Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks

Abstract

A novel extraction protocol is described with which metabolites, proteins and RNA are sequentially extracted from the same sample, thereby providing a convenient procedure for the analysis of replicates as well as exploiting the inherent biological variation of independent samples for multivariate data analysis. A detection of 652 metabolites, 297 proteins and clear RNA bands in a single Arabidopsis thaliana leaf sample was validated by analysis with gas chromatography coupled to a time of flight mass spectrometer for metabolites, two-dimensional liquid chromatography coupled to mass spectrometry for proteins, and Northern blot analysis for RNA. A subset of the most abundant proteins and metabolites from replicate analysis of different Arabidopsis accessions was merged to form an integrative dataset allowing both classification of different genotypes and the unbiased analysis of the hierarchical organization of proteins and metabolites within a real biochemical network.

Full text

Short Communication
Wolfram Weckwerth
Kathrin Wenzel
Oliver Fiehn
Max-Planck-Institut
für Molekulare
Pflanzenphysiologie,
Golm, Germany
Process for the integrated extraction, identification
and quantification of metabolites, proteins and RNA
to reveal their co-regulation in biochemical networks
A novel extraction protocol is described with which metabolites, proteins and RNA
are sequentially extracted from the same sample, thereby providing a convenient pro-
cedure for the analysis of replicates as well as exploiting the inherent biological varia-
tion of independent samples for multivariate data analysis. A detection of 652 metab-
olites, 297 proteins and clear RNA bands in a single Arabidopsis thaliana leaf sample
was validated by analysis with gas chromatography coupled to a time of flight mass
spectrometer for metabolites, two-dimensional liquid chromatography coupled to
mass spectrometry for proteins, and Northern blot analysis for RNA. A subset of the
most abundant proteins and metabolites from replicate analysis of different Arabidop-
sis accessions was merged to form an integrative dataset allowing both classification
of different genotypes and the unbiased analysis of the hierarchical organization of
proteins and metabolites within a real biochemical network.
Keywords: Gas chromatography-time of flight mass spectrometer / Metabolomics / Multi-
dimensional chromatography / Network topology / Plant systems biology / Transcript pro-
filing PRO 0500
Arabidopsis thaliana plants were cultivated in phytotrons
under highly controlled light, gas and temperature con-
ditions assuring approximately identical environmental
conditions for each plant sample. Biological variation
among independent samples of the same genotypes is
attributed to the inherent fluctuation of the biochemical
network due to slight environmental differences.
30–100 mg samples of Arabidopsis leaves at a develop-
mental stage 1.1 [1] were harvested and immediately
frozen in liquid nitrogen. Tissue was homogenized under
liquid nitrogen using a Retsch mill. Two mL of a single
phase solvent mixture of methanol/chloroform/water
2.5:1:1 v/v/v kept at 2207C was added to the tissue and
thoroughly mixed at 47C for 30 min to precipitate proteins
and DNA/RNA and to disassociate metabolites from
membrane and cell wall components. After centrifuga-
tion, the remaining pellet consisting of DNA/RNA, pro-
teins, starch, membranes, and cell wall components was
extracted in a second step with 1 mL methanol/chloro-
form 1:1 v/v at 2207C. The organic solvent extracts were
combined and used for metabolite analysis via GC-TOF.
For that purpose the chloroform phase was separated
from the water/methanol phase by adding 500 mL water.
The resulting water/methanol phase contained all hydro-
philic metabolites such as sugars, amino acids and
organic acids, and the chloroform phase all the lipophilic
compounds, lipids, chlorophyll and waxes. The remaining
white pellet was further partitioned according to the
scheme in Fig. 1. The pellet was extracted with 1 mL
extraction buffer (0.05 MTris, pH 7.6; 0.5% SDS; 1%
b-mercaptoethanol) and 1 mL water saturated phenol for
1hat377C. After centrifugation at 14 000 gthe remaining
pellet was used for cell wall synthesis (data not shown).
The phenol phase was separated from the buffer phase
and the proteins were precipitated with ice-cold acetone
at 2207C overnight, washed three times with ethanol
and dried at room temperature. Remaining protein in the
RNA-buffer phase was precipitated with 200 mL chloro-
form. After centrifugation and separation of the buffer
phase, 40 mL of acetic acid and 1 mL ethanol were added
Correspondence: Dr. Wolfram Weckwerth, Max-Planck-Institut
für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, D-14476
Golm, Germany
E-mail: weckwerth@mpimp-golm.mpg.de
Fax: 149-331-567-8134
Abbreviation: FW, fresh weight
78 Proteomics 2004, 4, 78–83
Supporting information for this article is available at www.
proteomics-journal.de or from the author at www.mpimp-
golm.mpg.de/fiehn/index-e.html.
2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de
DOI 10.1002/pmic.200200500

Proteomics 2004, 4, 78–83 Connectivities in biochemical networks 79
Figure 1. A separation scheme
for the integrative extraction of
metabolites, proteins and RNA
from single samples enabling
correlation analysis among
these compound classes. Multi-
ple system snapshots allow the
analysis of dynamic biochem-
ical interaction networks as a
response of the observed geno-
type-environment-phenotype re-
lationship [25].
to precipitate the RNA at 47C for 30 min. The pellet was
washed with one volume 3 Msodium acetate, and two
times with one volume 70% ethanol. The remaining pellet
was dissolved in 100 mL RNAse-free water. Amounts and
purity of RNA were checked by absorbance at 260 nm
and gel electrophoresis in agarose. Construction of Ara-
bidopsis isopropyl-malate synthase (IPMS) probes for
hybridization and Northern blots were performed using
standard protocols.
For GC-TOF MS (Leco Pegasus II GC-TOF mass spec-
trometer; Leco, St. Joseph, MI, USA) analysis, the organic
phase was dried and dissolved in 50 mL of methoxamine
hydrochloride (20 mg/mL pyridine) and incubated at
307C for 90 min with continuous shaking. Then 80 mLof
N-methyl-N-trimethylsilyltrifluoroacetamid (MSTFA) was
added to derivatize polar functional groups at 377C for
30 min. The derivatized samples were stored at room
temperature for 120 min before injection. GC-TOF analy-
sis was performed on an HP 5890 gas chromatograph
with tapered, deactivated split/splitless liners containing
glasswool (Agilent, Böblingen, Germany) and 1 mL split-
less injection at 2307C injector temperature. The GC was
operated at constant flow of 1 mL/min helium and a 40 m
0.25 mm id 0.25 mm RTX-5 column with 10 m integrated
precolumn. The temperature gradient started at 807C,
was held isocratic for 2 min, and subsequently ramped
at 157C/min to a final temperature of 3307C which was
held for 6 min. Twenty spectra per second were recorded
between m/z 85–500. Peak identification and quantifica-
tion were performed using the Pegasus software package
(Leco). Reference chromatograms were defined that had
a maximum of detected peaks over a signal/noise thresh-
old of 20 and used for automated peak identification
based on mass spectral comparison to a standard NIST
98 library [2]. Automated assignments of unique fragment
ions for each individual metabolite were taken as default
as quantifiers, and manually corrected where necessary.
All artifactual peaks caused by column bleeding or phtal-
ates and polysiloxanes derived from MSTFA hydroly-
zation were manually identified and removed from the
results table. All data were normalized to plant mg fresh
weight (FW) and internal references and log-transformed.
t-test, correlation analysis, and variance analysis were
performed in Microsoft Excel 5.0.
The dried protein pellet was dissolved in freshly prepared
1Murea in 0.05 MTris buffer pH 7.6. The complex protein
mixture was digested with modified trypsin (Böhringer
Mannheim, Mannheim, Germany) according to the manu-
facturer’s instructions. The tryptic digest was dried down
and dissolved in 300 mL water (1% formic acid). Insoluble
2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de

