29
Science Supporting Online Material doi 10.1126/science.1086716, p. 1 Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and intensity values for 685 genes with differential expression. Table S3. Genotyping primers Materials and Methods Growth conditions and inoculations All experiments were performed as previously described (S1). Arabidopsis thaliana (L.) Heyhn. and squash (Cucurbita maxima, cultivar Hybrid Kuta) (Park Seed, Greenwood, SC) were grown in growth chambers at 22°C with a 14-hour photoperiod of approximately 125 µEinsteins m –2 s –1 in the 400- to 700-nm range. Powdery mildew (Erysiphe cichoracearum UCSC1) was cultured on squash for 10–12 days and was then applied to Arabidopsis by using 1.3-m settling towers. Identification and cloning of pmr4 alleles Alleles of pmr4 were isolated during screens looking for either a gain of resistance to E. cichoracearum or for alterations in the nonhost papillae response to the nonhost barley powdery mildew (Blumeria graminis f.sp. hordei CR3). Previously pmr4-1 had been mapped to the top of chromosome 4 in a cross to Wassilewskija-0 (S1). Noting the presence of a glucan synthase-like gene (GSL5) within our mapping interval (S2), we ordered T-DNA insertion line SALK_2911 [Salk Institute Genomic Analysis Laboratory’s T-DNA project;(S3)] (S4) from the Arabidopsis Biological Resource Center. This line segregated for powdery mildew resistance. The identity of PMR4 was confirmed by cycle sequencing the open reading frames of our other pmr4 alleles following manufacturer’s instruction on an ABI 310 Sequenator (Applied Biosystems). Cytology Fungal growth, lesion staining with trypan blue, and callose staining with analine blue were performed as described (S1). To assay callose elicitation by dichlobenil (Chem Service), seedlings were germinated on 1 µM dichlobenil plates as described (S5), and then stained with aniline blue as above. For chitin elicitation, drops of 1 mg/mlacid hydrolyzed crab shell chitin (Sigma) in water were applied to 3-week-old plants, which were harvested and stained with aniline blue after 24 hours. Barley powdery mildew (Blumeria graminis f.sp. hordei CR3) was grown on barley line Algerian-S (CI-16138) (S6) and inoculated onto Arabidopsis by using the inoculation tower method previously described (S1). Barley plants were grown under the same conditions as Arabidopsis for 1 week before infection for maintenance of the inoculum. Three-week-old Arabidopsis plants were inoculated with barley powdery mildew, and leaf samples were taken 2 days later. Callose was stained with aniline blue. For TEM processing, leaf tissue at 24 hours after inoculation with E. cichoracearum was cut into small pieces in fixative (3% glutaraldehyde in buffer) and placed in fixative for 2 hours (S7). A 0.05 M potassium-phosphate buffer (pH 6.8) was

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Page 1: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Science Supporting Online Materialdoi 10.1126/science.1086716, p. 1

Supporting Online Material for Nishimura et al., 1086716Materials and MethodsTable S1. Alleles of PMR4Table S2. Ratio and intensity values for 685 genes with differential expression.Table S3. Genotyping primers

Materials and Methods

Growth conditions and inoculationsAll experiments were performed as previously described (S1). Arabidopsis thaliana (L.)Heyhn. and squash (Cucurbita maxima, cultivar Hybrid Kuta) (Park Seed, Greenwood,SC) were grown in growth chambers at 22°C with a 14-hour photoperiod ofapproximately 125 µEinsteins m–2 s–1 in the 400- to 700-nm range. Powdery mildew(Erysiphe cichoracearum UCSC1) was cultured on squash for 10–12 days and was thenapplied to Arabidopsis by using 1.3-m settling towers.

Identification and cloning of pmr4 allelesAlleles of pmr4 were isolated during screens looking for either a gain of resistance to E.cichoracearum or for alterations in the nonhost papillae response to the nonhost barleypowdery mildew (Blumeria graminis f.sp. hordei CR3). Previously pmr4-1 had beenmapped to the top of chromosome 4 in a cross to Wassilewskija-0 (S1). Noting thepresence of a glucan synthase-like gene (GSL5) within our mapping interval (S2), weordered T-DNA insertion line SALK_2911 [Salk Institute Genomic AnalysisLaboratory’s T-DNA project;(S3)] (S4) from the Arabidopsis Biological ResourceCenter. This line segregated for powdery mildew resistance. The identity of PMR4 wasconfirmed by cycle sequencing the open reading frames of our other pmr4 allelesfollowing manufacturer’s instruction on an ABI 310 Sequenator (Applied Biosystems).

CytologyFungal growth, lesion staining with trypan blue, and callose staining with analine bluewere performed as described (S1). To assay callose elicitation by dichlobenil (ChemService), seedlings were germinated on 1 µM dichlobenil plates as described (S5), andthen stained with aniline blue as above. For chitin elicitation, drops of 1 mg/mlacidhydrolyzed crab shell chitin (Sigma) in water were applied to 3-week-old plants, whichwere harvested and stained with aniline blue after 24 hours.

Barley powdery mildew (Blumeria graminis f.sp. hordei CR3) was grown onbarley line Algerian-S (CI-16138) (S6) and inoculated onto Arabidopsis by using theinoculation tower method previously described (S1). Barley plants were grown under thesame conditions as Arabidopsis for 1 week before infection for maintenance of theinoculum. Three-week-old Arabidopsis plants were inoculated with barley powderymildew, and leaf samples were taken 2 days later. Callose was stained with aniline blue.

For TEM processing, leaf tissue at 24 hours after inoculation with E.cichoracearum was cut into small pieces in fixative (3% glutaraldehyde in buffer) andplaced in fixative for 2 hours (S7). A 0.05 M potassium-phosphate buffer (pH 6.8) was

Page 2: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Science Supporting Online Materialdoi 10.1126/science.1086716, p. 2

used thoughout the protocol. Tissue was rinsed in buffer and post-fixed in 2% OsO4 inbuffer for 2 hours. After rinsing in buffer, the samples were dehydrated in an ethanolseries and embedded in Spurr’s resin (Electron Microscopic Sciences). Thin sections wereobtained using a diamond knife on a Reichert OM2 ultramicrotome, stained in 2% uranylacetate (pH 5.0), followed by 0.01 M lead citrate (pH 12), and viewed with a Philips 201transmission electron microscope.

ImmunolocalizationArabidopsis rosettes from 3-week-old plants were inoculated, and leaves were collectedafter 3 days. For wounding experiments, leaves were wounded with scissors 1 day beforecollection. The immunolocalization protocol was adapted from Sugimoto et al. (S8).Leaves were fixed in PEMT buffer (50 mM Pipes, 2 mM EGTA, 2 mM MgSO4, 0.05%Triton X-100, pH 7.2) containing 1.5% formaldehyde and 0.5% glutaraldehyde for 40min and washed with PEMT buffer three times for 10 min each. Then the leaves wererinsed quickly three times in PEM buffer. The leaves were digested with 0.5% cellulase(Sigma) and 0.025% pectolyase Y-23 (ICN Biomedicals) in PEM buffer for 15 min.After digestion the leaves were quickly rinsed in PEM buffer three times. The leaveswere then treated with –20°C methanol for 10 min and then rehydrated in PBS (0.9%NaCl, 10 mM sodium phosphate; pH 7.2) for 10 min. Leaves were incubated with 1mg/ml NaBH4 in PBS for 20 min to reduce free aldehyde groups. Leaves were washed inincubation buffer (PBS with 50 mM glycine) for 30 min. Leaves were incubated with a200:1 dilution of anti-callose antibodies (S9) in PBS (Biosupplies, Australia) overnight atroom temperature, followed by rinsing in incubation buffer three times for 10 min each.The leaves were then incubated with Alexa 488-conjugated secondary antibodies(Molecular Probes) for 3 hours at 37°C. The leaves were then stained with 0.1 mg/mlpropidium iodide (Molecular Probes) for 6 hours at room temperature to visualize bothfungal structures and plant cell walls. Fluorescence was imaged using a Bio-Rad confocalmicroscope.

Construction of double mutantsThe mutant alleles used for the construction of double mutants with pmr4-1 were NahG(S10), npr1-1 (S11), pad4-1 (S12), Etr1-1 (S13), and coi1-1 (S14). All of the mutant lineswere in the Columbia background. We performed all experiments using a pmr4-1 linethat had been backcrossed two times. We generated the double mutants by standardgenetic crosses, following the mutations with CAPS markers. In the cases when themutation did not lead to a change in a restriction site, we generated derived CAPSmarkers using the dCAPS Webtool (S15). Table S3 lists the primers used for genotyping,CAPS and dCAPS markers are indicated by the inclusion of the enzyme name in theprimer names. The Etr1-1 (S16), NahG (S17) and coi1-1 (S14) primers have beenpreviously described.

Expression analysisFour replicates of samples of Columbia-0 (Col-0; wild-type) and pmr4-1 were collectedfrom either uninfected plants or plants infected with powdery mildew for 3 days. TotalRNA was extracted from the plants using the TriZol method (S18) (Gibco-BRL) and

Page 3: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Science Supporting Online Materialdoi 10.1126/science.1086716, p. 3

purified with a silica membrane column (Qiagen, Rneasy) essentially as described in(S19). Biotinylated complementary RNA (cRNA) (20 µg) was prepared as described(S20) from the purified total RNA. The resulting cRNA was used to hybridize ATH1Arabidopsis GeneChips (Affymetrix) by using the manufacturer’s protocols. The arrayimages were analyzed with the Affymetrix Microarray Suite 5.0 with the target intensityset to 500. The expression levels of the genes were analyzed by using GeneSpring 4.2software (Silicon Genetics) with the chip-to-chip signal variation minimized bynormalizing signal intensities to the averaged (n = 4) intensity values of uninoculatedCol-0 using the expression levels of the top 50th percentile of genes on the arrays. Genesthat consistently increase or decrease in their expression levels relative to the expressionlevel in uninoculated Columbia-0 samples were identified using the SignificanceAnalysis of Microarrays software (S21) with a false-positive setting of less than 1. Thislist was further narrowed by selecting genes showing ��WZRIROG�FKDQJH�LQ�H[SUHVVLRQlevels relative to uninoculated Columbia-0 plants. Expression data sets have beendeposited in the Gene Expression Omnibus (accession numbers: GSE431, GSM6227,GSM6544, GSM6571-GSM6584) at the National Center for Biotechnology Information(S22, S23).

ReferencesS1. J. Vogel, S. Somerville, Proc. Natl. Acad. Sci. U.S.A. 97, 1897 (2000).S2. T. A. Richmond, C. R. Somerville, Plant Physiol. 124, 495 (2000).S3. http://signal.salk.edu/cgi-bin/tdnaexpressS4. J. R. Ecker, Plant Physiol. 129, 405 (2002).S5. T. C. Nickle, D. W. Meinke, Plant J. 15, 321 (1998).S6. J. G. Moseman, Crop Sci. 12, 681 (1972).S7. H. H. Edwards, Can. J. Bot. 80, 1121 (2002).S8. K. Sugimoto, R. E. Williamson, G. O. Wasteneys, Plant Physiol. 124, 1493 (2000).S9. P. J. Meikle, I. Bonig, N. J. Hoogenraad, A. E. Clarke, B. A. Stone, Planta 185, 1

(1991).S10. K. Lawton et al., Mol. Plant Microbe Interact. 8, 863 (1995).S11. H. Cao, S. A. Bowling, A. S. Gordon, X. Dong, Plant Cell 6, 1583 (1994).S12. D. Jirage et al., Proc. Natl. Acad. Sci. U.S.A. 96, 13583 (1999).S13. C. Chang, S. F. Kwok, A. B. Bleecker, E. M. Meyerowitz, Science 262, 539 (1993).S14. D. X. Xie, B. F. Feys, S. James, M. Nieto-Rostro, J. G. Turner, Science 280, 1091

(1998).S15. M. M. Neff, J. D. Neff, J. Chory, A. E. Pepper, Plant J. 14, 387 (1998).S16. J. Hua, E. M. Meyerowitz, Cell 94, 261 (1998).S17. K. Morris et al., Plant J. 23, 677 (2000).S18. P. Chomczynski, N. Sacchi, Anal. Biochem. 162, 156 (1987).S19. K. Ramonell et al., Mol. Plant Pathol. 3, 301 (2002).S20. R. Hernan et al., Cancer Res. 63, 140 (2003).S21. V. G. Tusher, R. Tibshirani, G. Chu, Proc. Natl. Acad. Sci. U.S.A. 98, 5116 (2001).S22. R. Edgar, M. Domrachev, A.E. Lash, Nucleic Acids Res. 30, 207-210 (2002).S23. www.ncbi.nlm.nih.gov/geo/

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Science Supporting Online Materialdoi 10.1126/science.1086716, p. 4

Table S1. Alleles of PMR4

Allelename

Linename

Population* Nucleotide change Amino acid change

pmr4-1 pmr4 Pmr G to A at nt 2220 Stop at aa 687pmr4-2 mil8-1 Mil A to G at nt 2031,

resulting in asplicing defect

Causes frame shiftmutation

pmr4-3 mil8-3 Mil G to A at nt 5491 Stop at aa 1717pmr4-4 mil8-8 Mil G to A at nt 1482 Stop at aa 494pmr4-5 86H3 No callose G to A at nt 1188 Stop at aa 396pmr4-6 82C2 No callose G to A at nt 2221 Stop at aa 687pmr4-7 87A3 No callose G to A at nt 3096 Stop at aa 979pmr4-8 146I4 No callose G to A at nt 3097 Stop at aa 979pmr4-9 62D2 No callose G to A at nt 5065 Stop at aa 1575

*Population from which the allele was recovered. Pmr, screen for powdery mildewresistant mutants; mil, screen for mutants that produce lesions following powderymildew attack; no callose, screen for mutants that do not produce callose in responseto inoculation with a non-host pathogen, barley powdery mildew (Blumeria graminisf. sp. hordei).

Page 5: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

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to G

B:M

905

08; s

upp

orte

d b

ycD

NA

: gi_

1668

60_

gb_

M90

508

.1_

AT

HR

PR

P1A

2663

85_a

t27

At1

g35

230

8.5

758

0.9

8911

.710

411.

716

2H

ypot

het

ical

pro

tein

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:2

657

72.

2595

50_a

t

Page 6: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 6

28A

t4g2

370

04.

710

40.

920

11.6

243

1.8

43P

utat

ive

Na+

/H+-e

xcha

ngin

g pr

otei

n N

a+/H

+-e

xcha

ngin

g pr

otei

n sl

r159

5--

Syn

echo

cyst

is s

p., E

MB

L:D

909

0225

4215

_at

29A

t4g2

183

05.

157

91.

011

211

.312

611.

517

0

Put

ativ

e pr

otei

n C

GI-

131

prot

ein,

Hom

o sa

pien

s, A

F15

188

9; s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

4645

.25

4385

_s_a

t

30A

t1g2

638

09.

639

60.

432

11.2

460

1.8

76

Hyp

oth

etic

al p

rote

in s

imila

r to

ret

icul

ine

oxid

ase-

like

prot

ein

GB

:CA

B45

850

GI:5

262

224

from

[A. t

halia

na];

supp

orte

d b

y cD

NA

:gi

_134

3083

9_gb

_AF

360

332.

1_A

F36

0332

2610

21_a

t

31A

t4g2

315

06.

570

91.

010

911

.112

152.

022

8S

erin

e/th

reon

ine

kina

se–l

ike

prot

ein

KI d

omai

n in

tera

ctin

g ki

nase

1 (

KIK

1), Z

ea

may

s25

4271

_at

32A

t1g2

639

04.

428

00.

962

11.0

682

1.3

87

Hyp

oth

etic

al p

rote

in s

imila

r to

ret

icul

ine

oxid

ase-

like

prot

ein

GB

:CA

B45

850

GI:5

262

224

from

[A. t

halia

na];

supp

orte

d b

y cD

NA

:gi

_152

9313

2_gb

_AY

0510

00.1

_26

1020

_at

33A

t1g6

862

05.

