Legends for Supporting Information
Figure S1. Phenotypes of the mutants used for whole-genome analyses of mutations. Wild type;
and mutants: Ar-57-al1 (a); Ar-365-as1 (b); and Ar-443-as1 (c) in the M3 generation, were
grown for 35 days after starting culture. In each panel, the wild type and mutant are placed on
the left and right side, respectively. Bars = 1 cm.
Figure S2. Confirmation of candidate deletions detected as positive peaks in array-CGH. The
detected regions were amplified by PCR using genomic DNA from seven individual M3 plants
in Ar-240-as1. (a) The deleted area was 2.9 kbp (chromosome 5: 22,269,224–22,272,104), as
estimated by the array-CGH. The fragments with 3.5 kbp and 0.5 kbp derive from the
non-deleted and deleted regions, respectively. These results indicate that the mutations were
separated in the M3 generation. (b) The deleted area was 0.6 kbp (chromosome 1:
29,374,384–29,374,957), as estimated by the array-CGH. The 1.4 kbp fragment was amplified
in the wild type (WT). If the mutants (MTs) have the deletion, 0.8 kbp fragments will be
amplified. However, all of the mutants have no bands. We interpret this to mean that the
deletion was accompanied by genomic rearrangements, and that the region was homozygously
contained in the mutants. M: size marker. The primers used for peak confirmation are listed in
Table S6.
Figure S3. Sequences of the breakpoints and rejoined junctions at deleted regions detected by
array-CGH. The sequences of the mutant lines induced by Ar- and Fe-ion beams were compared
to wild type. The sequences in the black boxes represent inserted filler DNA, and
microhomologies in the rejoining sites are boxed. In the sequences at the junctions, homologous
regions are represented by lines drawn between wild-type and mutant sequences; italics are used
to indicate reversed sequences.
Figure S4. Sequences in the peripheral regions of genomic rearrangements revealed by genome
resequencing. The sequences in black boxes represent base substitutions or insertions; other
notations are the same as in Supplementary Figure S3. For the breakpoints in the genome of
mutant lines (a), the sequences of the mutant lines were compared to wild type, and junction
numbers were assigned to each break end, corresponding to Figure 2, these being located both
upstream (u) and downstream (d) of the junction. Deletion sizes at the breakpoints and loci of
genes split by genomic rearrangements are indicated. (b) The genomic positions and sequences
of duplicated fragments. The junction numbers are described for both fragment ends. In the
rejoined junctions (c), sequences from the high copy number regions, including loci of
AT2G01010 or AT3G41768, were inserted within junctions 18 and 25.
Figure S5. Screening of heavy-ion beam induced mutations from candidate mutations detected
by SAMtools. The sequence reads from the resequencing of the three mutant genomes are
visualized by IGV. (a) Base substitutions, deletions, and insertions that were commonly
observed in at least three mutants were excluded as background mutations likely harbored in the
ecotype Col-0 kept in our laboratory. (b) Base substitutions and deletions that were detected just
following poly-A sequences. (c) Deletions detected at the beginning of microsatellite sequences:
(AT)n. These candidates in and around repeat sequences were judged as errors that likely
occurred in the process of sequencing or mapping and were excluded from those identified as
heavy-ion beam induced mutations.
Table S1. Characteristics of deleted areas represented in Figure 1.
Table S2. Mapping results of mutant sequencing reads onto the reference genome sequence.
Table S3. Total numbers of candidate mutations detected by the three algorithms.
Table S4. List of specific mutations, including bese substitutions, deletions, and insertions,
derived from Ar-ion irradiation.
Table S 5. High signal Peaks (≥ 1.2) detected by array-CGH.
Table S6. Primers used for confirmation of detected peaks in the array-CGH.