80 W. Weckwerth et al. Proteomics 2004, 4, 78–83
material was removed by centrifugation. An aliquot of the
digest (,100 mg protein) was injected onto two-dimen-
sional chromatography on a Thermofinnigan ProteomeX
system (Thermofinnigan, San Jose, CA, USA) coupled to
an LCQ DecaXp ion trap. The chromatographic separa-
tion was done according to manufacturer’s instructions.
After a 12 cycle run the MS/MS spectra were searched
against an A. thaliana database (downloaded from the
TAIR homepage www.arabidopsis.org) using TurboSe-
quest implemented in Bioworks 3.0 (Thermofinnigan).
Matches were filtered according to Wolters et al. [3] using
the multiple scoring filter of Bioworks 3.0. For the quanti-
fication approach aliquots of the complex tryptic digest
of Arabidopsis leaf protein (50 mg) were analyzed using
1-D reversed-phase chromatography. Quantification was
achieved by integrating peak areas of target peptides
representative for proteins. These peak areas were nor-
malized to the sum of internal standard peptides that
had been added to the mixture [4, 5].
All quantitative metabolite and protein data were normal-
ized to internal standards and FW. Principal component
analysis (PCA) and hierarchical cluster analysis (HCA) for
pattern recognition was performed according to Fiehn
et al. [6] using Pirouette software (Infometrix, Woodinville,
WA, USA). The integrative data set of metabolites and
proteins was log10 transformed. The HCA was performed
using Euclidian distances and complete linkage grouping.
Variance analyses were performed in MS Excel 5.0.
At the systems level, gene function is regarded as de-
pendent on developmental stage, environmental condi-
tions and expression levels of other genes, resulting in dy-
namic changes in transcript, protein and metabolite pro-
files. Thus, the next stage of understanding necessitates
that biological tissues be described in depth on different
levels, i.e. not only at the level of transcripts or protein
expression, but also at the metabolite level and with con-
sideration to the dynamic interaction of different gene
products [7–11]. Here, we propose a novel extraction pro-
tocol for the integrative analysis of metabolites, proteins
and RNA from the same sample. For each replicate,
30–100 mg FW leaf tissue of an individual A. thaliana plant
was extracted at 47C with chloroform/methanol/water
(1:2.5:1 v/v/v) according to the scheme illustrated in
Fig. 1. This single-phase mixture proved to have improved
extraction strength for metabolites in comparison to the
former extraction protocol utilizing a methanol/water mix-
ture for 15 min at 707C. However, when chloroform was
left out of the cold extraction mix, i.e. if methanol/water
extraction mixtures were used at 2207C, a strong de-
crease in sucrose content was detected in subsequent
GC-TOF MS analysis, concomitant with a sharp increase
in fructose and glucose contents. This indicates that
chloroform may inhibit sucrose cleaving enzyme activity,
e.g. invertase or sucrose synthase, by precipitating these
enzymes.
Total metabolite analysis was performed with GC-TOF
MS [12] (Fig. 2A) enabling the detection and quantification
of 652 metabolites (see Supplementary Table 1). Replica-
tion of metabolite analysis revealed a high recovery and a
mean coefficient of variance (CV) of 10%. In a subsequent
step, proteins and mRNA were isolated from the remain-
ing cell residue using buffer/phenol extraction and phase
separation (see Fig. 1). In Fig. 2C, a comparison of this
method with a conventional RNA extraction method is
shown. The extraction procedure achieves a higher level
of RNA recovery than does a typical RNA isolation kit
extraction (see above) with 30% CV in 28 samples. To
test the utility of the mRNA for hybridization we analyzed
the expression of IPMS from Arabidopsis (Fig. 2D). The
average amount of total protein extracted according to
Fig. 1 was 1.3 mg per 100 mg FW with 17% CV. The over-
all extraction process resulted in good recovery of metab-
olites, proteins and transcripts. After complete extraction,
the remaining cell pellet was used for cell wall analysis
giving rise to clear and typical cell wall profiling (data not
shown). The protein fraction was analyzed using shotgun
proteomics [3, 13, 14].
The complex mixture of the tryptic Arabidopsis leaf pro-
tein digest was analyzed by 2-D capillary LC and MS/MS
on an ion trap mass spectrometer (LCQ Deca Xp Plus)
and a subsequent database search performed using Tur-
boSequest implemented in ThermoFinnigan Bioworks
3.0. In a single Arabidopsis Col2 leaf sample extracted
according to the scheme in Fig. 1, 586 peptides and 297
corresponding proteins were identified using very strin-
gent criteria to avoid false positives (see above and Sup-
plementary Table 2). A classification of detected proteins
from one sample is shown in Fig. 2B. We applied the inte-
grative extraction process to two Arabidopsis genotypes,
C24 and Col2, to test if we were able to determine differ-
ent biochemical phenotypes and general biochemical
patterns using this strategy. C24 and Col2 showed an
overlap of 153 proteins (see Supplementary Table 2). The
data-dependent detection of peptides was strongly con-
tingent on the estimated abundance of the corresponding
proteins in the digest such as ribulose-1,5-biphosphate
carboxylase/oxygenase (RUBISCO) [15]. Thus, the high
number of nonoverlapping proteins also indicates differ-
ences in the protein-profiles of these different genotypes.
A set of 22 proteins appearing in both varieties was
chosen for the quantification approach. These proteins
were quantified by integrating their corresponding pep-
tide areas in a 1-D LC-MS/MS analysis and normalizing
these areas to internal standard peptides [4, 5]. Analytical
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Proteomics 2004, 4, 78–83 Connectivities in biochemical networks 81
Figure 2. Analysis of metabolites, proteins, and tran-
scripts extracted from a single Arabidopsis leaf sample.
A, GC-TOF MS direct analysis of hydrophilic and lipophilic
metabolites. B, Functional characterization of identified
proteins from a single Arabidopsis Col2 leaf sample.
Majority of the proteins are chloroplast-related. C, Com-
parison of the integrative extraction protocol with a con-
ventional plant RNA extraction kit. D, RNA blot analysis of
Arabidopsis isopropylmalate synthase (IPMS) transcripts
(two isoforms, GI9758 and GI9759360) in three replicate
samples of Arabidopsis Col2 leafs extracted according
to the scheme in Fig. 1.
precision was tested by adding internal standard pep-
tides to the sample. The deviation of the internal stand-
ards, in other words, the technical variation of the
extrac-