023

20.

945

10.7

489

2.2

104

Unk

now

n pr

otei

n; s

upp

orte

d b

y cD

NA

: gi_

1433

5125

_gb

_AY

0372

42.1

_26

2229

_at

34A

t4g1

189

07.

712

111.

015

810

.416

442.

032

1P

rote

in k

inas

e–lik

e pr

otei

n K

I dom

ain

inte

ract

ing

kina

se 1

-Z

eam

ays,

PIR

2:T

0205

325

4869

_at

35A

t2g0

445

04.

996

21.

019

910

.019

702.

345

8P

utat

ive

mut

T d

omai

n pr

otei

n26

3852

_at

36A

t4g0

070

05.

469

21.

012

79.

812

452.

329

2P

utat

ive

phos

phor

ibos

ylan

thra

nila

te tr

ansf

eras

e25

5630

_at

37A

t1g2

124

06.

428

91.

046

9.8

444

1.7

80H

ypot

het

ical

pro

tein

2595

59_a

t

38A

t3g1

101

09.

213

690.

915

09.

714

792.

233

1P

utat

ive

dise

ase

resi

stan

ce p

rote

in s

imila

r to

dis

ease

res

ista

nce

prot

ein

GB

:AA

C7

8591

[Ly

cope

rsic

on e

scul

entu

m]

2564

31_s

_at

39A

t4g0

449

05.

317

21.

031

9.6

299

1.7

63P

utat

ive

rece

pto

r-lik

e pr

otei

n ki

nase

2553

40_a

t40

At1

g13

470

8.4

1147

1.0

133

9.6

1332

3.5

491

Hyp

oth

etic

al p

rote

in p

redi

cted

by

GE

NS

CA

N +

2593

85_a

t41

At5

g22

570

5.3

272

1.0

509.

549

51.

998

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to D

NA

-bin

ding

pro

tein

2498

90_a

t

42A

t5g1

847

06.

715

931.

023

79.

422

331.

740

9P

utat

ive

prot

ein

S-r

ecep

tor

kina

se P

K3

prec

urso

r, m

aize

, PIR

:T02

753;

sup

port

ed

by

full-

leng

th c

DN

A: C

eres

:154

037.

2499

83_a

t

43A

t3g0

183

04.

311

10.

519

9.2

232

2.1

57

Hyp

oth

etic

al p

rote

in s

imila

r to

cal

mod

ulin

-like

pro

tein

GB

:CA

B42

906

[A. t

hal

iana

];P

fam

HM

M h

it: E

F h

and;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es: 7

252

.25

8947

_at

44A

t4g3

413

53.

933

81.

086

9.0

785

1.3

136

Glu

cosy

ltran

sfer

ase

-like

pro

tein

imm

edia

te-e

arly

sal

icyl

ate-

indu

ced

gluc

osyl

tran

sfer

ase,

Nic

otia

na ta

bacu

m,

PIR

2:T

0374

7; s

upp

orte

d b

y cD

NA

gi:1

4334

981

2532

68_s

_at

45A

t1g0

245

06.

147

71.

077

9.0

694

2.0

160

Unk

now

n pr

otei

n26

0904

_at

46A

t5g3

967

04.

764

21.

013

68.

912

042.

129

4

Cal

cium

-bin

ding

pro

tein

–lik

e cb

p1 c

alci

um-b

indi

ng p

rote

in, L

otus

japo

nicu

s,E

MB

L:L

JA25

180

8; s

uppo

rted

by

cDN

A:

gi_1

6648

829_

gb_

AY

058

192.

1_

2494

17_a

t

47A

t2g3

598

04.

523

40.

853

8.8

478

0.9

56S

imila

r to

har

pin-

indu

ced

prot

ein

hin1

from

toba

cco;

sup

port

ed b

y fu

ll-le

ngth

cDN

A: C

eres

:264

18.

2639

48_a

t

48A

t5g5

239

05.

524

60.

845

8.7

389

2.3

103

Pho

toas

sim

ilate

-res

pons

ive

prot

ein

PA

R-l

ike

prot

ein;

sup

port

ed

by

full-

leng

thcD

NA

: Cer

es:1

7872

.24

8333

_at

49A

t4g0

450

03.

334

81.

010

58.

790

71.

920

2P

utat

ive

rece

pto

r-lik

e pr

otei

n ki

nase

2553

41_a

t

50A

t3g2

683

06.

086

01.

014

38.

512

241.

521

8P

utat

ive

cyto

chro

me

P-4

50 s

imila

r to

cyt

ochr

ome

P-4

50

71B

2 G

B:O

6578

8 [A

.th

alia

na]

2582

77_a

t

51A

t3g5

133

06.

239

80.

864

8.4

551

2.0

128

Put

ativ

e pr

otei

n se

vera

l hyp

oth

etic

al p

rote

ins-

-A. t

halia

na; s

uppo

rted

by

cDN

A:

gi_1

5010

763_

gb_A

Y04

5683

.1_

2520

98_a

t52

At2

g18

690

6.3

1790

1.0

287

8.4

2387

1.4

409

Unk

now

n pr

otei

n; s

upp

orte

d b

y cD

NA

: gi_

1451

7479

_gb

_AY

0395

75.1

_26

6017

_at

53A

t5g6

400

05.

767

01.

011

88.

195

51.

619

13(

2),5

-Bis

phos

phat

e nu

cleo

tidas

e (e

mb|

CA

B05

889.

1)24

7314

_at

54A

t1g7

841

06.

125

91.

042

8.0

350

1.3

59H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

ene

Mar

k.hm

m; s

uppo

rted

by

full-

leng

th c

DN

A:

Cer

es:1

57.

2608

04_a

t55

At1

g14

870

6.6

1634

01.

024

648.

020

502

2.5

6130

Unk

now

n pr

otei

n26

2832

_s_a

t56

At4

g31

800

4.5

622

1.0

138

7.9

1102

1.1

150

Exp

ress

ed p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 4

069

2.25

3485

_at

57A

t4g3

983

04.

929

20.

959

7.8

458

1.9

115

Put

ativ

e L-

asco

rbat

e o

xida

se L

-asc

orba

te o

xida

se, C

ucum

is s

ativ

us,

PIR

1:K

SK

VA

O25

2862

_at

Page 7: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 7

58A

t1g5

189

06.

447

61.

074

7.6

571

1.4

109

Ligh

t rep

ress

ible

rec

epto

r pr

otei

n ki

nase

, put

ativ

e si

mila

r to

ligh

t rep

ress

ible

rece

ptor

pro

tein

kin

ase

GI:1

3216

86 fr

om [A

. th

alia

na]

2463

68_a

t59

At2

g32

210

2.3

860.

933

7.5

251

2.6

90U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:316

65.

2656

70_s

_at

60A

t3g2

561

04.

745

40.

897

7.5

724

1.4

170

AT

Pas

e II,

put

ativ

e si

mila

r to

GB

:AA

D34

706

from

[Hom

o sa

pien

s] (

Bio

chem

.B

ioph

ys. R

es. C

omm

un. 2

57 (

2), 3

33-3

39 (

1999

))25

6756

_at

61A

t5g1

076

05.

696

261.

017

237.

313

136

2.0

3487

Nuc

leoi

d D

NA

-bin

ding

pro

tein

cnd

41–l

ike

prot

ein;

nuc

leoi

d D

NA

-bin

ding

pro

tein

cnd4

1, c

hlor

opla

st, c

omm

on to

bacc

o, P

IR:T

0199

625

0445

_at

62A

t5g4

605

04.

050

61.

012

67.

291

81.

114

1P

eptid

e tr

ansp

orte

r24

8932

_at

63A

t3g5

093

03.

933

51.

086

7.1

614

1.5

140

BC

S1

prot

ein-

like

prot

ein

Hom

o sa

pien

s h-

bcs1

(B

CS

1) m

RN

A, n

ucle

ar g

ene

enco

ding

mito

chon

dria

l pro

tein

whi

ch is

invo

lved

in th

e e

xpre

ssio

n of

func

tiona

lm

itoch

ondr

ial u

biqu

inol

-cyt

ochr

ome

c re

duct

ase

com

plex

pro

babl

y vi

a th

e c

2521

31_a

t64

At5

g55

450

3.8

4090

1.0

1087

7.1

8096

2.0

2174

Unk

now

n pr

otei

n; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:4

309

.24

8062

_at

65A

t3g6

042

03.

089

41.

030

07.

121

661.

544

8P

utat

ive

prot

ein

prib

5, R

ibes

nig

rum

, EM

BL:

RN

I757

8; s

uppo

rted

by

full-

leng

thcD

NA

: Cer

es:3

1361

.25

1400

_at

66A

t1g1

034

04.

669

21.

014

97.

010

492.

131

6H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

EN

SC

AN

; su

ppo

rted

by

cDN

A:

gi_1

3937

239_

gb_A

F37

297

5.1

_AF

3729

7526

4434

_at

67A

t2g4

236

04.

517

20.

838

6.9

263

1.4

55P

utat

ive

RIN

G z

inc

finge

r pr

otei

n26

5853

_at

68A

t1g0

385

04.

384

51.

019

16.

913

421.

529

9H

ypot

het

ical

pro

tein

pre

dict

ed b

y ge

nef

inde

r; s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

:C

eres

:271

253.

2650

67_a

t

69A

t1g6

696

04.

217

10.

840

6.9

287

1.4

602,

3-O

xido

squa

lene

-tri

terp

enoi

d cy

clas

e, p

utat

ive

sim

ilar

to 2

,3-o

xido

squa

lene

-tr

iterp

enoi

d cy

clas

e G

I:273

8027

from

[A. t

hal

iana

]25

5912

_at

70A

t3g2

501

04.

063

01.

015

86.

810

781.

320

4

Dis

ease

res

ista

nce

prot

ein,

put

ativ

e si

mila

r to

GB

:AA

D13

301

from

[Lyc

oper

sico

nes

cule

ntum

], co

ntai

ns P

fam

pro

files

: PF

0056

0 le

ucin

e-ri

ch r

epea

t (23

cop

ies)

2571

00_a

t

71A

t3g4

748

04.

990

91.

018

56.

812

581.

224

1P

utat

ive

calc

ium

-bin

ding

pro

tein

cal

cium

bin

ding

dom

ains

(E

F h

and)

of s

ever

alpr

otei

ns25

2417

_at

72A

t3g5

724

06.

335

341.

055

76.

837

731.

810

29β-

1,3-

Glu

cana

se25

1673

_at

73A

t3g4

978

02.

739

91.

014

26.

896

31.

624

0P

utat

ive

prot

ein;

sup

port

ed

by

full-

leng

th c

DN

A: C

eres

: 403

02.

2522

34_a

t74

At4

g14

630

1.4

550.

835

6.7

235

1.1

54G

erm

in p

recu

rsor

oxa

late

oxi

dase

2455

67_a

t

75A

t2g2

946

03.

810

80.

928

6.7

189

0.7

28P

utat

ive

glut

athi

one

S-t

rans

fera

se; s

uppo

rted

by

cDN

A:

gi_1

4423

533_

gb_A

F38

700

4.1

_AF

3870

0426

6267

_at

76A

t4g1

249

03.

116

361.

052

86.

735

561.

051

8

pEA

RL

I 1-l

ike

prot

ein;

A.

thal

iana

pE

AR

LI 1

mR

NA

, PID

:g87

1780

; sup

por

ted

bycD

NA

: gi_

1545

047

0_g

b_A

Y05

233

6.1

_25

4832

_at

77A

t5g3

890

04.

340

20.

993

6.7

629

1.7

158

frnE

pro

tein

–lik

e; fr

nE p

rote

in, D

eino

cocc

us r

adio

dura

ns, P

IR:E

7549

1; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:109

82.

2494

81_a

t78

At5

g25

260

4.6

235

0.9

526.

735

31.

910

2N

odul

in –

like

pro

tein

; nod

ulin

, Gly

cine

max

, EM

BL:

AF

065

435

2469

27_s

_at

79A

t1g4

413

04.

688

0.4

156.

712

91.

230

Nuc

ellin

, put

ativ

e si

mila

r to

nuc

ellin

GI:2

2902

01 f

rom

[Hor

deum

vul

gare

]24

5738

_at

80A

t5g5

542

05.

528

50.

952

6.6

346

1.4

93U

nkno

wn

prot

ein

2480

83_a

t81

At2

g30

770

4.2

299

1.0

716.

445

91.

286

Put

ativ

e cy

toch

rom

e P

-450

2675

67_a

t82

At1

g67

920

5.1

251

1.0

496.

431

01.

679

Unk

now

n pr

otei

n; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

310

2.26

0005

_at

83A

t1g7

471

04.

310

711.

024

66.

315

871.

537

3

Isoc

hori

smat

e sy

nth

ase

(ics

I); i

dent

ical

to is

ocho

rism

ate

synt

hase

(ic

sI)

GB

:AF

0780

80 (

cata

lyze

s ch

oris

mic

aci

d to

isoc

hori

smic

aci

d P

lant

Ph

ysio

l. 11

8(4

), 1

536

(199

8));

sup

port

ed b

y cD

NA

: gi_

3348

076_

gb_

AF

078

080.

1_A

F07

808

026

2177

_at

84A

t3g1

310

03.

514

70.

532

6.3

273

1.1

56

AB

C tr

ansp

orte

r, p

utat

ive

sim

ilar

to A

tMR

P4

(tra

nspo

rt o

f glu

tath

ione

-con

juga

tes

into

the

vacu

ole)

GB

:CA

A05

625

[A. t

halia

na];

cont

ains

Pfa

m p

rofil

e: P

F00

005

AB

C tr

ansp

orte

r25

7185

_at

85A

t5g4

589

01.

238

0.9

306.

218

76.

319

0S

enes

cenc

e-sp

ecifi

c cy

stei

ne p

rote

ase

SA

G12

; ide

ntic

al to

sen

esce

nce-

spec

ific

prot

ein

SA

G12

GI:1

0463

73 fr

om [A

. th

alia

na]

2489

18_a

t86

At3

g28

580

2.8

460.

916

6.2

102

1.4

24H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

ene

Mar

k.hm

m25

6989

_at

87A

t2g2

640

01.

944

01.

023

06.

214

521.

536

1U

nkno

wn

prot

ein

sim

ilar

to G

P|2

2448

27|g

nl|P

ID|e

3268

18|Z

9733

624

5035

_at

Page 8: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 8

88A

t1g5

959

04.

850

90.

810

46.

265

21.

923

5H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

ene

Mar

k.hm

m; s

uppo

rted

by

full-

leng

th c

DN

A:

Cer

es:9

9553

.26

2072

_at

89A

t5g1

192

03.

229

41.

092

6.1

564

1.6

150

Fru

ctos

idas

e–lik

e pr

otei

n; fr

ucto

sida

se, C

icho

rium

inty

bus,

EM

BL:

CIF

RU

CT

OS

;su

ppor

ted

by

cDN

A: g

i_16

9745

74_g

b_A

Y06

0553

.1_

2503

02_a

t

90A

t3g5

048

03.

822

461.

058

06.

135

731.

810

93H

ypot

het

ical

pro

tein

; sup

port

ed b

y cD

NA

:gi

_136

0573

5_gb

_AF

361

849.

1_A

F36

1849

2521

70_a

t

91A

t1g6

688

04.

611

011.

023

96.

014

741.

740

4P

rote

in k

inas

e, p

uta

tive

cont

ains

Pfa

m p

rofil

e: P

F00

069:

Eu

kary

otic

pro

tein

kin

ase

dom

ain

2563

66_a

t92

At4

g14

365

3.9

1597

1.0

411

6.0

2462

1.7

704

Exp

ress

ed p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 3

780

9.24

5329

_at

93A

t4g3

699

03.

023

41.

