Fig. S1 Scattered matrix plot presenting the distribution RPKM values for different
comparisons between WT, WT[+], SO-KO and SO-KO[+]. This Matrix plot was
generated using 20th to 100th percentile filtered data, which were log 2 scaled and
quantile normalized in Genespring. Data were not baseline transformed.
1
Fig. S2 GO analysis of fivefold regulated transcripts. Different comparison pairs
provided transcripts which could be connected in different amounts to several defined
GO classes. Utilized GO groups were chosen according to the enrichment of
transcripts within those classes (p-value < 0.1). GO terms which are not significantly
enriched were marked with a star. The following terms were identified:

belonging to
CELLULAR COMPONENT
=
CELL, CELL PART, ORGANELLE, ORGANELLE
PART, EXTRACELLULAR REGION, MACROMOLECULAR COMPLEX;

transcripts associated to
BIOLOGICAL PROCESS
=
RESPONSE TO STIMULUS, METABOLIC
PROCESS, CELLULAR PROCESS, LOCALIZATION, ESTABLISHMENT OF LOCALIZATION,
MULTI-ORGANISM PROCESS, IMMUNE SYSTEM PROCESS, BIOLOGICAL REGULATION,
RHYTHMIC PROCESS AND GROWTH;
2

connected to
MOLECULAR FUNCTION
= BINDING, TRANSPORTER ACTIVITY, NUCLEIC ACID
BINDING, ENZYME REGULATOR ACTIVITY, ELECTRON CARRIER ACTIVITY
and
CATALYTIC
ACTIVITY.
WT vs. WT[+] (a) presented the lowest amount of GO terms identified for the different
transcripts, followed by the genotypic comparison WT vs. SO-KO (c). SO-KO vs. SOKO[+] (b) and WT[+] vs. SO-KO[+] (d) showed the highest diversity of GO terms
which implicates that in these comparisons most transcript alterations took place due
to SO2 fumigation, especially belonging to
DEFENSE
and
STRESS RESPONSE,
to TRANSPORT and CATALYTIC ACTIVITIES, as metabolically expected.
3
as well as
Fig. S3 KEGG Metabolic Pathways of the four different comparison pairs using
fivefold data: The Metabolic pathway map for A: WT vs. WT[+], B: SO-KO vs. SOKO[+], C: WT vs. SO-KO and D: WT[+] vs. SO-KO[+] was generated using “KEGG
Mapper
–
SearchColor
Pathway”
tool
(www.genome.jp/kegg/tool/map_pathway2.html) which is associated to the KEGG
database (www.genome.jp/kegg/kegg2.html). Pathways are colored according to the
differentially expressed genes as presented in the color range.
4
Fig. S4 SO [At3G01910] splice variants and mRNA fragment mapping for WT,
WT[+], SO-KO and SO-KO[+]: Fig. S4a presents the three different splice variants of
SO. Fig S4b shows WT and WT[+] transcript mappings, these were highlighted with a
check mark (green), to underline the propriety of the mapping of mRNA fragments
according to the different splice variants. Correct exon mapping is shown in green
boxes. Fig S4c illustrates transcript mapping of SO-KO and SO-KO[+], which is
highlighted with a red cross due to the wrong mapping. Red boxes depict mRNA
fragments which were mapped onto intron sequences. This happened in most cases
for SO-KO and SO-KO[+], although green boxes show the occurrence of correct
exon reads for SO-KO and SO-KO[+] as well. CLC-workbench (CLC bio, Mühltal,
Germany) was used for mapping.
5
Fig. S5 SO [At3G01910] mRNA mapping for WT, WT[+], SO-KO and SO-KO[+]: Fig.
S5a shows WT transcript fragments, mapped onto the exon structure of the three SO
splice variants, in Fig. S5b this is presented for SO-KO, Figs. S5c, d show the WT[+]
6
and the SO-KO[+]. Green lines describe correctly mapped mRNA fragments, those
were especially identified for WT and WT[+]. SO-KO and SO-KO[+] showed several
reads mapped on introns, those were marked with a red line. CLC-workbench (CLC
bio, Mühltal, Germany) was used for mapping. Although SO-KO should not be able to
produce SO mRNA, plants attempt by all means to start SO synthesis, especially
after SO2 fumigation.
7