tion process, stability of electrospray and matrix effects,
was ,25% CV. Each genotype was represented by ten
independent samples. The relative integrals of the pep-
tides in each sample were normalized to the FW of the
corresponding sample.
The metabolites in the corresponding samples were iden-
tified and quantified with GC-TOF. Fourteen of the most
abundant metabolites were normalized to the internal
standard and FW and combined with the protein data
(normalized to internal peptide-standard and FW) to form
an integrated dataset.
A homogeneous dataset was achieved by applying log10
transformation as described in [16]. Essential for the anal-
ysis is to test if we are able to discriminate between the
two genotypes, to see if they have different biochemical
phenotypes in identical environments. We applied princi-
pal component analysis (PCA) according to Fiehn et al.
[6]. Both Col2 and C24 were completely separated into
genotype-clusters (Fig. 3A). In contrast to NMR or other
fingerprinting methods, the individual identification of
compounds by our method enables the investigation of
distinct metabolite-protein co-regulations in a multitude
of samples. Examples are given in Figs. 3B and 3C.
Based on the detection of these fundamental correlations
in an integrative dataset (for instance a distance or a Pear-
sons matrix) and a comparison with hypothetical reaction
pathway networks, it is possible to expose instantaneous
connectivities in a regulatory network representing a
snapshot of the actual state of the system [17–20].
To make use of such a refined analysis it is important to
differentiate biological variability and technical measure-
ment error. The quantified proteins showed an overall
variability of ,39% whereas individual variation was up
to 70%, exceeding clearly the overall analytical precision
of ,25% CV. The same has been observed for meta-
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82 W. Weckwerth et al. Proteomics 2004, 4, 78–83
Figure 3. Principal component and hierarchi-
cal cluster analysis of metabolites and pro-
teins. A, Integrated PCA of metabolites and
proteins reveals complete clustering of the
two genotypes. B, Scatter plot of a metabo-
lite/protein-pair and a protein-pair for two dif-
ferent Arabidopsis accessions, C24 and Col2.
The data are generated using the integrative
extraction method. Co-regulation in these plots
is defined as a linear correlation depending on the correlation coefficient (R2). C, HCA of a merged
metabolite-protein dataset (for details see text). Abbreviations of proteins and metabolites: RUBISCO
activase: ribulose-1,5-bisphosphate carboxylase/oxygenase activase (S04048); RUBISCO: ribulose-
1,5-bisphosphate carboxylase/oxygenase (NP_051067); GAPDH: glyceraldehyde-3-phosphate de-
hydrogenase (AAD10209); asc peroxidase: L-ascorbate peroxidase (S20866); put kinase: protein
kinase, putative (At3g24550); SUC: sucrose; FUC: fucose; SHI: shikimate; CP12 like: CP12 protein
precursor-like protein (At3g62410); ATPsynthase: ATP synthase CF1 beta chain (NP_051066); perox-
idase: peroxidase, putative (At3g49120); put protein: protein, putative (At3g63190); put TK: transke-
tolase-like protein (At3g60750), put aldolase: putative fructose-bisphosphate aldolase (AF428455_1);
put oxidase: glycolate oxidase (At3g14420); GST protein: spindly (gibberellin signal transduction
protein) (At3g11540); ATPase: ATPase alpha subunit (NP_051044); EF-1: translation elongation fac-
tor eEF-1 alpha chain (gene A4) (S08534); catalase: catalase (AAB07026); put protein: protein,
putative (At3g47140); P-protein like: (At4g33010); put protein: protein, putative (At3g57190); PS I
RC: putative photosystem I reaction center subunit II precursor (At1g03130); PS I SUI: photo-
system I subunit III precursor (CAB52747); CIT: citrate; XYL: xylose; TRE: trehalose; SIN: sinapi-
nate; GAL: galacturonate; CITMA: citramalate; ASP: aspartate; GLUC: gluconate; MAL: malate;
INO: inositol; FUM: fumarate.
bolites according to Fiehn et al. [6]. We calculated the
ratio of standard deviation to the mean for every variable,
metabolite, and protein. These ratios appeared not to be
correlated to the means (rmetabolites 50.38 and rproteins 5
0.23), indicating that the relative variation of these com-
pounds does not depend on their abundance. This is in-
dicative of high biological variation among independent
samples, even samples collected from tissues at seem-
ingly identical developmental stage and grown under
highly controlled environmental conditions.
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Proteomics 2004, 4, 78–83 Connectivities in biochemical networks 83
In Fig. 3C, a hierarchical analysis of the set of quantified
proteins and metabolites is shown. C24 and Col2 data-
sets are merged together to detect biochemical patterns
conserved for both genotypes. A strongly conserved
pattern for both varieties is detected for Calvin cycle
enzymes such as RUBISCO and 3-glyceraldehyde de-
hydrogenase (GAPDH), which is in agreement with the
literature [21]. Metabolites included in this cluster are
sucrose and fucose suggesting the coordination of
sucrose synthesis and degradation and photosynthetic
activity. Surprisingly, ascorbate peroxidase is integrated
into the Calvin cycle/sucrose cluster giving hints to the
connectivity of the oxidative state and carbohydrate
metabolism in plants. Inside the metabolite cluster, bio-
chemically related structures such as malate and fuma-
rate and carbohydrates form subclusters as expected.
These observed correlative patterns of metabolites and
proteins suggest that connectivities with the underlying
biochemical network can be adopted [17] but are not
straightforwardly derivable from real biochemical net-
works at a systems level, pinpointing the need for extend-
ing these comprehensive studies. Additionally, the analy-
sis of theoretical network topologies gives many hints
about evolutionary relationships and regulation in bio-
chemical networks [22–24] and delivers models which
can be compared with the experimental network topolo-
gies discussed in this work. Many of the metabolites and
proteins have unknown or putative structures and func-
tions. Using a more comprehensive dataset and ulti-
mately including quantitative transcript expression data,
the integrative extraction protocol has the potential to
unravel relationships among these compounds and to
assign their linkage to already known functions in bio-
chemical networks.
We thank Megan McKenzie for revising the manuscript.
Received December 23, 2002
Revised March 8, 2003
Accepted May 23, 2003
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2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de