077

5.9

457

1.4

119

Hea

t sho

ck tr

ansc

ript

ion

fact

or H

SF

4; s

uppo

rted

by

cDN

A:

gi_1

6199

20_g

b_U

6801

7.1

_AT

U68

017

2462

14_a

t94

At1

g13

340

2.0

215

1.0

107

5.9

642

1.5

167

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

2594

10_a

t95

At2

g41

850

2.5

540.

922

5.8

132

4.0

88P

utat

ive

poly

gala

ctur

onas

e26

0492

_at

96A

t3g2

621

04.

784

71.

018

05.

810

491.

731

3C

ytoc

hrom

e P

-450

, pu

tativ

e c

onta

ins

Pfa

m p

rofil

e: P

F00

067

cyt

ochr

ome

P-4

5025

7623

_at

97A

t2g3

268

04.

418

081.

040

95.

723

231.

249

4P

utat

ive

dise

ase

resi

stan

ce p

rote

in26

7546

_at

98A

t5g6

095

03.

774

81.

020

35.

711

421.

634

0

Put

ativ

e ph

ytoc

hela

tin s

ynth

etas

e–lik

e; p

uta

tive

phyt

oche

latin

syn

thet

ase,

A.

thal

iana

, EM

BL:

AT

H67

8724

7604

_at

99A

t1g0

293

04.

612

361

1.0

2687

5.6

1553

01.

539

53

Glu

tath

ione

S-t

rans

fera

se, p

utat

ive

sim

ilar

to g

luta

thio

ne S

-tra

nsfe

rase

GI:8

6095

5fr

om [H

yosc

yam

us m

utic

us];

supp

orte

d b

y cD

NA

: gi

_152

1560

7_g

b_A

Y05

033

2.1

_26

2119

_s_a

t

100

At3

g45

860

3.9

3712

1.0

955

5.6

5294

1.7

1680

Pro

tein

kin

ase–

like;

rec

epto

r-lik

e pr

otei

n ki

nase

RL

K3,

A. t

hal

iana

,E

MB

L:A

TH

0116

7425

2549

_at

101

At1

g74

360

5.0

298

0.9

605.

533

32.

012

2

Put

ativ

e re

cep

tor

prot

ein

kina

se s

imila

r to

bra

ssin

oste

roid

-ins

ensi

tive

1G

B:A

AC

498

10 (

put

ativ

e re

cept

or p

rote

in k

inas

e); c

onta

ins

Pfa

m p

rofil

es:

PF

0056

0 le

ucin

e-ri

ch r

epea

t (17

rep

eats

), P

F0

0069

Eu

kary

otic

pro

tein

kin

ase

dom

ain

2602

39_a

t

102

At4

g18

250

4.4

334

1.0

755.

541

61.

410

7R

ecep

tor

seri

ne/th

reon

ine

kina

se–l

ike

prot

ein;

rec

epto

r se

rine

/thre

onin

e ki

nase

PR

5K,

PA

TC

HX

:G12

3568

025

4660

_at

103

At4

g23

810

4.6

582

0.9

123

5.5

692

1.5

213

Put

ativ

e pr

otei

n A

R4

11--

A. t

hal

iana

(th

ale

cres

s), P

ID:g

166

9603

; su

ppor

ted

by

cDN

A: g

i_13

507

100_

gb_

AF

272

748

.1_A

F2

7274

825

4231

_at

104

At2

g14

560

4.0

1015

21.

025

645.

414

425

2.5

6504

Unk

now

n pr

otei

n26

5837

_at

105

At2

g24

850

2.5

915

1.0

354

5.4

1892

1.0

339

Put

ativ

e ty

rosi

ne a

min

otra

nsfe

rase

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

4570

.26

3539

_at

106

At2

g13

810

2.9

267

1.0

925.

348

51.

514

3P

utat

ive

aspa

rtat

e am

inot

rans

fera

se; s

uppo

rted

by

cDN

A:

gi_1

5982

837_

gb_A

Y05

7526

.1_

2656

58_a

t

107

At5

g58

940

4.4

232

0.8

535.

328

01.

687

Rec

epto

r-lik

e pr

otei

n ki

nase

pre

curs

or–l

ike;

rec

epto

r-lik

e pr

otei

n ki

nase

pre

curs

or,

Mad

agas

car

peri

win

kle,

PIR

:T10

060

2477

40_a

t

108

At1

g30

900

3.9

773

1.0

200

5.2

1080

1.6

323

Put

ativ

e va

cuol

ar s

ortin

g re

cept

or s

imila

r to

(gi

|303

3390

); s

imila

r to

ES

Tdb

j|C72

582

2651

61_a

t

109

At1

g01

340

3.2

201

0.9

625.

232

81.

811

3

Cyc

lic n

ucle

otid

e an

d ca

lmod

ulin

-reg

ulat

ed io

n ch

anne

l, pu

tativ

e si

mila

r to

cyc

licnu

cleo

tide

and

calm

odul

in-r

egul

ated

ion

chan

nel G

B:C

AB

401

28 G

I:458

120

1 fr

om[A

. tha

liana

]; su

ppor

ted

by

cDN

A:

gi_8

5158

82_g

b_A

F27

2002

.1_A

F27

226

1027

_at

110

At5

g42

900

5.0

579

1.0

114

5.1

590

1.5

188

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (p

ir||T

0522

6); s

uppo

rted

by

full-

leng

thcD

NA

: Cer

es:9

6.24

9174

_at

111

At1

g35

710

3.3

2789

1.0

834

5.1

4257

2.0

1645

Pro

tein

kin

ase,

pu

tativ

e si

mila

r to

man

y pr

edic

ted

prot

ein

kina

ses

2613

39_a

t11

2A

t3g4

864

04.

017

30.

533

5.1

223

1.4

63H

ypot

het

ical

pro

tein

2523

45_a

t11

3A

t1g7

696

03.

321

431.

060

55.

030

992.

314

18U

nkno

wn

prot

ein;

sup

por

ted

by

cDN

A: g

i_13

9261

84_g

b_A

F37

0567

.1_A

F37

0567

2649

58_a

t

114

At4

g23

220

3.5

498

1.0

132

5.0

670

1.5

202

Ser

ine/

thre

onin

e ki

nase

–lik

e pr

otei

n; s

erin

e/th

reon

ine

kina

se, B

rass

ica

oler

acea

;su

ppor

ted

by

cDN

A: g

i_14

4234

17_g

b_A

F38

6946

.1_A

F38

6946

2542

55_a

t11

5A

t4g1

937

04.

114

30.

935

5.0

179

1.9

68H

ypot

het

ical

pro

tein

2545

71_a

t11

6A

t3g1

395

02.

321

00.

783

5.0

456

1.1

96H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

ene

Mar

k.hm

m25

8203

_at

117

At1

g09

080

2.9

120

1.0

415.

020

61.

253

Put

ativ

e lu

min

al b

indi

ng p

rote

in. S

imila

r to

Ara

bido

psis

lum

inal

bin

ding

pro

tein

2646

48_a

t

Page 9: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 9

(gb|

D89

342)

118

At2

g19

190

4.5

391

0.9

875.

044

41.

110

3P

utat

ive

rece

pto

r-lik

e pr

otei

n ki

nase

2674

36_a

t

119

At5

g26

920

3.2

958

1.0

299

4.9

1489

1.5

448

Cal

mod

ulin

-bin

ding

–lik

e pr

otei

n; c

alm

odul

in-b

indi

ng p

rote

in T

CB

60, N

icot

iana

taba

cum

, E

MB

L:U

589

7124

6821

_at

120

At5

g39

520

1.2

140

1.0

114

4.9

564

1.6

192

Exp

ress

ed p

rote

in p

redi

cted

pro

tein

, Syn

echo

cyst

is s

p., P

IR:S

7715

2; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

: 533

1.24

9454

_at

121

At1

g05

340

1.6

106

0.5

514.

934

50.

969

Unk

now

n pr

otei

n E

ST

gb|

AT

TS

0295

com

es fr

om th

is g

ene;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:2

0380

.26

4580

_at

122

At2

g30

140

3.6

980

1.0

273

4.9

1338

1.7

473

Put

ativ

e gl

ucos

yltr

ansf

eras

e26

7300

_at

123

At5

g08

240

3.8

377

1.0

994.

948

91.

211

8P

utat

ive

prot

ein

2505

75_a

t12

4A

t5g2

023

03.

427

871.

081

64.

940

481.

082

6B

lue

copp

er b

indi

ng p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:7

767.

2460

99_a

t

125

At5

g50

200

4.2

1496

1.0

359

4.8

1739

1.5

531

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (p

ir||T

0556

2); s

uppo

rted

by

full-

leng

thcD

NA

: Cer

es: 1

5839

7.24

8551

_at

126

At5

g17

760

2.3

415

1.0

174

4.8

844

1.8

316

BC

S1-

like

prot

ein;

h-b

cs1,

Hom

o sa

pien

s, E

MB

L:A

F0

2684

9; s

uppo

rted

by

cDN

A:

gi_1

5810

570_

gb_A

Y05

6324

.1_

2500

62_a

t12

7A

t5g4

623

02.

424

11.

098

4.8

491

1.4

142

Unk

now

n pr

otei

n; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

549

5.24

8889

_at

128

At2

g18

680

4.2

326

1.0

764.

837

21.

713

6U

nkno

wn

prot

ein

2660

71_a

t

129

At2

g46

400

2.9

640

1.0

224

4.7

1051

1.4

315

Put

ativ

e W

RK

Y-t

ype

DN

A b

indi

ng p

rote

in; s

upp

orte

d b

y cD

NA

:gi

_154

3027

6_gb

_AY

0462

75.1

_26

3783

_at

130

At1

g15

520

2.0

336

1.0

162

4.6

787

1.2

190

AB

C tr

ansp

orte

r, p

utat

ive

sim

ilar

to A

BC

tran

spor

ter

GI:9

2797

16 fr

om [A

. th

alia

na]

2617

63_a

t

131

At4

g35

180

3.7

283

0.9

764.

635

41.

511

4

Am

ino

acid

per

mea

se–l

ike

prot

ein

Lily

mR

NA

, Li

lium

long

iflor

um, g

b:D

2181

4;su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:364

61.

2531

81_a

t

132

At5

g24

530

3.2

5775

1.0

1799

4.6

8576

1.5

2801

Fla

vano

ne 3

-hyd

roxy

lase

-lik

e pr

otei

n; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:14

9654

.24

9754

_at

133

At1

g61

800

3.4

499

1.0

147

4.6

684

1.4

208

Glu

cose

-6-p

hosp

hate

/pho

spha

te-t

rans

loca

tor

prec

urso

r, p

utat

ive

sim

ilar

togl

ucos

e-6-

phos

phat

e/ph

osph

ate-

tran

sloc

ator

pre

curs

or G

I:299

759

1 fr

om [P

isum

sativ

um];

supp

orte

d b

y cD

NA

: gi_

145

9617

2_gb

_A

Y04

287

4.1_

2644

00_a

t13

4A

t2g4

300

02.

819

31.

067

4.6

307

0.9

67N

AM

(no

api

cal m

eris

tem

)-lik

e pr

otei

n26

5260

_at

135

At5

g67

450

5.2

207

0.5

374.

617

02.

490

Cys

2/H

is2-

typ

e zi

nc fi

nger

pro

tein

1 (

dbj

|BA

A85

108.

1)24

6993

_at

136

At3

g01

290

3.6

2162

1.0

594

4.5

2690

1.5

941

Unk

now

n pr

otei

n si

mila

r to

hyp

othe

tical

pro

tein

GB

:CA

A10

289

[Cic

er a

riet

inum

];su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

: 108

086

.25

9272

_at

137

At4

g02

380

3.8

2645

1.0

689

4.5

3100

1.3

888

Cod

ed fo

r b

y A

. tha

liana

cD

NA

T46

835

sim

ilar

to s

ever

al s

mal

l pro

tein

s (~

100

aa)

that

are

indu

ced

by

hea

t, a

uxi

n, e

thyl

ene

and

wo

undi

ng s

uch

as P

has

eolu

sau

reus

indo

le-3

-ace

tic a

cid

indu

ced

prot

ein

AR

G (

SW

:322

92);

sup

port

ed25

5479

_at

138

At3

g07

650

3.7

376

0.8

100

4.5

452

1.4

147

Unk

now

n pr

otei

n si

mila

r to

zin

c fin

ger

prot

ein

GB

:BA

A33

206

[Ory

za s

ativ

a]25

9244

_at

139

At1

g21

110

5.8

167

0.2

154.

513

01.

236

O-M

eth

yltr

ans

fera

se, p

utat

ive

sim

ilar

to G

B:A

AF

2835

3 fr

om [F

raga

ria

x an

anas

sa]

2614

50_s

_at

140

At5

g52

750

3.6

976

1.0

269

4.5

1206

1.3

357

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (e

mb|

CA

A71

173.

1); s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

9542

.24

8327

_at

141

At1

g73

800

2.3

781

1.0

333

4.5

1488

1.7

583

Exp

ress

ed p

rote

in; s

upp

orte

d b

y cD

NA

: gi

_166

4869

9_g

b_A

Y05

812

6.1

_26

0046

_at

142

At4

g12

280

3.0

1005

1.0

331

4.4

1478

1.8

597

Cop

per

amin

e o

xida

se li

ke p

rote

in (

frag

men

t2);

cop

per

amin

e o

xida

se--

Cic

erar

ietin

um,P

ID:e

1335

964

2548

33_s

_at

143

At2

g38

860

3.2

2000

1.0

617

4.4

2817

1.5

923

Unk

now

n pr

otei

n; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

140

31.

2661

67_a

t14

4A

t2g4

713

03.

438

21.

011

24.

449

12.

022

9P

utat

ive

alco

hol d

ehyd

roge

nase

2667

61_a

t

145

At1

g33

950

1.3

290.

922

4.4

930.

826

AIG

1-lik

e pr

otei

n si

mila

r to

AIG

1 pr

otei

n G

B:P

5412

0 (A

. th

alia

na),

NT

GP

4G

B:A

AD

095

18 (

Nic

otia

na ta

bac

um);

con

tain

s P

fam

pro

file:

PF

0073

5 c

ell d

ivis

ion

prot

ein

(mem

bers

of t

his

fam

ily b

ind

GT

P)

2601

17_a

t

146

At3

g25

020

3.2

311

1.0

974.

343

51.

919

4

Dis

ease

res

ista

nce

prot

ein,

put

ativ

e si

mila

r to

GB

:AA

D13

301

from

[Lyc

oper

sico

nes

cule

ntum

], co

ntai

ns P

fam

pro

files

: PF

0056

0 le

ucin

e-ri

ch r

epea

t (24

cop

ies)

2571

01_a

t

Page 10: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 10

147

At2

g14

580

3.0

160

0.8

524.

323

12.

211

7P

utat

ive

path

oge

nesi

s re

late

d-1

(PR

1) p

rote

in26

6383

_at

148

At4

g13

900

3.3

303

1.0

904.

339

01.

311

9P

utat

ive

dise

ase

resi

stan

ce p

rote

in H

cr9-

9A, L

ycop

ersi

con

pim

pine

llifo

lium

,gb

:AJ0

022

3625

4741

_s_a

t

149

At3

g13

790

4.1

748

1.0

184

4.3

803

1.2

232

β-F

ruct

ofur

anos

idas

e 1

iden

tical

to G

B:S

3721

2 fr

om [A

. tha

liana

]; su

ppor

ted

by

cDN

A: g

i_15

027

838_

gb_

AY

045

776.

1_

2567

87_a

t

150

At3

g60

140

0.3

160.

524

4.3

135

3.3

112

β-G

luco

sida

se-li

ke p

rote

in; s

eve

ral β

-glu

cosi

dase

s--d

iffer

ent s

peci

es; s

uppo

rted

by

cDN

A: g

i_1

0834

547

_gb_

AF

1593

76.1

_AF

159

376

2514

28_a

t15

1A

t5g4

078

03.

