomes, we
conducted a synteny analysis between subgenomes of C. songoricaand our O. kokonorica pseudochromosomes. We found that eachC. songorica chromosome corresponded with a pair of O.
kokonorica pseudochromosomes, and vice versa (Figure 1C). Based on
genome synteny and K s values, we divided the O. kokonoricapseudochromosomes into A and B subgenomes. We found that high
collinearity among the two genomes by visualizing the synteny blocks.
For subgenomes A of the two species, each pair of chromosomes
corresponded very well, while for subgenomes B, two pairs of large
interchromosomal rearrangements were revealed between chromosomes B2 and
B5, and between B1 and B8. When using O. thomaeum , a diploid
close relative to the two allotetraploid species, as a reference, we
found no interchromosomal rearrangement events between O.
kokonorica and O. thomaeum (Figure 1D), indicating that these
large interchromosomal rearrangements occurred specifically in C.
songorica .