Supporting Information
for Proteomics
DOI 10.1002/pmic.200200500
Wolfram Weckwerth, Kathrin Wenzel and Oliver Fiehn
Process for the integrated extraction, identification and
quantification of metabolites, proteins and RNA to reveal their
coregulation in biochemical networks
ª2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de

Supplementary Table 1. Identified metabolites of known structure
A list of all detected metabolites including classification of unknowns can be found on http://www.mpimp-golm.mpg.de/fiehn/index-e.html

Supplementary Table 2. Identified proteins
ProteinID Function Peptides Found in
identified
NP_051067 riblose 1,5-bisphosphate carboxylase/oxygenase large chain 23 Col2/C24
NP_051066
A
TP synthase CF1 beta chain 10 Col2/C24
S04048 ribulose-bisphosphate carboxylase activase (EC 6.3.4.-) precursor 8 Col2/C24
NP_051044
A
TPase alpha subunit 13 Col2/C24
A
AL38341 chlorophyll a/b-binding protein 5 Col2/C24
CAB40384 16 kDa polypeptide of oxygen-evolving complex 9 Col2/C24
A
t3g01500 carbonic anhydrase, chloroplast precursor 8 Col2/C24
A
t3g60750 transketolase - like protein 6 Col2/C24
A
t4g10340 light-harvesting chlorophyll a/b binding protein 7 Col2/C24
GCST_MESCR
A
minomethyltransferase, mitochondrial precursor (Glycine cleavage system T protein) (GCVT) 7 Col2/C24
A
AD10209 glyceraldehyde 3-phosphate dehydrogenase A subunit 4 Col2/C24
A
t2g30860 glutathione transferase, putative 4 Col2/C24
A
t1g06680 photosystem II oxygen-evolving complex 23 (OEC23) 5 Col2/C24
A
T5g25980 myrosinase TGG2 5 Col2/C24
A
t5g35630 glutamate-ammonia ligase (EC 6.3.1.2) precursor, chloroplast 4 Col2/C24
S08534 translation elongation factor eEF-1 alpha chain (gene A4) 3 Col2/C24
A
t3g55800 sedoheptulose-bisphosphatase precursor 3 Col2/C24
A
t1g03130 putative photosystem I reaction center subunit II precursor 4 Col2/C24
A
AM12979 chlorophyll a/b-binding protein CP29 4 Col2/C24
A
t3g26060 putative peroxiredoxin 4 Col2/C24
NP_051054 photosystem II protein D2 3 Col2/C24
A
t2g40840 glycosyl hydrolase family 77 (4-alpha-glucanotransferase) 1 Col2/C24
BAB08951 2-cys peroxiredoxin-like protein 3 Col2/C24
A
AM62639 unknown 2 Col2/C24
A
t1g12900 putative calcium-binding protein, calreticulin 1 Col2/C24
A
t1g44575 photosystem II 22kDa protein, putative 4 Col2/C24
A
t4g05180 oxygen-evolving complex protein 16, chloroplast precursor (OEC16) 4 Col2/C24
NP_051072 cytochrome f 3 Col2/C24
A
F217459_1 heat shock protein 70 2 Col2/C24
A
t1g64290 hypothetical protein 1 Col2/C24
A
t5g26000 glycosyl hydrolase family 1, myrosinase precursor 3 Col2/C24
A
t3g57190 putative protein 1 Col2/C24
A
AK64040 unknown protein 4 Col2/C24
A
F428455_1 putative fructose-bisphosphate aldolase 1 Col2/C24
A
t1g32060 phosphoribulokinase precursor 2 Col2/C24
BAA20945 beta subunit of coupling factor one 2 Col2/C24
A
t2g39730 auxin-regulated protein 1 Col2/C24
A
t1g20020 ferredoxin--NADP reductase precursor, putative 3 Col2/C24
A
t3g08940 putative chlorophyll a/b-binding protein 3 Col2/C24
NP_051055 photosystem II 44 kDa protein 3 Col2/C24
A
t3g03530 expressed protein, supported by cDNA: gi_14335155 1 Col2/C24
A
t2g14380 putative retroelement pol polyprotein 3 Col2/C24
A
t3g26490 non-phototropic hypocotyl, putative 1 Col2/C24
A
t5g66520 selenium-binding protein-like 1 Col2/C24
CAB52747 photosystem I subunit III precursor 2 Col2/C24
A
AK68813 H+-transporting ATP synthase-like protein 2 Col2/C24
A
t3g22520 unknown protein 1 Col2/C24
A
t3g63140 mRNA binding protein precursor - like 1 Col2/C24
A
t1g79040 photosystem II polypeptide, putative 2 Col2/C24
A
t5g20290 putative protein 1 Col2/C24
A
t1g49290 hypothetical protein 1 Col2/C24
A
t5g13160 protein kinase-like 1 Col2/C24
A
t5g24630 unknown protein 1 Col2/C24
A
t1g36990 hypothetical protein 1 Col2/C24
A
96754 Similar to part of disease resistance protein [imported] 1 Col2/C24
T05822 hypothetical protein T5K18.170 1 Col2/C24
A
t3g57330 potential calcium-transporting ATPase 11, plasma membrane-type (Ca2+-ATPase, isoform 11) 1 Col2/C24
A
t4g25430 hypothetical protein 1 Col2/C24
A
t1g16240 expressed protein 1 Col2/C24
A
t1g48280 expressed protein 1 Col2/C24
A
AM62447 glycine-rich RNA binding protein 7 1 Col2/C24
BAB08888 gene_id:MIJ24.6~ref|NP_013897.1~similar to unknown protein 1 Col2/C24