436

661.

010

944.

346

441.

516

32A

min

o ac

id p

erm

ease

2493

46_a

t

152

At2

g39

210

3.2

1213

1.0

374

4.2

1585

1.5

551

Nod

ulin

-lik

e pr

otei

n; s

uppo

rted

by

cDN

A:

gi_1

6930

478_

gb_A

F41

959

3.1

_AF

4195

9326

6993

_at

153

At4

g39

030

2.9

683

1.0

233

4.2

983

1.4

322

Put

ativ

e pr

otei

n D

NA

dam

age-

indu

cibl

e pr

otei

n--S

ynec

hocy

stis

sp.

,PIR

2:S

773

6425

2921

_at

154

At1

g56

060

2.7

300

1.0

112

4.2

468

1.5

172

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

2620

85_a

t15

5A

t4g3

856

03.

287

0.9

274.

211

51.

444

Pho

spho

lipas

e lik

e pr

otei

n A

. tha

liana

pE

AR

LI 4

mR

NA

, P

ID:g

8717

82

2529

77_a

t15

6A

t2g0

443

02.

732

81.

011

94.

249

61.

619

2P

utat

ive

mut

T d

omai

n pr

otei

n26

3854

_at

157

At1

g51

800

4.9

322

1.0

664.

128

21.

498

Rec

epto

r pr

otei

n ki

nase

, put

ativ

e co

nta

ins

Pfa

m p

rofil

es: P

F00

069:

Euk

aryo

ticpr

otei

n ki

nase

dom

ain,

mul

tiple

PF

0056

0: L

euci

ne-r

ich

repe

at25

6169

_at

158

At1

g43

910

2.3

171

1.0

754.

131

41.

612

6U

nkno

wn

prot

ein

2595

07_a

t

159

At1

g77

510

3.6

2481

1.0

691

4.1

2840

1.3

940

Put

ativ

e th

iore

doxi

n si

mila

r to

pro

tein

dis

ulfid

e is

omer

ase

prec

urso

r G

B:P

2982

8[M

edic

ago

sativ

a]; P

fam

HM

M h

it: T

hior

edo

xins

2597

57_a

t16

0A

t5g5

274

02.

916

01.

053

4.1

215

1.2

64P

utat

ive

prot

ein

sim

ilar

to u

nkno

wn

prot

ein

(em

b|C

AA

7117

3.1)

2483

21_a

t16

1A

t5g6

734

03.

430

21.

088

4.1

358

1.6

142

Put

ativ

e pr

otei

n st

rong

sim

ilari

ty to

un

know

n pr

otei

n (p

ir||T

0051

8)24

6988

_at

162

At1

g76

040

2.3

102

0.9

444.

019

22.

096

Cal

cium

-dep

ende

nt p

rote

in k

inas

e, p

utat

ive

sim

ilar

to c

alci

um-d

epen

dent

pro

tein

kina

se G

B:A

AC

2542

3 G

I:328

3996

[Nic

otia

na ta

bacu

m]

2626

71_a

t16

3A

t5g4

391

02.

119

41.

091

4.0

368

1.1

99P

utat

ive

prot

ein

sim

ilar

to u

nkno

wn

prot

ein

(ref

|NP

_000

212.

1)24

9096

_at

164

At5

g59

670

3.2

578

1.0

182

4.0

723

2.1

394

Ser

ine/

thre

onin

e-sp

ecifi

c pr

otei

n ki

nase

–lik

e pu

tativ

e; p

rote

in s

erin

e /th

reon

ine

kina

se, S

orgh

um b

icol

or, E

MB

L:S

BR

LK1

2476

84_a

t

165

At2

g31

880

3.1

5854

1.0

1863

4.0

7363

1.5

2917

Put

ativ

e re

cep

tor-

like

prot

ein

kina

se; s

uppo

rted

by

cDN

A:

gi_1

6648

754_

gb_A

Y05

8153

.1_

2634

78_a

t16

6A

t3g2

644

02.

326

10.

911

13.

943

51.

213

3U

nkno

wn

prot

ein;

sup

por

ted

by

cDN

A: g

i_16

6122

99_g

b_A

F43

9843

.1_A

F43

9843

2568

83_a

t

167

At1

g73

805

2.7

538

0.9

198

3.9

780

1.5

311

Put

ativ

e ca

lmod

ulin

-bin

ding

pro

tein

sim

ilar

to c

alm

odul

in-b

indi

ng p

rote

inG

B:A

AB

3724

6 [N

icot

iana

taba

cum

]26

0068

_at

168

At1

g51

920

3.1

220

0.9

683.

927

70.

760

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

2463

70_a

t

169

At2

g20

145

2.6

224

1.0

863.

933

81.

311

6E

xpre

ssed

pro

tein

; sup

por

ted

by

cDN

A:

gi_1

3605

516_

gb_A

F36

158

4.1

_AF

3615

8426

5597

_at

170

At1

g34

180

2.1

111

1.0

523.

920

81.

161

Hyp

oth

etic

al p

rote

in s

imila

r to

NA

M-l

ike

prot

ein

GI:8

8096

51

from

[A. t

halia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

197

7.26

2542

_at

171

At3

g63

380

3.9

658

1.0

168

3.9

673

1.0

164

Ca2

+-t

rans

port

ing

AT

Pas

e–lik

e pr

otei

n; C

a2+-t

rans

port

ing

AT

Pas

e, c

alm

odul

in-

stim

ulat

ed, w

ild c

abba

ge, P

IR:T

1445

325

1176

_at

172

At3

g09

940

2.5

278

1.0

109

3.9

426

1.4

155

Put

ativ

e m

ono

deh

ydro

asco

rbat

e re

duct

ase

(NA

DH

) si

mila

r to

mon

odeh

ydro

asco

rbat

e re

duct

ase

(NA

DH

) G

B:J

U01

82

[Cuc

umis

sat

ivus

];su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

: 111

60.

2589

41_a

t17

3A

t3g2

854

03.

291

81.

028

73.

911

251.

542

7H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

ene

Mar

k.hm

m25

6596

_at

174

At3

g51

440

2.4

202

1.0

833.

932

11.

512

5

Muc

in -

like

prot

ein

hem

omuc

in, D

roso

phila

mel

anog

aste

r, E

MB

L:D

M42

014;

supp

orte

d b

y cD

NA

: gi_

1343

0723

_gb

_AF

3602

74.1

_AF

3602

7425

2068

_at

175

At2

g47

800

2.3

246

1.0

105

3.9

406

1.6

174

Glu

tath

ione

-con

juga

te tr

ansp

orte

r A

tMR

P4

iden

tical

to G

B:A

J00

2584

; su

ppor

ted

by

cDN

A: g

i_7

7165

82_

gb_A

F24

350

9.1

_AF

2435

0926

6464

_at

176

At1

g08

450

3.0

3459

1.0

1139

3.8

4387

1.4

1609

Cal

retic

ulin

, put

ativ

e si

mila

r to

cal

retic

ulin

GB

:AA

C49

697

GI:2

052

383

from

[A.

thal

iana

]; su

ppor

ted

by

cDN

A:

gi_2

052

382_

gb_

U66

345.

1_A

TU

6634

526

1692

_at

177

At1

g21

250

3.3

5987

1.0

1816

3.8

7019

1.7

3144

Hyp

oth

etic

al p

rote

in; s

uppo

rted

by

cDN

A: g

i_14

5325

85_

gb_A

Y03

9917

.1_

2595

61_a

t

Page 11: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 11

178

At1

g67

980

1.9

225

1.0

115

3.8

444

1.3

155

Put

ativ

e S

-ade

nosy

l-L-

met

hion

ine:

tran

s-ca

ffeoy

l-C

oen

zym

e A

3-O

-m

ethy

ltran

sfer

ase;

sim

ilar

to S

-ade

nosy

l-L-

met

hion

ine:

tran

s-ca

ffeo

yl-C

oenz

yme

A3-

O-m

ethy

ltran

sfer

ase

GB

:AA

A62

426

[A

. tha

liana

] (fu

nctio

n =

dis

ease

resi

stan

ce);

sup

port

ed26

0015

_at

179

At4

g03

450

3.1

548

1.0

173

3.8

676

1.6

281

Hyp

oth

etic

al p

rote

in s

imila

r to

hyp

othe

tical

pro

tein

enc

ode

d b

y F

CA

1, G

enB

ank

acce

ssio

n nu

mbe

r Z

9733

625

5406

_at

180

At4

g33

050

3.3

1855

1.0

560

3.8

2140

1.8

1034

Put

ativ

e pr

otei

n25

3414

_at

181

At1

g21

520

2.4

503

1.0

202

3.8

765

1.3

266

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

2609

19_a

t

182

At4

g20

110

1.8

478

1.0

261

3.7

999

1.5

390

Vac

uola

r so

rtin

g re

cept

or-li

ke p

rote

in B

P-8

0 va

cuol

ar s

ortin

g re

cept

or, P

isum

sativ

um, P

AT

CH

X:G

1737

222

2545

00_a

t

183

At3

g10

500

2.7

702

1.0

258

3.7

970

1.5

399

Unk

now

n pr

otei

n N

-ter

min

us s

imila

r to

unk

now

n pr

otei

n G

B:A

AD

256

13 [A

.th

alia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 3

8529

.25

8921

_at

184

At1

g15

790

2.5

188

1.0

733.

727

41.

611

9U

nkno

wn

prot

ein

2594

89_a

t

185

At3

g09

270

3.0

205

1.0

673.

725

41.

393

Put

ativ

e gl

utat

hion

e tr

ans

fera

se s

imila

r to

glu

tath

ione

tran

sfer

ase

GB

:CA

A71

784

[Gly

cine

max

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:215

46.

2590

40_a

t

186

At5

g40

690

3.2

150

0.8

473.

717

21.

891

Put

ativ

e pr

otei

n pr

edic

ted

prot

eins

, A.

thal

iana

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

:C

eres

:115

39.

2493

77_a

t18

7A

t1g0

366

02.

318

01.

080

3.7

293

1.8

146

Unk

now

n un

know

n26

4832

_at

188

At1

g45

145

2.3

2000

1.0

862

3.7

3154

1.4

1210

Thi

ored

oxi

n, p

utat

ive;

sim

ilar

to th

iore

doxi

n G

I:992

966

from

[A. t

halia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 3

236

.26

0943

_at

189

At4

g12

500

1.9

261

1.0

135

3.6

488

0.8

112

pEA

RL

I 1-l

ike

prot

ein

A. t

halia

na; p

EA

RL

I 1 m

RN

A, P

ID:g

8717

8025

4819

_at

190

At4

g21

850

2.8

636

1.0

229

3.6

817

0.9

218

Put

ativ

e pr

otei

n C

GI-

131

prot

ein,

Hom

o sa

pien

s, A

F15

188

9; s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:2

4573

.25

4387

_at

191

At3

g52

430

1.7

247

1.0

142

3.6

506

1.5

226

Put

ativ

e pr

otei

n ot

her

hyp

othe

tical

pro

tein

s in

A. t

halia

na; s

uppo

rted

by

cDN

A:

gi_6

4573

30_g

b_A

F18

8329

.1_

AF

188

329

2520

60_a

t

192

At1

g07

000

2.6

703

1.0

264

3.5

955

1.5

421

Leuc

ine

zipp

er p

rote

in, p

utat

ive;

sim

ilar

to le

ucin

e zi

pper

pro

tein

GI:1

017

7020

from

[A. t

halia

na]

2560

50_a

t

193

At4

g01

700

2.7

381

1.0

139

3.5

495

1.3

183

Put

ativ

e ch

itina

se s

imila

r to

pea

nut t

ype

II ch

itina

se, G

enB

ank

acc

essi

on n

umbe

rX

8232

9, E

.C.

3.2.

1.1

425

5595

_at

194

At4

g04

540

2.6

1133

1.0

433

3.5

1523

1.3

593

Put

ativ

e re

cep

tor-

like

prot

ein

kina

se25

5344

_s_a

t19

5A

t1g1

774

52.

515

001.

059

53.

520

671.

589

6U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

: 205

82.

2594

03_a

t19

6A

t4g0

175

02.

968

0.9

233.

588

1.4

35H

ypot

het

ical

pro

tein

T15

B16

.825

5564

_s_a

t19

7A

t3g5

240

02.

613

911.

052

73.

518

301.

052

8S

ynta

xin-

like

prot

ein

synt

4; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:372

48.

2520

53_a

t

198

At5

g27

420

2.8

475

1.0

160

3.4

561

1.3

228

RIN

G-H

2 zi

nc fi

nger

pro

tein

-lik

e; R

ING

-H2

zinc

fing

er p

rote

in A

TL6

--A

. tha

liana

,E

MB

L:A

F13

201

6; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:106

078.

2467

77_a

t

199

At5

g52

810

3.1

962

1.0

309

3.4

1065

1.3

422

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to o

rnith

ine

cycl

odea

min

ase;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

1467

8.24

8330

_at

200

At5

g37

600

2.9

1017

71.

035

563.

412

581

1.3

4488

Glu

tam

ate-

amm

onia

liga

se; s

uppo

rted

by

cDN

A:

gi_1

6226

386_

gb_A

F42

838

6.1

_AF

4283

8624

9581

_at

201

At1

g19

020

1.7

310

1.0

172

3.4

587

0.9

160

Exp

ress

ed p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 3

101

5.25

9479

_at

202

At1

g62

300

2.5

230

1.0

913.

433

11.

095

Unk

now

n pr

otei

n si

mila

r to

put

ativ

e D

NA

-bin

ding

pro

tein

GI:7

268

215

from

[A.

thal

iana

]; su

ppor

ted

by

cDN

A:

gi_1

265

8409

_gb

_A

F33

171

2.1_

AF

3317

1226

4746

_at

203

At3

g26

220

2.2

181

1.0

803.

427

21.

714

0

Cyt

ochr

ome

P-4

50 m

onoo

xyge

nase

(C

YP

71B

3); i

dent

ical

to c

ytoc

hrom

e P

-450

mon

ooxy

gena

se (

CY

P71

B3)

GB

:D78

602

[A. t

halia

na] (

Pla

nt M

ol. B

iol.

37 (

1), 3

9-52

(19

98))

; sup

port

ed b

y cD

NA

: gi_

316

4133

_db

j_D

786

02.1

_D78

602

2576

24_a

t20

4A

t1g6

550

03.

295

31.

029

83.

310

381.

441

5U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:251

36.

2646

35_a

t20

5A

t5g6

080

02.

428

21.

011

43.

337

91.

315

2P

utat

ive

prot

ein

farn

esyl

ate

d pr

otei

n G

MF

P5

, Gly

cine

max

, EM

BL:

U64

916

2475

94_a

t20

6A

t5g1

038

02.

245

511.

020

243.

368

271.

122

22P

utat

ive

prot

ein

vari

ous

pred

icte

d pr

otei

ns, A

. tha

liana

2504

35_a

t

Page 12: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 12

207

At3

g60

540

2.2

817

1.0

361

3.3

1222

1.2

421

Tra

nspo

rt p

rote

in s

ubun

it–lik

e S

61B

_AR

AT

H P

RO

TE

IN T

RA

NS

PO

RT

PR

OT

EIN

SE

C61

β S

UB

UN

IT, A

. tha

liana

, SW

ISS

PR

OT

:S61

B_

AR

AT

H25

1422

_at

208

At3

g23

110

3.7

591

1.0

158

3.3

546

1.8

288

Dis

ease

res

ista

nce

prot

ein,

put

ativ

e si

mila

r to

Hcr

2-5b

GB

:AA

C78

595

[Lyc

oper

sico

n es

cule

ntum

] (P

lant

Cel

l 10,

191

5-1

926

(19

98))

; con

tain

s P

fam

prof

ile: P

F00

560

leuc

ine

rich

rep

eat (

20 c

opie

s)25

7763

_s_a

t

209

At4

g25

000

2.0

214

1.0

104

3.3

349

1.5

157

α-A

myl

ase–

like

prot

ein;

α-a

myl

ase,

Vig

na m

ung

o, P

IR2:

S10

514

; sup

port

ed b

yfu

ll-le

ngth

cD

NA

: Cer

es:3

059.

