Supporting Information legends to Figs S1–S7 and Videos S1 & S2
Fig. S1 A homologous gene dotplot of Rice (R) and Sorghum (S) and the formation of
Sorghum karyotype. The dotplot is shown with grids, with blue lines to separate different
chromosomes, green lines to separate 10 Mb regions, and gray lines to show 1 Mb regions.
As noted in the main text, chromosomes in their latest common ancestor of considered
grasses correspond to rice chromosomes, respectively. (1) The formation of S1: Ancestral
chromosome R10 formed a ring near its telomeres, and the ring broke near telomeres to form
a free-end chromosome and a satellite chromosome. Eventually, the free-end chromosome
was nested into R3 in its centromere region to form S1. The satellite chromosome might have
been lost during evolution. (2) The formation of S2: Ancestral chromosome R9 formed a ring
near its telomeres, and the ring broke near telomeres to form a free-end chromosome and a
satellite chromosome. Eventually, the free-end chromosome was nested into R7 in its
centromere region to form S1. The satellite chromosome might have been lost during
evolution. (3) A DNA inversion occurred in the terminal region of S3 short arm. (4) A DNA
inversion occurred in the middle part of S4 long arm. (5) A DNA inversion occurred in the
middle part of S5 short arm. (6) A DNA inversion occurred in the terminal part of S7 long
arm. (7) A DNA inversion occurred in the terminal region of S8 long arm. (8) A DNA
inversion occurred in the pericentromeric region of S10 short arm. (9) S6 and R4 are
orthologous chromosomes, which preserved much of their common ancestral chromosome.
(10) S9 and R5 are orthologous chromosomes, which preserved much of their commonly
ancestral chromosome.
Fig. S2 A homologous gene dotplot of Rice (R) and Brachypodium. The dotplot is shown
with grids, with blue lines to separate different chromosomes, green lines to separate 10 Mb
regions, and gray lines to show 1 Mb regions. As noted in the main text, chromosomes in
their latest common ancestor of considered grasses correspond to rice chromosomes,
respectively.
(1) The formation of B1: Two chromosome fusions occurred, likely with R7 firstly nest into
R3, then R6 nested into the already-nested chromosome; The nesting events occurred at the
peri-aentromeric regions of the acceptor chromosomes; The centromere from R6 was taken as
the neo-chromosome centromere.
(2) The formation of B2: One chromosome fusion occurred, with R5 nested into its
paralogous chromosome R1, produced in the whole-genome duplication.
(3) The formation of B3: Two chromosome fusions occurred, likely with R8 firstly nested
into R2, then R10 nest into the already-nested neo-chromosome.
(4) The formation of B4: Two chromosome fusions occurred, likely with R9 firstly nested
into R12, then R11 nested into the already-nested neo-chromosome.
(5) B5 and R4 are orthologous chromosomes, which preserved much of their commonly
ancestral chromosome.
Fig. S3 DNA distribution and gene synteny. (a) The line graph (above) shows distribution of
genes, paralogous genes within rice, genes with orthologs in other grasses, and classified
repetitive sequences along rice chromosome 2 (R2).The dot plot (below) shows gene synteny
between R2 (green and yellow box) and R4 (yellow) and R6 (green). (b) The line graph
(above) shows distributions of different types of DNA as in (A) along R3.The dot plot
(below) shows gene synteny between R3 (Red-gray), and R7 (Gray), R10 (Red) and R12
(Red-blue).
Fig. S4 A homologous gene dotplot of Sorghum and maize and the formation of maize
karyotype. The dotplot is shown with grids, with blue lines to separate different
chromosomes, green lines to separate 10 Mb regions, and vertical and horizontal gray lines to
show 1 Mb and 5 Mb regions, respectively. In essence, the horizontally aligned sorghum
chromosomes represent ancestral Panicoideae chromosomes, and each had 2 copies after
specific whole-genome duplication in maize lineage. (1) The formation of M1: One of two
intermediate chromosomes, produced by S7-S8 cross-over, was nested into a S1. The other
intermediate chromosome formed M10.
(2) The formation of M2: A S5 was nested into a S2; and nn inversion in the intermediate
chromosome occurred; then was end-end joined to a S6.
(3) The formation of M3: A S8 nested into a S3, with primary inversion occurred.
(4) The formation of M4: A S7 was nested into a S5; then inversion occurred in the
intermediate chromosome, which was end-end joined with a S4.
(5) The formation of M5: The formation of M5: One of two intermediate chromosomes,
produced by a S1-S10 cross-over, was end-end joined with a S4, then inversions occurred.
The other intermediate chromosome formed M9.
(6) The formation of M6: A S10 was nested into a S9, and primary inversions occurred.
(7) The formation of M7: M7 is an old Panicoideae chromosome represented orthologous to
S2.
(8) The formation of M8: A S9 was nested into a S3.
(9) The formation of M8: One of two intermediate chromosomes, produced by a S1-S10
cross-over, evolved as an independent chromosome M9.
(10) The formation of M10: One of two intermediate chromosomes, produced by a S7-S8
cross-over, then end-end joined with a S6; The other intermediate chromosome are used to
form M1.
Fig. S5 Grass genome repatterning.
Fig. S6 A homologous gene dotplot of Arabidopsis thaliana and Arabidopsis lyrata to show
karyotype formation in the former. "Add." show sequences unassembled. Chromosomes,
shown with rectangular blocks, are arranged horizontally and vertically to the dotplot.
Fig. S7 Arabidopsis genomes’ repatterning.
Video S1 Dynamic changes during grass genome repatterning.
Video S2 Dynamic changes during grass genome repatterning.