A
AM62639 unknown 2 Col2/C24
A
t1g12900 putative calcium-binding protein, calreticulin 1 Col2/C24
A
t1g44575 photosystem II 22kDa protein, putative 4 Col2/C24
A
t4g05180 oxygen-evolving complex protein 16, chloroplast precursor (OEC16) 4 Col2/C24
NP_051072 cytochrome f 3 Col2/C24
A
F217459_1 heat shock protein 70 2 Col2/C24
A
t1g64290 hypothetical protein 1 Col2/C24
A
t5g26000 glycosyl hydrolase family 1, myrosinase precursor 3 Col2/C24
A
t3g57190 putative protein 1 Col2/C24
A
AK64040 unknown protein 4 Col2/C24
A
F428455_1 putative fructose-bisphosphate aldolase 1 Col2/C24
A
t1g32060 phosphoribulokinase precursor 2 Col2/C24
BAA20945 beta subunit of coupling factor one 2 Col2/C24
A
t2g39730 auxin-regulated protein 1 Col2/C24
A
t1g20020 ferredoxin--NADP reductase precursor, putative 3 Col2/C24
A
t3g08940 putative chlorophyll a/b-binding protein 3 Col2/C24
NP_051055 photosystem II 44 kDa protein 3 Col2/C24
A
t3g03530 expressed protein, supported by cDNA: gi_14335155 1 Col2/C24
A
t2g14380 putative retroelement pol polyprotein 3 Col2/C24
A
t3g26490 non-phototropic hypocotyl, putative 1 Col2/C24
A
t5g66520 selenium-binding protein-like 1 Col2/C24
CAB52747 photosystem I subunit III precursor 2 Col2/C24
A
AK68813 H+-transporting ATP synthase-like protein 2 Col2/C24
A
t3g22520 unknown protein 1 Col2/C24
A
t3g63140 mRNA binding protein precursor - like 1 Col2/C24
A
t1g79040 photosystem II polypeptide, putative 2 Col2/C24
A
t5g20290 putative protein 1 Col2/C24
A
t1g49290 hypothetical protein 1 Col2/C24
A
t5g13160 protein kinase-like 1 Col2/C24
A
t5g24630 unknown protein 1 Col2/C24
A
t1g36990 hypothetical protein 1 Col2/C24
A
96754 Similar to part of disease resistance protein [imported] 1 Col2/C24
T05822 hypothetical protein T5K18.170 1 Col2/C24
A
t3g57330 potential calcium-transporting ATPase 11, plasma membrane-type (Ca2+-ATPase, isoform 11) 1 Col2/C24
A
t4g25430 hypothetical protein 1 Col2/C24
A
t1g16240 expressed protein 1 Col2/C24
A
t1g48280 expressed protein 1 Col2/C24
A
AM62447 glycine-rich RNA binding protein 7 1 Col2/C24
BAB08888 gene_id:MIJ24.6~ref|NP_013897.1~similar to unknown protein 1 Col2/C24
A
t3g14420 glycolate oxidase, putative 1 Col2/C24
A
AM65044 60S acidic ribosomal protein P2 1 Col2/C24
A
t2g29450 glutathione transferase (103-1A) 1 Col2/C24
A
AM98072 unknown protein 1 Col2/C24
A
F428455_1 putative fructose-bisphosphate aldolase 1 Col2/C24
A
t3g50820 photosystem II oxygen-evolving complex 33 (OEC33) 1 Col2/C24
A
t3g14415 glycolate oxidase 1 Col2/C24
A
t2g20230 expressed protein 1 Col2/C24
A
t2g13360 alanine-glyoxylate aminotransferase 1 Col2/C24
A
t5g42650 allene oxide synthase 1 Col2/C24
A
t2g05100 light-harvesting chlorophyll a/b binding protein 1 Col2/C24
A
t5g38750 putative protein 1 Col2/C24
A
t3g44890 RP19 gene for chloroplast ribosomal protein CL9 1 Col2/C24
A
t3g45590 putative protein 1 Col2/C24
A
t5g56810 F-box protein 1 Col2/C24
A
t1g69070 hypothetical protein 1 Col2/C24
A
t2g15325 hypothetical protein 1 Col2/C24
A
t3g63190 putative protein 1 Col2/C24
A
t1g13800 hypothetical protein 1 Col2/C24
A
t3g30843 hypothetical protein 1 Col2/C24
S49030 RNA-binding protein RNP-D precursor 1 Col2/C24
A
AM66135 unknown 1 Col2/C24
A
t4g37460 putative protein 1 Col2/C24
A
t5g44870 disease resistance protein (TIR-NBS-LRR class), putative1 Col2/C24
Supplementary Table 2. Continued

A
t2g47610 60S ribosomal protein L7
A
1 Col2/C24
A
t5g25590 putative protein 1 Col2/C24
A
AM63618 putative rubisco subunit binding-protein alpha subunit 1 Col2/C24
A
t5g23700 putative protein 1 Col2/C24
NP_051045
A
TP synthase CF0 B chain 1 Col2/C24
A
t3g23400 expressed protein 1 Col2/C24
A
t2g40630 expressed protein 1 Col2/C24
A
t4g22780 Translation factor EF-1 alpha - like protein 1 Col2/C24
A
t1g04800 unknown protein 1 Col2/C24
A
t1g20060 kinesin-related protein 1 Col2/C24
A
t5g60120
A
PETALA2 protein - like 1 Col2/C24
A
t2g01620 expressed protein 1 Col2/C24
A
t2g27000 cytochrome p450 family 1 Col2/C24
A
t5g17370 hypothetical protein 1 Col2/C24
A
t5g09660 microbody NAD-dependent malate dehydrogenase 1 Col2/C24
A
t4g31050 putative protein 1 Col2/C24
A
t2g37310 hypothetical protein 1 Col2/C24
A
t5g49120 putative protein 1 Col2/C24
A
t3g24550 protein kinase, putative 1 Col2/C24
A
t2g26940 putative C2H2-type zinc finger protein 1 Col2/C24
T51531 biotin carboxyl carrier protein homolog T20K14.140 [imported] 1 Col2/C24
A
t5g16860 putative protein 1 Col2/C24
BAB10393 contains similarity to En/Spm-like transposon 1 Col2/C24
A
t4g18820 putative protein 1 Col2/C24
A
t5g01730 putative protein 1 Col2/C24
A
t1g80910 myrosinase precursor, putative 1 Col2/C24
A
t2g05170 expressed protein 1 Col2/C24
A
t5g42920 putative protein 1 Col2/C24
A
t5g51200 putative protein 1 Col2/C24
A
t3g53720 putative protein 1 Col2/C24
A
t5g22450 putative protein 1 Col2/C24
A
t1g22410 3-deoxy-D-arabino-heptulosonate 7-phosphate, putative 1 Col2/C24
A
t4g30990 putative protein 1 Col2/C24
A
t3g20860 putative serine/threonine protein kinase 1 Col2/C24
A
t3g05470 unknown protein 1 Col2/C24
A
t1g06380 hypothetical protein 1 Col2/C24
A
t3g47140 putative protein 1 Col2/C24
A
t5g01630 putative protein 1 Col2/C24
A
t5g39960 putative protein 1 Col2/C24
A
t2g35300 similar to late embryogenesis abundant proteins 1 Col2/C24
A
t4g30830 putative protein 1 Col2/C24
A
t1g68940 hypothetical protein 1 Col2/C24
A
t1g79680 WAK-like kinase (WLK) 1 Col2/C24
A
t3g66658 betaine aldehyde dehydrogenase, putative 1 Col2/C24
A
t4g19320 hypothetical protein 1 Col2/C24
A
t3g49350 GTPase activating -like protein 1 Col2/C24
A
t1g16140 WAK-like kinase (WLK) 1 Col2/C24
A
t3g04740 hypothetical protein 1 Col2/C24
A
t3g60890 putative protein 1 Col2/C24
A
t2g07010 putative retroelement pol polyprotein 1 Col2/C24
A
t5g02060 putative protein 1 Col2/C24
A
t3g60310 putative protein 1 Col2/C24
A
AA32797 geranylgeranyl pyrophosphate synthase 1 Col2/C24
BAB09274 histidine kinase-like protein 1 Col2/C24
A
t1g72500 hypothetical protein 1 Col2/C24
A
t3g42320 putative protein 1 Col2/C24
H86321 hypothetical protein F6A14.10 [imported] 1 Col2/C24
A
t5g58980 random slug protein - like 1 Col2/C24
A
t5g14350 putative protein 1 Col2/C24
A
t4g27720 putative protein 1 Col2/C24
S20866 L-ascorbate peroxidase (EC 1.11.1.11) precursor 3 Col2/C24
A
t3g62410 CP12 protein precursor-like protein 1 Col2/C24
A
t3g49120 peroxidase, putative 1 Col2/C24
Supplementary Table 2. Continued