2541

01_a

t

210

At1

g48

210

2.5

542

0.9

214

3.3

724

1.8

391

Pto

kin

ase

inte

ract

or 1

, pu

tativ

e s

imila

r to

GB

:AA

C61

805

from

[Lyc

oper

sico

nes

cule

ntum

] (C

ell 8

3 (6

), 9

25-9

35 (

1995

)); s

upp

orte

d b

y cD

NA

:gi

_154

5119

5_gb

_AY

0546

78.1

_26

0728

_at

211

At1

g02

220

2.1

871.

040

3.3

135

1.5

63N

AM

(no

api

cal m

eris

tem

)-lik

e pr

otei

n, p

utat

ive;

sim

ilar

to N

AM

(no

api

cal

mer

iste

m)-

like

prot

ein

GI:9

7595

89 fr

om (

A. t

halia

na)

2641

48_a

t

212

At1

g72

280

2.7

179

1.0

673.

321

91.

071

Dis

ulfid

e bo

nd fo

rmat

ion

prot

ein,

put

ativ

e si

mila

r to

GI:6

6429

25 f

rom

[Mus

mus

culu

s]25

9852

_at

213

At3

g21

520

1.6

127

1.0

783.

325

61.

297

Hyp

oth

etic

al p

rote

in25

7540

_at

214

At5

g45

380

2.5

795

1.0

316

3.3

1033

1.8

559

Ure

a ac

tive

tran

spor

ter-

like

prot

ein

2489

70_a

t21

5A

t5g4

854

03.

486

11.

025

13.

389

41.

334

133

-kD

sec

reto

ry p

rote

in-l

ike;

sup

port

ed b

y cD

NA

: gi_

152

9298

0_g

b_A

Y0

5092

4.1_

2486

86_a

t

216

At1

g32

940

2.2

347

1.0

157

3.3

516

1.2

196

Sub

tilis

in-li

ke s

erin

e pr

otea

se c

onta

ins

sim

ilari

ty to

sub

tilas

e; S

P1

GI:9

957

714

from

[Ory

za s

ativ

a]26

1240

_at

217

At3

g07

520

2.9

553

1.0

190

3.3

621

1.5

296

Unk

now

n pr

otei

n si

mila

r to

put

ativ

e gl

utam

ate

rece

ptor

GB

:AA

D09

173

[A.

thal

iana

] and

put

ativ

e lig

and-

gate

d io

nic

chan

nel G

B:A

AC

3323

7 [A

. th

alia

na]

2590

65_a

t21

8A

t5g5

387

02.

122

81.

010

83.

335

41.

112

0P

utat

ive

prot

ein

cont

ains

sim

ilarit

y to

ph

ytoc

yani

n/e

arly

nod

ulin

-lik

e pr

otei

n24

8236

_at

219

At1

g79

450

1.7

671.

038

3.3

123

1.1

49

Hyp

oth

etic

al p

rote

in s

imila

r to

unk

now

n pr

otei

n G

I:458

597

6 fr

om [A

. th

alia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:9

482

8.26

2942

_at

220

At2

g24

160

2.8

292

1.0

101

3.3

337

1.6

165

Put

ativ

e di

seas

e re

sist

ance

pro

tein

2659

93_a

t22

1A

t5g4

283

02.

842

31.

014

93.

349

31.

421

0N

-Hyd

roxy

cinn

amo

yl b

enzo

yltr

ansf

eras

e-lik

e pr

otei

n24

9188

_at

222

At4

g39

950

2.1

1501

1.0

698

3.2

2257

1.4

967

Cyt

ochr

ome

P-4

50–l

ike

prot

ein;

cyt

ochr

ome

P-4

50,

Sin

apis

alb

a, A

F06

949

4;su

ppor

ted

by

cDN

A: g

i_15

0281

34_g

b_A

Y04

6017

.1_

2528

27_a

t

223

At2

g17

040

2.9

1393

1.0

472

3.2

1536

1.2

615

NA

M (

no a

pica

l mer

iste

m)-

like

prot

ein;

sim

ilar

to p

etun

ia N

AM

(X

9220

5) a

nd A

.th

alia

na s

eque

nces

AT

AF

1 (X

7475

5) a

nd A

TA

F2

(X74

756)

; pro

bab

le D

NA

-bi

ndin

g pr

otei

n; s

uppo

rted

by

cDN

A:

gi_1

360

5646

_gb

_A

F36

180

4.1_

AF

3618

0426

3584

_at

224

At4

g08

850

3.0

1766

1.0

594

3.2

1920

1.6

934

Rec

epto

r pr

otei

n ki

nase

-lik

e pr

otei

n; r

ecep

tor

prot

ein

kina

se-l

ike

prot

ein-

-A.

thal

iana

, PIR

2:T

0589

825

5116

_at

225

At2

g04

460

1.9

174

1.0

933.

230

51.

918

1P

utat

ive

retr

oele

men

t pol

pol

ypro

tein

2638

51_a

t

226

At4

g23

610

2.7

252

1.0

953.

231

01.

413

6H

ypot

het

ical

pro

tein

; sup

port

ed b

y cD

NA

:gi

_139

3713

4_gb

_AF

372

921.

1_A

F37

2921

2542

29_a

t22

7A

t3g2

647

02.

516

41.

064

3.2

208

1.5

95U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:483

6.

2568

77_a

t22

8A

t2g3

055

02.

362

01.

026

43.

286

51.

336

9P

utat

ive

lipas

e; s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 2

070

43.

2674

96_a

t

229

At3

g12

220

2.0

690.

625

3.1

101

0.8

34S

erin

e ca

rbo

xype

ptid

ase,

put

ativ

e co

nta

ins

Pfa

m p

rofil

e: P

F00

450

seri

neca

rbo

xyp

eptid

ase;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es: 3

4525

.25

6265

_at

230

At4

g37

370

3.3

307

1.0

923.

129

21.

513

6C

ytoc

hrom

e P

-450

–lik

e pr

otei

n; c

ytoc

hrom

e P

-450

, Gly

cyrr

hiza

ech

inat

a,A

B00

1379

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:2

536

98.

2530

46_a

t

231

At1

g71

880

2.4

1222

1.0

516

3.1

1630

1.6

833

Suc

rose

tran

spor

t pro

tein

SU

C1

ide

ntic

al to

GB

:S38

197

from

[A. t

hal

iana

];su

ppor

ted

by

cDN

A: g

i_15

1462

67_g

b_A

Y04

9275

.1_

2601

43_a

t

232

At5

g48

380

2.2

2318

1.0

1042

3.1

3269

1.4

1454

Rec

epto

r-lik

e pr

otei

n ki

nase

; sup

port

ed b

y cD

NA

:gi

_136

0582

6_gb

_AF

367

312.

1_A

F36

7312

2486

98_a

t

233

At3

g17

790

2.2

702

1.0

320

3.1

1000

1.7

541

Aci

d ph

osph

atas

e ty

pe 5

ide

ntic

al to

GB

:CA

B6

3938

fro

m [A

. tha

liana

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:113

666.

2581

58_a

t23

4A

t4g0

095

52.

515

70.

860

3.1

193

1.6

100

Exp

ress

ed p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 9

381

8.25

5627

_at

Page 13: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 13

235

At1

g73

260

0.9

190

1.0

163

3.1

518

2.6

435

Put

ativ

e tr

ypsi

n in

hibi

tor

sim

ilar

to tr

ypsi

n in

hibi

tor

prop

eptid

e G

B:A

AB

689

64[B

rass

ica

oler

acea

]; co

ntai

ns P

fam

pro

file:

PF

0019

7 T

ryps

in a

nd

prot

ease

inhi

bito

rs; s

uppo

rted

by

cDN

A: g

i_15

4509

71_

gb_A

Y05

4566

.1_

2601

01_a

t

236

At2

g02

930

2.4

9473

1.0

3984

3.1

1252

91.

455

73

Put

ativ

e gl

utat

hion

e S

-tra

nsfe

rase

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:2

7915

.;su

ppor

ted

by

cDN

A: g

i_11

0959

95_g

b_A

F28

8181

.1_A

F28

8181

2667

46_s

_at

237

At2

g26

440

3.2

2459

1.0

775

3.1

2391

1.5

1165

Put

ativ

e pe

ctin

este

rase

2450

52_a

t

238

At4

g12

720

2.2

2803

1.0

1293

3.1

3950

1.1

1478

Gro

wth

fact

or–l

ike

prot

ein

antis

ense

bas

ic fi

brob

last

gro

wth

fact

or G

FG

--R

attu

sno

rveg

icus

, PID

:g1

5186

35;

sup

port

ed

by

full-

leng

th c

DN

A: C

eres

:148

575.

2547

84_a

t23

9A

t1g0

156

02.

554

61.

021

93.

168

01.

636

7M

AP

kin

ase,

put

ativ

e si

mila

r to

MA

P k

inas

e 5

GI:4

2398

89 fr

om [Z

ea m

ays]

2594

28_a

t24

0A

t3g5

442

02.

523

61.

093

3.1

283

1.0

103

Cla

ss IV

chi

tinas

e (C

HIV

)25

1895

_at

241

At1

g72

240

2.3

131

0.9

563.

017

11.

062

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

2598

50_a

t24

2A

t4g2

321

02.

821

21.

077

3.0

237

1.5

115

Ser

ine/

thre

onin

e ki

nase

–lik

e pr

otei

n; s

erin

e/th

reon

ine

kina

se, B

rass

ica

oler

acea

2542

43_a

t24

3A

t1g7

206

03.

072

41.

023

43.

072

71.

332

4U

nkno

wn

prot

ein

2563

37_a

t

244

At5

g38

210

2.5

250

0.9

993.

032

21.

414

3P

rote

in k

inas

e–lik

e pr

otei

n; w

all-

asso

ciat

ed k

inas

e 4

(wak

4),

A. t

halia

na,

EM

BL

:AT

H96

9524

9550

_at

245

At2

g02

810

2.2

542

1.0

241

3.0

728

1.4

347

Unk

now

n pr

otei

n; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:3

544

1.26

7483

_at

246

At4

g25

110

2.4

271

1.0

113

3.0

360

1.3

145

Put

ativ

e pr

otei

n e

xten

sin,

Cat

hara

nthu

s ro

seus

, D86

853

2540

93_a

t

247

At1

g76

970

2.2

406

1.0

182

3.0

546

1.3

239

Unk

now

n pr

otei

n co

ntai

ns s

imila

rity

to s

eed

prot

ein

B32

E G

I:190

46

from

[Hor

deum

vul

gare

]26

4951

_at

248

At3

g54

150

2.3

215

1.0

933.

027

71.

211

8E

mbr

yoni

c ab

unda

nt p

rote

in–l

ike

embr

yoni

c ab

unda

nt p

rote

in E

MB

34,

Pic

eagl

auca

, PIR

:T09

281;

sup

port

ed

by

full-

leng

th c

DN

A: C

eres

: 652

9.

2518

84_a

t24

9A

t5g1

069

51.

850

21.

027

73.

082

91.

132

4E

xpre

ssed

pro

tein

; sup

por

ted

by

full-

leng

th c

DN

A: C

eres

: 10

3171

.24

6018

_at

250

At3

g51

890

2.2

513

1.0

235

3.0

697

1.3

306

Put

ativ

e pr

otei

n pr

otei

n A

t2g4

006

0--A

. th

alia

na, E

MB

L:A

F00

210

9; s

uppo

rte

d by

full-

leng

th c

DN

A: C

eres

:934

27.

2463

05_a

t25

1A

t5g5

982

01.

615

70.

999

3.0

300

1.3

132

Zin

c fin

ger

prot

ein

Zat

12; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:405

76.

2476

55_a

t

252

At1

g34

750

2.2

445

1.0

198

3.0

587

1.5

301

Pro

tein

pho

spha

tase

typ

e 2C

, pu

tativ

e s

imila

r to

GB

:AA

D17

805

from

(Lo

tus

japo

nicu

s) (

Pro

c. N

atl.

Aca

d. S

ci. U

.S.A

. 96

(4),

173

8-17

43

(199

9))

2624

08_a

t

253

At5

g14

930

2.1

250

1.0

116

3.0

349

1.3

150

Put

ativ

e pr

otei

n di

seas

e re

sist

ance

pro

tein

ED

S1,

A. t

halia

na, P

IR:T

4885

9;su

ppor

ted

by

cDN

A: g

i:86

9916

924

6600

_at

254

At4

g28

390

2.0

685

1.0

336

3.0

1028

1.0

329

AD

P,A

TP

car

rier

-like

pro

tein

; AD

P,A

TP

car

rier

pro

tein

-ric

e, P

IR2:

S33

630;

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:4

203

6.25

3776

_at

255

At5

g64

510

3.0

204

1.0

683.

020

21.

510

4P

utat

ive

prot

ein

sim

ilar

to u

nkno

wn

prot

ein

(pir

|T03

813)

2472

93_a

t25

6A

t3g4

865

02.

626

90.

891

2.9

275

1.0

108

Hyp

oth

etic

al p

rote

in25

2346

_at

257

At5

g54

720

2.5

110

1.0

442.

912

91.

466

Put

ativ

e pr

otei

n si

mila

r to

Unk

now

n pr

otei

n (g

b|A

AD

328

84.1

)24

8123

_at

258

At3

g48

090

1.6

483

1.0

290

2.9

851

1.1

323

Dis

ease

res

ista

nce

prot

ein

ED

S1;

sup

por

ted

by

cDN

A:

gi_1

5028

150_

gb_A

Y04

6025

.1_

2523

73_a

t

259

At1

g07

050

2.7

1415

1.0

520

2.9

1554

1.5

825

Hyp

oth

etic

al p

rote

in c

onta

ins

sim

ilarit

y to

pho

tope

riod

sen

sitiv

ity q

uant

itativ

e tr

ait

locu

s (H

d1)

GI:1

1094

203

from

[Ory

za s

ativ

a]; s

uppo

rted

by

full-

leng

th c

DN

A:

Cer

es:1

955.

2560

60_a

t

260

At1

g33

720

2.2

328

1.0

152

2.9

445

1.4

214

Cyt

ochr

ome

P-4

50,

puta

tive

sim

ilar

to C

YT

OC

HR

OM

E P

450

76C

2 G

B:O

6463

7fr

om [A

. tha

liana

]26

1986

_s_a

t

261

At5

g01

540

2.8

406

1.0

147

2.9

425

1.2

177

Rec

epto

r-lik

e pr

otei

n ki

nase

; rec

epto

r lik

e pr

otei

n ki

nase

-A.

thal

iana

,E

MB

L:A

TLE

CG

EN

E; s

uppo

rted

by

cDN

A:

gi_1

3605

542_

gb_A

F36

159

7.1

_AF

3615

9725

1054

_at

262

At1

g51

780

2.2

345

1.0

156

2.9

448

1.0

158

Au

xin

conj

ugat

e h

ydro

lase

(IL

L5)

iden

tical

to a

uxi

n co

njug

ate

hyd

rola

se [A

.th

alia

na] (

ILL5

) G

I:572

564

9;co

ntai

ns n

onc

onse

nsus

AT

acc

epto

r sp

lice

site

at

exo

n325

6178

_s_a

t26

3A

t1g2

415

02.

117

61.

083

2.9

240

1.5

124

Unk

now

n pr

otei

n26

4867

_at

Page 14: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 14

264

At5

g60

900

2.9

1615

1.0

556

2.9

1602

1.5

825

S-r

ecep

tor

kina

se h

omol

og 2

pre

curs

or; S

-rec

epto

r ki

nase

hom

olog

2 p

recu

rsor

,A

. tha

liana

, PIR

:S2

7754

2476

02_a

t

265

At3

g49

340

2.1

190

1.0

902.