A
t3g11540 spindly (gibberellin signal transduction protein) 1 Col2/C24
A
AB07026 catalase 3 Col2/C24
A
t4g33010 P-Protein - like protein 3 Col2/C24
RBS1_ARATH Ribulose bisphosphate carboxylase small chain 1A, chloroplast precursor (RuBisCO small subunit 1A) 6 Col2/C24
A
t3g45140 lipoxygenase AtLOX2 7Col2
S11852 photosystem II oxygen-evolving complex protein 1 precursor8Col2
A
t5g54270 light-harvesting chlorophyll a/b binding protein, putative 3Col2
JQ1286 glyceraldehyde-3-phosphate dehydrogenase (NADP) (phosphorylating) (EC 1.2.1.13) B precursor, chloropla
s
8Col2
A
t1g56190 phosphoglycerate kinase, putative 7Col2
A
t3g04120 glyceraldehyde-3-phosphate dehydrogenase C subunit (GapC) 3Col2
A
t2g02930 glutathione transferase, putative 5Col2
A
AA50156 carbonic anhydrase 5Col2
A
T4g37930 glycine hydroxymethyltransferase-like protein 5Col2
A
t4g04640 coded for by A. thaliana cDNA AA041141 5Col2
T52072 hypothetical protein g5bf [imported] 5Col2
NP_051058 photosystem I P700 apoprotein A2 5Col2
A
T3g48870
A
tClpC endopeptidase Clp ATP-binding chain C 5Col2
T12970 hypothetical protein T6H20.190 3Col2
A
96602 elongation factor EF-2 [imported] 5Col2
A
t2g39730 Rubisco activase 3Col2
CAA70862 ferredoxin-dependent glutamate synthase 4Col2
A
F326861_1 putative photosystem I subunit PSI-E 3Col2
A
AN31836 putative 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase 4Col2
A
T4g38970 putative fructose-bisphosphate aldolase 2Col2
T52314 chlorophyll a/b-binding protein Lhcb6 [imported] 4Col2
A
t2g35370 glycine decarboxylase complex H-protein 2Col2
NP_051084 photosystem II 47 kDa protein 2Col2
A
t4g13400 putative protein 1Col2
A
AN31832 putative chloroplast translation elongation factor EF-Tu precursor 3Col2
A
t5g38410 ribulose bisphosphate carboxylase small chain 3b precursor 3Col2
A
AA32813 plasma membrane proton pump H+ ATPase 3Col2
NP_051039 photosystem II protein D1 3Col2
A
t4g18480 protein ch-42 precursor, chloroplast 3Col2
S16582 fructose-bisphosphatase (EC 3.1.3.11) precursor, chloroplast 4Col2
A
t5g47210 putative protein 2Col2
JT0901 chaperonin 60 beta precursor 3Col2
CAA74895 ribosomal protein L4 1Col2
A
t1g76030 vacuolar ATP synthase subunit B 2Col2
S33707 DNA-damage repair protein DRT112 precursor 1Col2
A
AN31859 putative heat shock protein 81-2 (HSP81-2) 3Col2
A
AM63250 cyanate lyase 1Col2
A
F360195_1 putative alanine aminotransferase 2Col2
A
t1g53310 phosphoenolpyruvate carboxylase 1, putative 2Col2
A
t2g26080 putative glycine dehydrogenase 2Col2
A
t1g04410 putative malate dehydrogenase 2Col2
A
t1g50250 chloroplast FtsH protease 2Col2
G84888 probable transketolase precursor [imported] 2Col2
A
AK73957 putative ftsH chloroplast protease 3Col2
A
F083913_1 annexin 2Col2
A
t1g77160 hypothetical protein 1Col2
A
t3g17820 glutamine synthetase, putative 2Col2
C84582 hypothetical protein At2g19880 [imported] 1Col2
A
t2g41560 potential calcium-transporting ATPase 4, plasma membrane-type (Ca2+-ATPase, isoform 4) 2Col2
A
AM62764 glutamine synthetase, putative 2Col2
A
t1g24706 F5A9.21, unknown 1Col2
A
t2g22010 unknown protein 1Col2
A
t5g14740 carbonic anhydrase 2 1Col2
A
t1g76180 dehydrin, putative 2Col2
A
F428455_1 putative fructose-bisphosphate aldolase 1Col2
A
t4g31700 ribosomal protein S6 - like 1Col2
A
t1g74060 putative 60S ribosomal protein L6 1Col2
A
t3g47070 putative protein 2Col2
A
t3g58730 v-ATPase subunit D (vATPD) 2Col2
Supplementary Table 2. Continued

A
t1g23740 putative auxin-induced protein 1Col2
CAA11554 2-oxoglutarate dehydrogenase, E3 subunit 2Col2
A
t2g21170 putative triosephosphate isomerase 2Col2
A
t3g46520 actin 12 1Col2
A
t1g19570 dehydroascorbate reductase, putative 2Col2
A
AM97062 unknown protein 1Col2
S71112 catalase (EC 1.11.1.6) 3, peroxisome/glyoxysome location signal (S-[RKH]-L) motif 1Col2
A
t4g13940 adenosylhomocysteinase 2Col2
NP_051087 photosystem II phosphoprotein 1Col2
A
t2g15620 ferredoxin--nitrite reductase 1Col2
A
t3g47470 light-harvesting chlorophyll a/b binding protein 1Col2
A
t4g35090 catalase 2 1Col2
S19226 cold-regulated protein cor47 2Col2
CAC35872 H+-transporting ATP synthase beta chain (mitochondrial)-like protein 2Col2
A
AB80700 glycolate oxidase 1Col2
A
t4g09000 14-3-3 protein GF14 chi (grf1) 1Col2
A
t2g34430 photosystem II type I chlorophyll a /b binding protein 1Col2
A
t4g34870 peptidylprolyl isomerase (cyclophilin) 2Col2
A
t1g16880 expressed protein 2Col2
A
t2g37660 expressed protein 2Col2
A
F360228_1 putative glutathione reductase 1Col2
A
t3g49910 60S ribosomal protein - like 2Col2
A
t5g15980 putative protein 2Col2
T52122 chaperonin 10 2Col2
A
t3g07570 unknown protein 1Col2
A
AM13161
A
TP-dependent transmembrane transporter, putative 1Col2
A
AB09585
A
DP glucose pyrophosphorylase small subunit 2Col2
A
t3g02090 putative mitochondrial processing peptidase 2Col2
A
t4g03430 putative pre-mRNA splicing factor 1Col2
A
t1g71240 hypothetical protein 1Col2
A
t4g31700 ribosomal protein S6 - like 1Col2
A
AK59424 putative DEF (CLA1) protein 1Col2
A
t5g55180 glycosyl hydrolase family 17 1Col2
A
t1g74770 hypothetical protein 1Col2
A
C012394_17 putative phytochrome A signaling protein 1Col2
A
t2g24820 putative Rieske iron-sulfur protein 1Col2
A
t2g36380
A
BC transporter family protein 1Col2
A
t2g35120 glycine decarboxylase complex H-protein 1Col2
A
AL32516 putative protein 1Col2
A
t1g50730 hypothetical protein 1Col2
A
t2g14470 putative helicase 2Col2
A
t1g67560 putative lipoxygenase 1Col2
A
t1g56190 phosphoglycerate kinase 1Col2
A
t4g12180 putative reverse transcriptase 1Col2
A
t3g51560 disease resistance protein (TIR-NBS-LRR class), putative1Col2
A
t1g50120 hypothetical protein 2Col2
G86301 probable retroelement polyprotein [imported] 1Col2
A
t5g16500 protein kinase-like protein 1Col2
A
t1g60860 GCN4-complementing protein 1Col2
CAB80674 putative protein transport factor 1Col2
A
t2g34610 hypothetical protein 1Col2
T01733 hypothetical protein A_IG002N01.31 2Col2
A
t2g07698 hypothetical protein 1Col2
A
t5g10790 ubiquitin-specific protease 22 (UBP22) 1Col2
A
t1g62810 amine oxidase, putative 1Col2
A
C069473_9 unknown protein 1Col2
A
t1g73980 unknown protein 1Col2
T50928 calmodulin-binding protein [imported] 1Col2
A
AM62795 60S ribosomal protein L27A 1Col2
A
t5g37670 low-molecular-weight heat shock protein - like 1Col2
A
t5g48010 pentacyclic triterpene synthase (04C11) (ATPEN1), putative 1Col2
A
t2g43560 FKBP-type peptidyl-prolyl cis-trans isomerase 1Col2
A
C007354_10 Strong similarity to gb|Y09533 involved in starch metabolism from Solanum tuberosum 1Col2
Supplementary Table 2. Continued

A
t1g13790 hypothetical protein 1Col2
A
t2g19380 RRM-containing RNA-binding protein 1Col2
A
t5g06240 unknown protein 1Col2
A
t1g67240 mutator-like transposase, putative 1Col2
CAA69802
A
TPase subunit 1 1Col2
A
t4g20890 tubulin beta-9 chain 1Col2
A
t2g40590 40S ribosomal protein S26 1Col2
BAA97188 emb|CAB87273.1~gene_id:MMI9.7~similar to unknown protein1Col2
A
t5g09860 expressed protein 1Col2
A
t1g60630 leucine-rich repeat transmembrane protein kinase 1Col2
A
t1g02500 s-adenosylmethionine synthetase 1Col2
A
F462865_1 unknown protein 1Col2
A
F424618_1 membrane-associated salt-inducible protein 1Col2
A
t1g05530 UDP-glycosyltransferase family 1Col2
A
t1g74680 Exostosin family 1Col2
A
t1g32470 glycine cleavage system H protein precursor, putative 1Col2
A
t2g47470 putative protein disulfide-isomerase 1Col2
T48997 epsin-like protein 1Col2
A
AK96795 acyl carrier protein (ACP) gene 1Col2
A
t2g16890 putative glucosyltransferase 1Col2
A
AL91646 unknown protein 1Col2
A
t5g59660 leucine-rich repeat transmembrane protein kinase, putative 2Col2
A
t5g66190 ferredoxin-NADP+ reductase 1C24
A
t3g22910 potential calcium-transporting ATPase 13, plasma membrane-type (Ca2+-ATPase, isoform 13) 1C24
A
t4g28750 photosystem I subunit PSI-E - like protein 1C24
A
t5g48310 putative protein 1C24
A
t5g28300 GTL1 - like protein 1C24
A
t1g29930 light-harvesting chlorophyll a/b binding protein 1C24
A
t5g09660 microbody NAD-dependent malate dehydrogenase 1C24
A
t3g11820 syntaxin SYP121 1C24
A
t5g40480 nuclear pore protein -like 1C24
A
t2g35920 putative ATP-dependent RNA helicase
A
1C24
A
t1g22490 expressed protein 1C24
A
t5g14070 glutaredoxin-like protein 1C24
NP_051048 ribosomal protein S2 1C24
A
t4g19750 glycosyl hydrolase family 18 1C24
A
t1g25340 myb-related transcription factor (cpm7), putative 1C24
A
t2g25140 HSP100/ClpB, putative 1C24
A
t2g20960 pEARLI 4 protein 1C24
A
t2g27480 putative calcium binding protein 1C24
A
AD03443 contains similarity to human RNA polymerase II complex component SRB7 (GB:U52960) 1C24
A
t5g03940 signal recognition particle 54CP protein precursor 1C24
A
t1g07430 protein phosphatase 2C (PP2C), putative 1C24
A
t4g07960 putative glucosyltransferase 1C24
A
t3g11630 putative 2-cys peroxiredoxin BAS1 precursor (thiol-specific antioxidant protein) 1C24
A
t4g01310 putative L5 ribosomal protein 1C24
A
t5g61250 glycosyl hydrolase family 79 (endo-beta-glucuronidase/heparanase) 1C24
A
t1g65010 hypothetical protein 1C24
A
t1g67810 unknown protein 1C24
A
t5g50260 cysteine proteinase 1C24
A
t5g64040 photosystem I reaction center subunit PSI-N precursor (PSI-N) 1C24
A
t5g24770 vegetative storage protein Vsp2 1C24
A
t4g28630
A
BC transporter family protein 1C24
A
t5g09730 glycosyl hydrolase family 3 1C24
A
t4g31300 20S proteasome beta subunit A (PBA1); 1C24
T05498 hypothetical protein T19K4.190 1C24
A
C000103_3 unknown protein 1C24
A
t5g09700 beta-glucosidase - like protein 1C24
A
t5g15200 40S ribosomal protein - like 1C24
A
t1g72300 leucine-rich repeat transmembrane protein kinase, putative 1C24
A
t3g14350 leucine-rich repeat transmembrane protein kinase, putative 1C24
A
t3g13160 expressed protein 1C24
A
t5g59660 leucine-rich repeat transmembrane protein kinase, putative 1C24
Supplementary Table 2. Continued