926

01.

199

Cys

tein

e pr

otea

se c

onta

ins

sim

ilari

ty to

cys

tein

e pr

otei

nase

GI:5

354

54 f

rom

[Aln

us g

lutin

osam

]25

2309

_at

266

At5

g22

530

1.8

651.

033

2.9

960.

519

Unk

now

n pr

otei

n; s

upp

orte

d b

y cD

NA

: gi_

1453

2613

_gb

_AY

0399

31.1

_24

9896

_at

267

At5

g53

110

1.9

213

1.0

111

2.9

320

0.8

85P

utat

ive

prot

ein

sim

ilar

to u

nkno

wn

prot

ein

(gb

AA

F25

996.

1)24

8298

_at

268

At4

g23

320

1.5

108

0.9

692.

919

61.

913

4S

erin

e/th

reon

ine

kina

se–l

ike

prot

ein;

ser

ine/

thre

onin

e ki

nase

, Bra

ssic

a ol

erac

ea25

4253

_at

269

At5

g09

290

1.3

204

0.9

149

2.9

427

1.4

220

3 (2

),5

-Bis

phos

phat

e nu

cleo

tidas

e-lik

e pr

otei

n 3

(2 )

,5 -

bisp

hosp

hate

nucl

eotid

ase-

-A. t

halia

na, E

MB

L:A

B01

9227

2459

32_a

t27

0A

t1g5

521

02.

212

161.

054

02.

915

421.

373

3U

nkno

wn

prot

ein

2596

55_a

t

271

At4

g05

020

2.5

585

0.9

236

2.8

685

1.1

268

Cod

ed fo

r b

y A

. tha

liana

cD

NA

W43

435;

sup

port

ed b

y cD

NA

:gi

_145

3246

3_gb

_AY

0398

56.1

_25

5259

_at

272

At4

g33

980

2.1

278

1.0

132

2.8

379

1.5

202

Put

ativ

e pr

otei

n; s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:8

161.

2533

22_a

t

273

At2

g41

100

2.3

6471

0.9

2773

2.8

8210

1.2

3571

Cal

mod

ulin

-like

pro

tein

iden

tical

to G

B:D

4584

8; s

uppo

rte

d b

y cD

NA

:gi

_159

8340

5_gb

_AF

424

577.

1_A

F42

4577

2670

83_a

t27

4A

t2g4

075

02.

324

151.

010

672.

829

881.

213

57H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

EN

SC

AN

and

ge

nefin

der

2573

82_a

t

275

At1

g67

360

1.7

956

1.0

541

2.8

1517

1.2

675

Str

ess-

rela

ted

prot

ein,

put

ativ

e si

mila

r to

str

ess-

rela

ted

prot

ein

GI:5

802

955

from

[Viti

s rip

aria

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:140

43.

2649

68_a

t27

6A

t5g2

421

02.

123

411.

011

282.

831

761.

011

62P

utat

ive

prot

ein

sim

ilar

to u

nkno

wn

prot

ein

(gb

AA

D29

063

.1)

2497

77_a

t

277

At1

g18

570

2.1

385

1.0

180

2.8

501

1.4

264

myb

fac

tor,

put

ativ

e s

imila

r to

myb

fact

or G

I:194

626

6 fr

om [O

ryza

sat

iva]

;su

ppor

ted

by

cDN

A: g

i_39

4146

5_gb

_A

F06

288

7.1

_AF

062

887

2557

53_a

t

278

At1

g28

480

2.2

287

1.0

126

2.8

364

1.1

138

Glu

tare

doxi

n, p

utat

ive

sim

ilar

to g

luta

redo

xin

GI:2

244

924

from

[A. t

halia

na];

supp

orte

d b

y cD

NA

: gi_

1335

8219

_gb

_AF

3250

30.2

_AF

3250

3026

1443

_at

279

At1

g21

120

3.7

900.

825

2.8

730.

822

Put

ativ

e A

TP

ase

sim

ilar

to G

B:A

AF

2835

3 fr

om [F

raga

ria

x a

nana

ssa]

2614

49_a

t28

0A

t5g6

215

01.

415

21.

094

2.8

268

0.8

84P

utat

ive

prot

ein

pred

icte

d pr

otei

n, A

. tha

liana

2474

87_a

t

281

At3

g14

990

1.5

1061

1.0

713

2.8

2054

1.0

693

4-M

eth

yl-5

(b-h

ydro

xyet

hyl

)-th

iazo

le m

onop

hosp

hate

bio

synt

hesi

s pr

otei

n, p

utat

ive

sim

ilar

to T

hiJ

GB

:AA

A82

704

[Esc

heri

chia

col

i]; li

kely

enc

odes

two

Thi

J su

buni

tsw

ithin

a s

ingl

e po

lype

ptid

e; s

uppo

rted

by

cDN

A: g

i_14

517

477

_gb_

AY

039

5725

7216

_at

282

At3

g14

620

2.6

1400

1.0

538

2.8

1495

1.6

895

Put

ativ

e cy

toch

rom

e P

-450

sim

ilar

to G

B:Q

0504

7 fr

om [C

atha

rant

hus

rose

us];

supp

orte

d b

y cD

NA

: gi_

1552

9168

_gb

_AY

0522

08.1

_25

8063

_at

283

At4

g20

860

2.0

129

0.9

632.

817

41.

277

Ber

beri

ne b

ridg

e en

zym

e–lik

e pr

otei

n; s

uppo

rted

by

cDN

A:

gi_1

4194

126_

gb_A

F36

726

9.1

_AF

3672

6925

4447

_at

284

At4

g17

670

2.5

491

1.0

198

2.8

548

1.3

257

Hyp

oth

etic

al p

rote

in; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:670

9.24

5401

_at

285

At3

g24

982

2.7

650.

519

2.7

661.

435

Dis

ease

res

ista

nce

prot

ein,

put

ativ

e, 3

par

tial s

imila

r to

GB

:AA

D13

301

from

[Lyc

oper

sico

n es

cule

ntum

], co

ntai

ns P

fam

pro

files

: PF

0056

0 le

ucin

e-ri

ch r

epea

t(1

9 co

pies

)25

7099

_s_a

t

286

At3

g08

720

2.4

146

1.0

612.

716

91.

276

Put

ativ

e ri

boso

mal

-pro

tein

S6

kina

se (

AT

PK

19);

iden

tical

to p

utat

ive

ribo

som

al-

prot

ein

S6

kina

se (

AT

PK

19)

GB

:D42

061

[A. t

halia

na] (

FE

BS

Let

t. 35

8 (2

), 1

99-

204

(199

5));

sup

port

ed

by

cDN

A: g

i_15

2927

84_

gb_A

Y05

0826

.1_

2586

82_a

t

287

At2

g02

390

1.6

384

1.0

238

2.7

647

0.8

200

Put

ativ

e gl

utat

hion

e S

-tra

nsfe

rase

; sup

port

ed b

y cD

NA

:gi

_154

5046

2_gb

_AY

0523

32.1

_26

6181

_at

288

At5

g46

350

2.3

289

1.0

123

2.7

346

1.0

135

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to W

RK

Y-t

ype

DN

A-b

indi

ng p

rote

in; s

uppo

rted

by

cDN

A: g

i_1

5384

212

_gb_

AF

4048

55.1

_AF

404

855

2488

96_a

t28

9A

t3g2

623

02.

040

70.

919

82.

755

91.

326

7C

ytoc

hrom

e P

-450

, pu

tativ

e c

onta

ins

Pfa

m p

rofil

e: P

F00

067

cyt

ochr

ome

P-4

5025

7625

_at

290

At2

g27

660

2.4

186

1.0

752.

720

31.

397

Hyp

oth

etic

al p

rote

in p

redi

cted

by

GE

NS

CA

N26

6247

_at

291

At5

g39

050

2.4

741

1.0

306

2.7

831

1.3

412

Acy

ltran

sfer

ase–

like

prot

ein.

Ant

hoc

yani

n 5-

arom

atic

acy

ltran

sfer

ase,

Gen

tiana

trifl

ora,

EM

BL:

AB

010

708;

sup

por

ted

by

cDN

A: g

i_1

5450

468

_gb_

AY

052

335.

1_

2494

94_a

t

292

At1

g09

560

2.1

2050

1.0

958

2.7

2592

1.4

1345

Ger

min

-like

pro

tein

. Id

entic

al to

Ara

bido

psis

ger

min

-like

pro

tein

, gi|1

7551

78.

Loca

tion

of E

ST

180

L10T

7, g

i|906

417;

sup

port

ed

by

cDN

A:

2645

06_a

t

Page 15: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 15

gi_1

3265

455_

gb_A

F32

467

8.2

_AF

3246

78

293

At1

g23

840

1.9

476

1.0

256

2.7

689

0.9

236

Unk

now

n pr

otei

n; s

upp

orte

d b

y cD

NA

: gi_

1433

5017

_gb

_AY

0371

88.1

_26

5189

_at

294

At2

g43

510

2.1

565

1.0

273

2.7

737

1.3

365

Put

ativ

e tr

ypsi

n in

hibi

tor;

sup

port

ed b

y cD

NA

: gi_

152

9271

0_gb

_A

Y05

078

9.1_

2605

51_a

t

295

At4

g28

490

2.2

484

1.0

216

2.7

587

1.3

282

Rec

epto

r-lik

e pr

otei

n ki

nase

5 p

recu

rsor

(R

LK5)

; sup

port

ed b

y cD

NA

:gi

_166

849_

gb_

M84

660

.1_A

TH

RLP

KC

2537

79_a

t29

6A

t1g2

414

02.

221

00.

794

2.7

254

0.9

90P

utat

ive

met

allo

prot

eina

se s

imila

r to

GB

:AA

B6

1099

2648

66_a

t

297

At1

g20

350

2.1

199

1.0

922.

724

81.

312

5

Mito

chon

dria

l inn

er m

embr

ane

tran

sloc

ase

com

pone

nt, p

uta

tive;

sim

ilar

tom

itoch

ondr

ial i

nner

mem

bran

e tr

ansl

ocas

e co

mpo

nent

Tim

17a

GI:4

3785

24 f

rom

[Mus

mus

culu

s]25

5941

_at

298

At1

g65

790

2.0

1169

1.0

578

2.7

1611

1.4

812

Rec

epto

r ki

nase

, put

ativ

e si

mila

r to

rec

epto

r ki

nase

1 [B

rass

ica

rapa

]G

B:B

AA

2367

626

2926

_s_a

t

299

At1

g60

740

0.5

240.

833

2.7

920.

829

Per

oxi

redo

xin,

put

ativ

e si

mila

r to

typ

e 2

pero

xire

doxi

n G

I:492

847

2 fr

om [B

rass

ica

rapa

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:108

62.;

sup

port

ed b

y fu

ll-le

ngth

cDN

A: C

eres

: 181

0.26

4923

_s_a

t30

0A

t1g5

220

02.

515

291.

060

42.

716

121.

275

8U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

: 166

14.

2598

41_a

t

301

At3

g50

900

2.0

173

0.9

762.

721

70.

978

Hyp

oth

etic

al p

rote

in; h

ypot

hetic

al p

rote

in--

A. t

halia

na c

hrom

osom

e 4

AP

2 co

ntig

,P

ID:e

3532

23; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:10

044.

2521

33_a

t30

2A

t4g1

561

02.

051

01.

025

12.

767

01.

231

5H

ypot

het

ical

pro

tein

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es: 2

601

9.24

5317

_at

303

At3

g13

380

2.1

247

1.0

117

2.7

316

1.0

130

Bra

ssin

oste

roid

rec

epto

r ki

nase

, put

ativ

e si

mila

r to

GB

:AA

C49

810

from

[A.

thal

iana

], co

ntai

ns P

fam

pro

files

: PF

0056

0 le

ucin

e-ri

ch r

epea

t (23

cop

ies)

2569

81_a

t

304

At5

g25

930

2.3

480

1.0

210

2.7

557

1.3

282

Rec

epto

r-lik

e pr

otei

n ki

nase

–lik

e; r

ecep

tor-

like

prot

ein

kina

se 5

, A

. tha

liana

,P

IR:S

277

5624

6858

_at

305

At3

g24

900

1.6

141

1.0

872.

624

41.

311

3

Leuc

ine-

rich

rep

eat d

isea

se r

esis

tanc

e pr

otei

n, p

utat

ive

sim

ilar

to N

L0C

GB

:AA

D1

3302

from

[Lyc

oper

sico

n es

cule

ntum

] ([M

ol. P

lant

Mic

robe

Inte

ract

. 12

(2),

93-

102

(199

9)]

2575

91_a

t

306

At2

g37

710

2.1

3528

1.0

1650

2.6

4315

1.3

2116

Put

ativ

e re

cep

tor-

like

prot

ein

kina

se s

ame

as G

B:X

959

09 (

poly

mor

phis

m e

xist

s at

a G

A r

epea

t. W

e fo

und

6 co

pies

in o

ur s

eque

nce,

whe

reas

onl

y 5

copi

es e

xist

inG

B:X

959

09)

2671

65_a

t30

7A

t5g6

664

02.

523

61.

095

2.6

254

1.0

93P

utat

ive

prot

ein

sim

ilar

to u

nkno

wn

prot

ein

(em

b C

AB

168

16.1

)24

7071

_at

308

At5

g44

810

1.8

285

1.0

154

2.6

406

1.2

182

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (g

b|A

AC

7913

9.1)

2545

21_a

t30

9A

t3g1

428

01.

392

0.9

702.

619

21.

180

Unk

now

n pr

otei

n25

8362

_at

310

At2

g17

290

1.8

268

1.0

150

2.6

400

1.3

191

Put

ativ

e ca

lmod

ulin

-dom

ain

prot

ein

kina

se C

PK

6 (c

alm

odul

in-d

omai

n pr

otei

nki

nase

isof

orm

6, a

cces

sion

U31

835)

; sup

port

ed b

y cD

NA

:gi

_122

0099

_dbj

_D28

582.

1_A

TH

AT

CD

PK

2648

51_a

t31

1A

t2g1

379

01.

812

371.

067

72.

617

611.

281

5P

utat

ive

rece

pto

r-lik

e pr

otei

n ki

nase

2641

07_s

_at

312

At5

g03

350

2.3

1294

11.

055

162.

614

838

1.3

7249

Put

ativ

e pr

otei

n25

0942

_at

313

At3

g56

710

2.2

2610

1.0

1200

2.6

3162

1.4

1711

Sig

A b

indi

ng p

rote

in; s

upp

orte

d b

y cD

NA

: gi

_145

9608

6_g

b_A

Y04

283

1.1

_24

6293

_at

314

At2

g41

250

1.3

388

1.0

294

2.6

762

1.5

432

Hyp

oth

etic

al p

rote

in p

redi

cted

by

GE

NS

CA

N a

nd g

ene

finde

r26

6363

_at

315

At5

g58

120

1.5

138

0.9

922.

624

41.

412

8

Res

ista

nce

prot

ein–

like;

dis

ease

res

ista

nce

prot

ein

RP

P1-

WsA

, A. t

halia

na,

EM

BL

:AF

098

962

2478

48_a

t31

6A

t1g7

517

01.

726

31.

015

52.

640

21.

320

2U

nkno

wn

prot

ein

2564

51_s

_at

317

At3

g45

290

1.7

471

1.0

267

2.6

691

1.1

295

Put

ativ

e pr

otei

n M

lo-h

1 pr

otei

n--H

orde

um

vul

gare

, PIR

:T05

952;

sup

port

ed b

ycD

NA

: gi_

1409

157

5_g

b_A

F3

6956

4.1

_AF

369

564

2525

72_a

t31

8A

t5g4

707

02.

070

51.

034

72.

690

21.