A
t5g66190 ferredoxin-NADP+ reductase 1C24
A
t3g22910 potential calcium-transporting ATPase 13, plasma membrane-type (Ca2+-ATPase, isoform 13) 1C24
A
t4g28750 photosystem I subunit PSI-E - like protein 1C24
A
t5g48310 putative protein 1C24
A
t5g28300 GTL1 - like protein 1C24
A
t1g29930 light-harvesting chlorophyll a/b binding protein 1C24
A
t5g09660 microbody NAD-dependent malate dehydrogenase 1C24
A
t3g11820 syntaxin SYP121 1C24
A
t5g40480 nuclear pore protein -like 1C24
A
t2g35920 putative ATP-dependent RNA helicase
A
1C24
A
t1g22490 expressed protein 1C24
A
t5g14070 glutaredoxin-like protein 1C24
NP_051048 ribosomal protein S2 1C24
A
t4g19750 glycosyl hydrolase family 18 1C24
A
t1g25340 myb-related transcription factor (cpm7), putative 1C24
A
t2g25140 HSP100/ClpB, putative 1C24
A
t2g20960 pEARLI 4 protein 1C24
A
t2g27480 putative calcium binding protein 1C24
A
AD03443 contains similarity to human RNA polymerase II complex component SRB7 (GB:U52960) 1C24
A
t5g03940 signal recognition particle 54CP protein precursor 1C24
A
t1g07430 protein phosphatase 2C (PP2C), putative 1C24
A
t4g07960 putative glucosyltransferase 1C24
A
t3g11630 putative 2-cys peroxiredoxin BAS1 precursor (thiol-specific antioxidant protein) 1C24
A
t4g01310 putative L5 ribosomal protein 1C24
A
t5g61250 glycosyl hydrolase family 79 (endo-beta-glucuronidase/heparanase) 1C24
A
t1g65010 hypothetical protein 1C24
A
t1g67810 unknown protein 1C24
A
t5g50260 cysteine proteinase 1C24
A
t5g64040 photosystem I reaction center subunit PSI-N precursor (PSI-N) 1C24
A
t5g24770 vegetative storage protein Vsp2 1C24
A
t4g28630
A
BC transporter family protein 1C24
A
t5g09730 glycosyl hydrolase family 3 1C24
A
t4g31300 20S proteasome beta subunit A (PBA1); 1C24
T05498 hypothetical protein T19K4.190 1C24
A
C000103_3 unknown protein 1C24
A
t5g09700 beta-glucosidase - like protein 1C24
A
t5g15200 40S ribosomal protein - like 1C24
A
t1g72300 leucine-rich repeat transmembrane protein kinase, putative 1C24
A
t3g14350 leucine-rich repeat transmembrane protein kinase, putative 1C24
A
t3g13160 expressed protein 1C24
A
t5g59660 leucine-rich repeat transmembrane protein kinase, putative 1C24
A
t3g05400 sugar transporter, putative 1C24
A
t5g54290 cytochrome c biogenesis protein precursor (gb|AAF35369.1) 1C24
A
t1g75350 chloroplast 50S ribosomal protein L31, putative 1C24
A
t1g75350 chloroplast 50S ribosomal protein L31, putative 1C24
A
t3g54890 light-harvesting chlorophyll a/b binding protein 1C24
A
t5g47180 VAMP (vesicle-associated membrane protein)-associated protein-like 1C24
A
t5g41610 Na+/H+ antiporter-like protein 1C24
A
C002423_15 unknown protein 1C24
A
t5g58490 cinnamoyl-CoA reductase - like protein 1C24
C86379 unknown protein 1C24
A
t1g19640 S-adenosyl-L-methionine:jasmonic acid carboxyl methyltransferase (JMT) 1C24
A
t5g04290 glycine-rich protein 1C24
A
t1g35680 50S ribosomal protein L21 chloroplast precursor (CL21) 1C24
NP_051097 ribosomal protein L22 1C24
A
t5g48600 chromosome condensation protein 1C24
A
t3g43190 sucrose synthase, putative 1C24
A
t3g26790 transcriptional regulator (FUSCA3) 1C24
A
t4g17300 asparagine--tRNA ligase 1C24
A
t1g31000 hypothetical protein 1C24
BAB02913 unknown protein 1C24
A
AK64154 unknown protein 1C24
A
AB61690 disease resistance protein homolog 1C24
Supplementary Table 2. Continued

A
t2g24490 putative replication protein A1 1C24
A
t5g66190 ferredoxin-NADP+ reductase 1C24
A
t3g22910 potential calcium-transporting ATPase 13, plasma membrane-type (Ca2+-ATPase, isoform 13) 1C24
A
t5g48310 putative protein 1C24
A
t5g28300 GTL1 - like protein 1C24
A
t1g29930 light-harvesting chlorophyll a/b binding protein 1C24
A
t5g09660 microbody NAD-dependent malate dehydrogenase 1C24
A
t3g11820 syntaxin SYP121 1C24
A
t3g51570 disease resistance protein (TIR-NBS-LRR class), putative1C24
A
t3g46530 disease resistance protein, RPP13-like (CC-NBS class), putative 1C24
A
t2g25710 biotin holocarboxylase synthetase 1C24
A
t2g12150 Mutator-like transposase 1C24
A
t5g32481
A
thila retroelement ORF1, putative 1C24
A
t3g24190 expressed protein 1C24
A
t1g19390 WAK-like kinase (WLK) 1C24
A
t4g22470 extensin - like protein 1C24
A
t1g47560 hypothetical protein 1C24
A
t2g16780 putative WD-40 repeat protein, MSI2 1C24
A
t1g18030 protein phosphatase 2C (PP2C), putative 1C24
A
t3g23790
A
MP-binding protein, putative 1C24
A
t1g66530 arginyl-tRNA synthetase 1C24
A
t1g48150 MADS-box protein 1C24
A
t4g14140 (cytosine-5-)-methyltransferase 1C24
A
t1g62940 4-coumarate:coenzyme A ligase, putative 1C24
A
t2g29500 putative small heat shock protein 1C24
A
t3g07980 putative MAP3K epsilon protein kinase 1C24
A
t4g23940 putative MAP3K epsilon protein kinase 1C24
A
t1g21810 myosin-like protein 1C24
A
t5g14950 glycosyl hydrolase family 38 (alpha-mannosidase) 1C24
A
t3g53280 cytochrome P450 monooxygenase 1C24
A
t2g41310 putative two-component response regulator 3 protein 1C24
A
t1g50410 DNA-binding protein, putative 1C24
A
t5g05340 peroxidase, putative 1C24
A
96721 probable peptide transporter 1C24
A
t2g26790 putative salt-inducible protein 1C24
A
t3g30570 putative reverse transcriptase 1C24
A
t1g74080 putative transcription factor 1C24
A
t3g21210 CHP-rich zinc finger protein, putative 1C24
A
t2g42270 U5 small nuclear ribonucleoprotein helicase, putative 1C24
A
t1g69320 CLE10, putative 1C24
A
t3g42950 polygalacturonase, putative 1C24
Supplementary Table 2. Continued