345

7P

rote

in s

erin

e th

reon

ine

kina

se-l

ike

2488

21_a

t

319

At3

g51

430

1.9

1159

1.0

609

2.6

1589

1.3

785

Muc

in -

like

prot

ein

hem

omuc

in, D

roso

phila

mel

anog

aste

r, E

MB

L:D

M42

014;

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:3

419

7.25

2117

_at

320

At5

g26

731

1.3

981.

071

2.6

185

0.6

56E

xpre

ssed

pro

tein

; sup

por

ted

by

full-

leng

th c

DN

A: C

eres

: 30

174.

2468

42_a

t32

1A

t2g4

615

02.

111

20.

953

2.6

141

1.2

64H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

EN

SC

AN

and

ge

nefin

der

2665

96_a

t

Page 16: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 16

322

At4

g11

850

2.4

233

1.0

952.

624

71.

514

6

Put

ativ

e ph

osph

olip

ase

D-g

amm

a; p

hosp

holip

ase

D-g

amm

a--A

.th

alia

na,P

ID:g

265

3885

; sup

port

ed

by

cDN

A:

gi_2

6538

84_g

b_A

F02

7408

.1_

AF

027

408

2548

47_a

t32

3A

t3g0

902

02.

131

91.

014

42.

638

01.

218

4U

nkno

wn

prot

ein

iden

tical

to G

B:A

AD

563

18 (

A. t

halia

na)

2592

11_a

t

324

At3

g56

400

1.7

4134

1.0

2416

2.6

6341

1.0

2484

DN

A-b

indi

ng p

rote

in-l

ike;

DN

A-b

indi

ng p

rote

in 4

WR

KY

4--N

icot

iana

taba

cum

,E

MB

L:A

F19

377

1; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:348

47.

2517

05_a

t32

5A

t4g2

952

02.

067

61.

033

42.

686

60.

931

4P

utat

ive

prot

ein;

sup

port

ed

by

full-

leng

th c

DN

A: C

eres

:142

647.

2536

87_a

t32

6A

t4g2

253

02.

319

81.

086

2.6

221

1.1

108

Put

ativ

e pr

otei

n em

bryo

-abu

ndan

t pr

otei

n (E

MB

34),

Pic

ea g

lauc

a, P

ID:g

135

053

125

4318

_at

327

At4

g23

480

2.4

2406

1.0

1012

2.6

2598

1.2

1192

Put

ativ

e pr

otei

n an

ne

xin

VII,

Dic

tyos

teliu

m d

isco

ideu

m, P

IR1:

LUD

O7

2542

62_a

t32

8A

t5g4

500

02.

520

91.

084

2.6

223

1.5

127

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to d

isea

se r

esis

tanc

e pr

otei

n24

8971

_at

329

At2

g44

380

3.2

103

0.8

322.

683

2.1

67U

nkno

wn

prot

ein

high

ly s

imila

r to

GP

|243

5515

|AF

024

504

2673

85_a

t33

0A

t1g6

142

02.

614

40.

956

2.6

143

1.7

97R

ecep

tor

kina

se, p

utat

ive

sim

ilar

to r

ecep

tor

kina

se G

I:166

692

from

[A. t

halia

na]

2647

66_a

t33

1A

t5g1

924

02.

631

671.

012

132.

530

861.

315

64P

utat

ive

prot

ein

pred

icte

d pr

otei

n, A

. tha

liana

2499

18_a

t

332

At4

g35

110

1.9

308

1.0

165

2.5

421

1.2

192

Put

ativ

e pr

otei

n pE

AR

LI 4

, A.

thal

iana

, PA

TC

HX

:G87

1782

; sup

port

ed b

y cD

NA

:gi

_143

2652

6_gb

_AF

385

717.

1_A

F38

5717

2531

73_a

t

333

At1

g09

970

2.3

1057

1.0

451

2.5

1151

1.2

544

Unk

now

n pr

otei

n S

imila

r to

A. t

halia

na r

ecep

tor-

like

prot

ein

kina

se(g

b|R

LK5_

AR

AT

H).

ES

Ts

gb|A

TT

S04

75,g

b|A

TT

S43

62 c

ome

from

this

gen

e26

4663

_at

334

At3

g54

640

2.2

2346

1.0

1072

2.5

2693

1.2

1337

Try

ptop

han

synt

has

e al

pha

chai

n; s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 4

0110

.25

1847

_at

335

At1

g22

180

1.9

353

1.0

187

2.5

475

1.1

213

Hyp

oth

etic

al p

rote

in c

onta

ins

Pfa

m p

rofil

e: P

F00

650

CR

AL/

TR

IO d

omai

n25

5923

_at

336

At3

g29

240

1.7

3256

1.0

1906

2.5

4830

1.1

2148

Unk

now

n pr

otei

n; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

214

35.

2577

45_a

t

337

At3

g26

590

2.4

351

1.0

148

2.5

374

1.4

211

Inte

gral

mem

bran

e pr

otei

n, p

utat

ive

con

tain

s P

fam

pro

file:

PF

0155

4un

char

acte

rize

d m

embr

ane

prot

ein

fam

ily; s

uppo

rted

by

cDN

A:

gi_1

6323

120_

gb_A

Y05

7664

.1_

2573

14_a

t

338

At1

g04

980

2.6

545

1.0

212

2.5

555

1.2

268

Dis

ulfid

e is

omer

ase-

rela

ted

prot

ein,

put

ativ

e si

mila

r to

GB

:AA

B50

217

from

[Hom

osa

pien

s]26

1167

_at

339

At3

g47

090

2.5

238

0.9

962.

524

41.

716

8R

ecep

tor

kina

se-l

ike

prot

ein;

rec

epto

r ki

nase

-lik

e pr

otei

n (X

a21)

, Ory

zalo

ngis

tam

inat

a, U

7272

525

2450

_s_a

t

340

At4

g26

270

1.8

689

1.0

374

2.5

931

1.2

453

Pyr

oph

osph

ate-

depe

nde

nt p

hosp

hofr

ucto

-1-k

inas

e; p

yrop

hosp

hate

-dep

end

ent

phos

phof

ruct

o-1-

kina

se, P

runu

s ar

men

iaca

, U93

272;

sup

por

ted

by

cDN

A:

gi_1

5146

207_

gb_A

Y04

9245

.1_

2539

87_a

t

341

At1

g22

400

1.6

250

1.0

155

2.5

398

1.1

176

UD

P-g

luco

se g

luco

syltr

ansf

eras

e, p

utat

ive

sim

ilar

to U

DP

-glu

cose

gluc

osyl

tran

sfer

ase

GI:6

5618

05 fr

om [S

orgh

um

bic

olor

]26

1934

_at

342

At4

g05

590

1.7

388

1.0

232

2.5

587

1.3

313

Put

ativ

e pr

otei

n h

ypot

het

ical

pro

tein

--A

. tha

liana

,PIR

:F71

409;

sup

port

ed

by

full-

leng

th c

DN

A: C

eres

:227

15.

2552

43_a

t

343

At3

g62

600

2.2

2503

1.0

1119

2.5

2887

1.3

1434

Put

ativ

e pr

otei

n H

IRA

inte

ract

ing

prot

ein

4 (d

naJ-

like)

--H

omo

sapi

ens,

EM

BL

:AJ0

013

09; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:3

729

2.25

1182

_at

344

At5

g42

050

1.6

3157

1.0

1919

2.5

4766

1.1

2057

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (s

p|P

3770

7); s

upp

orte

d b

y fu

ll-le

ngth

cDN

A: C

eres

:690

3.24

9237

_at

345

At5

g41

740

2.5

322

0.9

126

2.5

312

1.4

178

Dis

ease

res

ista

nce

prot

ein-

like

2492

64_s

_at

346

At1

g79

680

2.1

256

1.0

122

2.5

301

1.2

149

Wal

l-ass

ocia

ted

kina

se 2

, put

ativ

e si

mila

r to

wal

l-as

soci

ated

kin

ase

2 G

I:482

6399

from

[A. t

halia

na]

2613

94_a

t34

7A

t2g4

644

02.

319

521.

083

12.

520

481.

613

12P

utat

ive

cycl

ic n

ucle

otid

e-re

gula

ted

ion

chan

nel p

rote

in26

3776

_s_a

t

348

At5

g28

540

1.6

4446

1.0

2718

2.5

6684

1.3

3665

Lum

inal

bin

ding

pro

tein

; sup

port

ed b

y cD

NA

:gi

_130

3694

_dbj

_D84

414.

1_A

TH

BIP

A24

5956

_s_a

t

349

At2

g25

000

1.9

304

1.0

161

2.5

394

1.0

159

Put

ativ

e W

RK

Y-t

ype

DN

A b

indi

ng p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

:C

eres

:300

71.

2635

36_a

t35

0A

t2g4

014

02.

182

20.

938

32.

594

31.

353

5P

utat

ive

CC

CH

-typ

e zi

nc fi

nger

pro

tein

als

o an

ank

yrin

-rep

eat

prot

ein

2633

79_a

t35

1A

t2g1

670

01.

659

21.

036

72.

489

51.

246

2A

ctin

dep

olym

eriz

ing

fact

or 5

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:2

6940

.26

5354

_at

352

At3

g48

080

2.4

355

1.0

146

2.4

358

1.6

239

Hyp

oth

etic

al p

rote

in25

2403

_at

Page 17: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 17

353

At1

g74

020

1.8

289

1.0

164

2.4

399

1.5

252

Put

ativ

e st

rict

osid

ine

synt

hase

ext

rem

ely

sim

ilar

to S

TR

ICT

OS

IDIN

E S

YN

TH

AS

E1/

2 P

RE

CU

RS

OR

GB

:P94

111

; sup

por

ted

by

cDN

A:

gi_1

4334

593_

gb_A

Y03

4970

.1_

2603

91_a

t35

4A

t5g2

366

01.

689

31.

053

92.

413

081.

583

0M

tN3-

like

prot

ein;

sup

port

ed b

y cD

NA

: gi_

3747

110_

gb_A

F0

9564

1.1_

AF

0956

4124

9800

_at

355

At3

g45

620

2.1

1289

1.0

618

2.4

1512

1.4

852

Put

ativ

e pr

otei

n H

uman

(H

326)

tran

slat

ed m

RN

A--

Hom

o sa

pien

s,E

MB

L:H

S06

631

2525

87_a

t

356

At4

g13

510

2.1

2581

1.0

1212

2.4

2923

1.3

1539

Am

mon

ium

tran

spor

t pro

tein

(A

MT

1); s

uppo

rted

by

cDN

A:

gi_1

4335

079_

gb_A

Y03

7219

.1_

2547

23_a

t35

7A

t5g4

841

01.

818

61.

010

52.

425

51.

718

1Li

gand

-gat

ed io

n ch

ann

el p

rote

in-l

ike;

glu

tam

ate

rece

ptor

-lik

e24

8701

_at

358

At1

g18

890

1.9

407

1.0

208

2.4

511

1.4

290

Cal

cium

-dep

ende

nt p

rote

in k

inas

e, p

utat

ive

sim

ilar

to c

alci

um-d

epen

dent

pro

tein

kina

se G

I:604

880

from

[A. t

halia

na];

sup

port

ed b

y cD

NA

:gi

_123

5716

_dbj

_D21

805.

1_A

TH

CD

PK

A26

1378

_at

359

At4

g24

190

1.7

7959

1.0

4598

2.4

1154

01.

257

01

HS

P 9

0-lik

e pr

otei

n H

SP

90 h

omol

og--

Cat

hara

nth

us r

oseu

s, P

IR2:

S39

558;

supp

orte

d b

y cD

NA

: gi_

1453

2541

_gb

_AY

0398

95.1

_25

4166

_at

360

At2

g47

000

1.4

114

0.9

802.

419

21.

084

Put

ativ

e A

BC

tran

spor

ter

rela

ted

to m

ulti

drug

res

ista

nce

prot

eins

and

P-

glyc

opro

tein

s26

6752

_at

361

At4

g28

400

1.5

792

1.0

538

2.4

1300

1.3

708

Pro

tein

pho

spha

tase

2C

-lik

e pr

otei

n; p

rote

in p

hosp

hata

se 2

C-f

issi

on y

east

,P

IR2:

S54

297

; sup

port

ed b

y cD

NA

: gi_

166

0458

4_g

b_A

Y0

5973

7.1_

2537

80_a

t36

2A

t1g1

436

02.

110

701.

050

92.

412

151.

471

7U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:693

7.

2614

85_a

t

363

At3

g28

930

2.4

990

1.0

416

2.4

1000

1.6

665

AIG

2-lik

e pr

otei

n si

mila

r to

AIG

2 pr

otei

n G

B:P

5412

1 fr

om [A

. tha

liana

]; su

ppo

rted

by

full-

leng

th c

DN

A: C

eres

:285

11.

2580

02_a

t

364

At1

g11

330

2.0

468

1.0

237

2.4

574

1.7

416

Rec

epto

r-lik

e pr

otei

n ki

nase

, put

ativ

e; s

imila

r to

rec

epto

r-lik

e pr

otei

n ki

nase

GB

:AA

C9

5353

GI:4

0080

10 fr

om [A

. th

alia

na]

2625

07_a

t

365

At2

g22

500

1.8

1258

1.0

699

2.4

1687

1.2

825

Put

ativ

e m

itoch

ondr

ial d

icar

boxy

late

car

rier

pro

tein

; sup

port

ed b

y fu

ll-le

ngth

cDN

A: C

eres

:207

23.

2640

00_a

t

366

At3

g61

190

1.9

135

1.0

702.

416

61.

184

Put

ativ

e pr

otei

n h

ypot

het

ical

pro

tein

F4I

18.2

6--A

. tha

liana

, P

IR:T

0247

1; s

upp

orte

db

y fu

ll-le

ngth

cD

NA

: Cer

es:3

0454

.25

1336

_at

367

At5

g61

790

2.1

5217

1.0

2521

2.4

6130

1.2

2983

Cal

nexi

n-lik

e pr

otei

n; c

alne

xin

hom

olog

, A. t

halia

na, E

MB

L:A

T08

315;

sup

port

edb

y fu

ll-le

ngth

cD

NA

: Cer

es:2

869.

2474

94_a

t36

8A

t2g2

871

01.

618

51.

011

02.

425

91.

213

3P

utat

ive

C2H

2-ty

pe z

inc

finge

r pr

otei

n lik

ely

a nu

clei

c ac

id b

indi

ng p

rote

in26

3411

_at

369

At2

g34

940

2.2

342

1.0

158

2.4

373

1.5

245

Put

ativ

e va

cuol

ar s

ortin

g re

cept

or26

7412

_at

370

At3

g01

420

0.7

511.

070

2.3

170

2.1

164

Fee

bly-

like

prot

ein

cont

ains

sim

ilari

ty to

feeb

ly p

rote

in G

B:S

7064

8 [L

ycop

ersi

con

escu

lent

um];

supp

orte

d b

y cD

NA

: gi

_145

959

98_

gb_A

Y04

2787

.1_

2589

57_a

t

371

At5

g58

620

1.7

139

0.9

802.

318

81.

310

6

Put

ativ

e pr

otei

n zi

nc fi

nger

tran

scri

ptio

n fa

ctor

, A. t

halia

na, P

IR:T

4988

9;su

ppor

ted

by

cDN

A: g

i_15

8098

17_g

b_A

Y05

4176

.1_

2477

95_a

t

372

At1

g67

970

2.1

1397

1.0

672

2.3

1572

1.2

805

Put

ativ

e he

at s

hock

tran

scri

ptio

n fa

ctor

con

tain

s P

fam

pro

file:

PF

0044

7 H

SF

-typ

eD

NA

-bin

ding

dom

ain;

N-t

erm

inal

por

tion

sim

ilar

to h

eat s

hock

tran

scri

ptio

n fa

ctor

prot

eins

: GB

:CA

A7

4397

[A

. th

alia

na],

GB

:S2

5478

[L

ycop

ersi

c25

9992

_at

373

At2

g40

350

1.5

650.

943

2.3

102

0.9

41A

P2

dom

ain

tran

scri

ptio

n fa

ctor

2638

23_s

_at

374

At2

g29

120

2.1

604

1.0

290

2.3

677

1.2

364

Put

ativ

e lig

and-

gate

d io

n ch

anne

l pro

tein

2667

82_a

t

375

At2

g04

400

2.0

2523

1.0

1276

2.3

2994

1.1

1472

Put

ativ

e in

dol

e-3-

glyc

erol

pho

spha

te s

ynth

ase;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

:C

eres

:300

6.26

3807

_at

376

At4

g16

660

2.0

998

1.0

495

2.3

1160

1.3

647

HS

P li

ke p

rote

in; s

uppo

rted

by

cDN

A:

gi_1

5293

148_

gb_

AY

051

008.

1_

2452

93_a

t37

7A

t5g5

312

01.

578

01.

050

52.

311

861.

261

0S

perm

idin

e sy

nth

ase;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:3

3021

.24

8248

_at

378

At3

g60

450

1.7

924

1.0

532

2.3

1240

1.3

672

Put

ativ

e pr

otei

n pr

ib5,

Rib

es n

igru

m, E

MB

L:R

NI7

578

; sup

port

ed b

y fu

ll-le

ngth

cDN

A: C

eres

:157

92.

2513

70_a

t

379

At4

g08

770

2.5

180

0.9

712.

316

51.

288

Per

oxi

dase

C2

prec

urso

r lik

e pr

otei

n; p

ero

xida

se (

EC

1.1

1.1.

7) C

2 p

recu

rsor

--A

rmor

acia

rus

tican

a,P

ID:d

1014

846

2551

10_a

t38

0A

t5g6

689

01.

781

0.9

492.

311

60.

738

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to d

isea

se r

esis

tanc

e pr

otei

n24

7064

_at

Page 18: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 18

381

At2

g26

190

1.7

1106

1.0

626

2.3

1462

1.3

829

Unk

now

n pr

otei

n; s

upp

orte

d b

y cD

NA

: gi_

1693

0468

_gb

_AF

4195

88.1

_AF

4195

8826

7381

_at

382

At4

g04

220

2.3

290

1.0

124

2.3

288

1.2

155

Put

ativ

e di

seas

e re

sist

ance

pro

tein

sim

ilar

to r

ecep

tor

prot

ein

kina

ses

2553

19_a

t

383

At5

g24

810

1.7

1113

1.0

652

2.3

1515

1.4

895

Put

ativ

e pr

otei

n U

BIQ

UIN

ON

E B

IOS

YN

TH

ES

IS P

RO

TE

IN A

AR

F--

Pro

vide

ncia

stua

rtii,

EM

BL:

AF

0021

65(N

-ter

min

us)

and

to E

ster

ase

ST

E1-

-Met

arhi

zium

anis

oplia

e, E

MB

L:A

J251

924

(C-t

erm

inus

)24

6976

_s_a

t

384

At1

g66

920

1.4

222

1.0

154

2.3

360

1.2

181

Rec

epto

r se

rine

/thre

onin

e ki

nase

PR

5K,

puta

tive

sim

ilar

to r

ecep

tor

seri

ne/th

reon

ine

kina

se P

R5

K G

I:123

5680

fro

m [A

. tha

liana

]24

5760

_s_a

t38

5A

t1g3

041

01.

738

51.

022

32.

351

41.

227

2A

BC

tran

spor

ter,

put

ativ

e c

onta

ins

Pfa

m p

rofil

e: P

F00

005:

AB

C tr

ansp

orte

r25

6308

_s_a

t

386

At1

g33

030

2.1

244

1.0

118

2.3

285

1.0

127

Cat

echo

l O-m

ethy

ltran

sfer

ase,

put

ativ

e si

mila

r to

cat

echo

l O-m

ethy

ltran

sfer

ase

GI:4

808

524

from

[Tha

lictr

um tu

bero

sum

]26

1216

_at

387

At2

g43

850

1.5

357

1.0

228

2.3

527

1.2

289

Put

ativ

e pr

otei

n ki

nase

con

tain

s a

prot

ein

kina

se d

omai

n pr

ofile

(P

DO

C00

100)

2605

62_a

t

388

At2

g26

560

2.2

5305

1.0

2376

2.3

5472

1.4

3346

sim

ilar

to la

tex

alle

rgen

from

He

vea

bras

ilien

sis;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

:C

eres

:199

9.24

5038

_at

389

At2

g40

080

2.3

635

0.9

276

2.3

714

1.0

274

Unk

now

n pr

otei

n; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:9

398

.26

7364

_at

390

At1

g67

810

2.9

431

1.0

148

2.3

340

1.6

232

F12

A21

.6 h

ypot

hetic

al p

rote

in24

5193

_at

391

At4

g17

500

1.7

130

0.9

772.

319

11.

411

5et

hyl

ene

resp

ons

ive

elem

ent b

indi

ng fa

ctor

1 (

fram

eshi

ft !)

; sup

port

ed b

y cD

NA

:gi

_343

4966

_dbj

_AB

008

103.

1_A

B00

8103

2452

52_a

t

392

At3

g28

480

1.7

1052

1.0

608

2.3

1398

1.3

775

SURO\O���K\GUR[\ODVH��SXWDWLYH�VLP

LODU�WR�352/</���+<'52;</$6(��68%81,7

PR

EC

UR

SO

R G

B:Q

1057

6 fr

om [C

aeno

rhab

ditis

ele

gans

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:833

0.25

7844

_at

393

At4

g39

270

1.5

186

1.0

122

2.3

285

1.0

126

Rec

epto

r pr

otei

n ki

nase

–lik

e pr

otei

n; r

ecep

tor

prot

ein

kina

se e

rect

a, A

. th

alia

na25

2940

_at

394

At3

g54

960

2.1

1291

1.0

619

2.3

1438

1.1

673

prot

ein

disu

lfide

-isom

eras

e-lik

e pr

otei

n; p

rote

in d

isul

phid

e is

omer

ase,

Fas

ciol

ahe

patic

a25

1840

_at

395

At5

g25

440

1.7

470

1.0

277

2.3

638

1.3

369

Put

ativ

e pr

otei

n ki

nase

ser

ine/

thre

onin

e/ty

rosi

ne-s

peci

fic p

rote

in k

inas

e A

PK

1--A

.th

alia

na, P

IR:S

2861

524

6943

_at

396

At5

g48

400

1.3

981.

077

2.3

175

1.1

89lig

and-

gate

d io

n ch

anne

l pro

tein

-lik

e; g

luta

mat

e re

cept

or-l

ike

2487

00_a

t

397

At1

g35

210

1.6

121

0.9

732.

316

61.

088

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

:C

eres

:422

17.

2457

55_a

t

398

At5

g01

550

2.7

128

0.9

472.

311

80.

959

Rec

epto

r lik

e pr

otei

n ki

nase

; rec

epto

r lik

e pr

otei

n ki

nase

--A

. tha

liana

,E

MB

L:A

TLE

CG

EN

E25

1096

_at

399

At1

g72

680

1.4

707

1.0

508

2.3

1157

1.3

651

Put

ativ

e ci

nnam

yl-a

lcoh

ol d

ehyd

rog

enas

e si

mila

r to

cin

nam

yl-a

lcoh

olde

hyd

roge

nase

GB

:AA

C35

846

[Med

icag

o sa

tiva]

2599

11_a

t40

0A

t1g3

339

02.

221

31.

093

2.3

214

1.7

169

RN

A h

elic

ase,

put

ativ

e si

mila

r to

GI:1

7429

09 fr

om (

Hom

o sa

pien

s)25

6511

_at

401

At3

g45

330

1.1

651.

056

2.3

130

1.1

63

Rec

epto

r-lik

e pr

otei

n ki

nase

; rec

epto

r lik

e pr

otei

n ki

nase

LR

K1-

-A.

thal

iana

,EM

BL:

AT

LEC

GE

NE

2525

96_a

t

402

At1

g21

750

2.0

5611

1.0

2776

2.3

6309

1.2

3368

Put

ativ

e pr

otei

n di

sulfi

de is

omer

ase

prec

urso

r S

imila

r to

gb|

Z11

499

prot

ein

disu

lfide

isom

eras

e fr

om M

edic

ago

sativ

a. E

ST

s gb

|AI0

996

93,

gb|R

652

26,

gb|A

A65

7311

, gb

|T43

068,

gb|

T42

754,

gb|

T14

005,

gb|

T76

445,

gb|

H36

733,

gb|T

4316

8 an

d g

2625

04_a

t

403

At4

g34

150

1.7

1740

1.0

1024

2.3

2331

1.2

1354

Put

ativ

e pr

otei

n h

ydro

xypr

olin

e-ri

ch g

lyco

prot

ein

prec

urso

r, N

icot

iana

taba

cum

,P

IR2:

S06

733

; sup

port

ed b

y cD

NA

: gi_

157

2431

5_g

b_A

F41

2098

.1_

AF

412

098

2532

84_a

t

404

At3

g55

950

1.5

145

1.0

942.

321

81.

211

8R

ecep

tor

kina

se–l

ike

prot

ein;

rec

epto

r ki

nase

hom

olog

CR

INK

LY4,

mai

ze,

PIR

:T04

108

2517

69_a

t

405

At1

g68

710

1.9

298

1.0

157

2.3

358

1.6

258

AT

Pas

e, p

utat

ive

sim

ilar

to c

hrom

affin

gra

nule

AT

Pas

e II

GB

:AA

D03

352

GI:4

115

341

from

[Bos

taur

us]

2622

75_a

t

406

At4

g29

810

1.6

1932

1.0

1181

2.3

2721

1.3

1528

MA

P k

inas

e ki

nase

2;

supp

orte

d b

y cD

NA

:gi

_143

2647

0_gb

_AF

385

688.

1_A

F38

5688

2536

46_a

t40

7A

t3g2

450

32.

157

591.

027

032.

361

191.

232

30E

xpre

ssed

pro

tein

; sup

por

ted

by

cDN

A:

gi_1

5912

240_

gb_

AY

056

398.

1_

2581

40_a

t40

8A

t5g5

461

01.

913

151.

068

12.

315

551.

284

6an

kyri

n-re

peat

-con

tain

ing

prot

ein-

like

2481

69_a

t40

9A

t1g7

270

01.

862

91.

035

52.

380

11.

139

6P

utat

ive

P-t

ype

tran

spor

ting

AT

Pas

e si

mila

r to

AT

Pas

e II

GB

:AA

D34

706

[Ho

mo

2599

10_a

t

Page 19: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 19

sapi

ens]

410

At5

g05

460

1.9

341

1.0

179

2.3

407

1.3

241

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to e

ndo-

β-N

-ace

tylg

luco

sam

inid

ase

2507

75_a

t41

1A

t2g3

829

01.

780

31.

046

02.

310

471.

256

9P

utat

ive

amm

oniu

m tr

ansp

orte

r26

7142

_at

412

At5

g57

220

2.2

149

0.9

672.

316

20.

662

Cyt

ochr

ome

P-4

5024

7949

_at

413

At2

g25

440

1.5

950.

963

2.3

147

0.7

51P

utat

ive

dise

ase

resi

stan

ce p

rote

in26

5659

_at

414

At5

g63

990

1.6

297

0.9

188

2.2

421

1.3

244

3(2)

,5-B

isph

osph

ate

nucl

eotid

ase;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:9

8980

.24

7318

_at

415

At1

g55

910

2.0

1052

1.0

525

2.2

1184

1.3

709

Exp

ress

ed p

rote

in; s

upp

orte

d b

y cD

NA

:gi

_152

9427

3_gb

_AF

410

328.

1_A

F41

0328

2606

01_a

t41

6A

t4g1

553

01.

710

511.

061

52.

213

971.

277

0p

yru

vate

,ort

hoph

osph

ate

diki

nase

2455

28_a

t

417

At4

g36

110

1.8

296

1.0

167

2.2

375

1.0

175

Put

ativ

e au

xin-

indu

ced

prot

ein;

hig

h si

mila

rity

to a

uxi

n-in

duce

d pr

otei

n 15

A,

soyb

ean,

PIR

2:JQ

109

6; s

uppo

rted

by

cDN

A:

gi_1

3194

817_

gb_A

F34

952

4.1

_AF

3495

2425

3103

_at

418

At4

g13

810

1.6

229

1.0

139

2.2

314

1.2

179

Put

ativ

e di

seas

e re

sist

ance

pro

tein

Cf-

4 ,L

ycop

ersi

con

hirs

utum

, gb:

AJ0

0223

525

4735

_at

419

At2

g30

250

1.8

621

1.0

342

2.2

760

1.2

428

Put

ativ

e W

RK

Y-t

ype

DN

A b

indi

ng p

rote

in; s

upp

orte

d b

y cD

NA

:gi

_150

2791

2_gb

_AY

0458

13.1

_26

7246

_at

420

At5

g20

400

1.4

218

1.0

149

2.2

335

1.3

196

eth

ylen

e-fo

rmin

g-en

zym

e-lik

e di

oxy

gen

ase-

like

prot

ein;

eth

ylen

e-fo

rmin

g-en

zym

e-lik

e di

oxyg

ena

se--

Pru

nus

arm

enia

ca, E

MB

L:U

9753

0; s

uppo

rted

by

full-

leng

thcD

NA

: Cer

es:3

8372

.24

6098

_at

421

At5

g51

570

1.7

1319

1.0

757

2.2

1705

1.0

748

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (g

b|A

AF

0349

7.1)

2484

10_a

t

422

At1

g69

930

1.4

102

1.0

722.

216

21.

291

Put

ativ

e gl

utat

hion

e tr

ans

fera

se s

imila

r to

glu

tath

ione

tran

sfer

ase

GB

:CA

A09

188

[Alo

pecu

rus

myo

suro

ides

]26

0405

_at

423

At4

g12

480

1.5

276

1.0

186

2.2

412

1.0

195

pEA

RL

I 1; s

uppo

rted

by

cDN

A: g

i_87

1779

_gb_

L43

080.

1_A

TH

PE

AR

2548

05_a

t42

4A

t5g4

099

01.

771

0.3

222.

289

0.5

29G

DS

L-m

otif

lipas

e/h

ydro

lase

-lik

e pr

otei

n24

9333

_at

425

At1

g42

990

1.7

1349

1.0

785

2.2

1740

1.1

873

bZIP

tran

scri

ptio

n fa

ctor

, put

ativ

e co

ntai

ns P

fam

pro

file:

PF

001

70: b

ZIP

tran

scri

ptio

n fa

ctor

; sup

port

ed b

y cD

NA

: gi_

1502

8322

_gb

_AY

0459

64.1

_25

9626

_at

426

At5

g23

850

1.2

232

1.0

187

2.2

415

1.2

224

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to u

nkno

wn

prot

ein

(em

b|C

AB

6201

2.1)

2498

06_a

t

427

At5

g37

740

1.6

554

1.0

341

2.2

769

1.2

412

Put

ativ

e pr

otei

n pr

edic

ted

prot

eins

, A.

thal

iana

; sup

port

ed b

y cD

NA

:gi

_158

1033

4_gb

_AY

0562

06.1

_24

9580

_at

428

At3

g47

780

1.6

118

1.0

722.

216

41.

188

AB

C-t

ype

tran

spor

t pro

tein

-lik

e pr

otei

n; tr

ansp

ort p

rote

in A

BC

-C, H

omo

sapi

ens,

PIR

2:S

7136

325

2383

_at

429

At4

g01

610

1.7

2931

1.0

1692

2.2

3727

1.4

2392

cath

epsi

n B

-lik

e cy

stei

ne p

rote

ase,

put

ativ

e si

mila

r to

cat

heps

in B

-lik

e cy

stei

nepr

otei

nase

GI:6

0917

5 fr

om [N

icot

iana

rus

tica]

; con

tain

s an

unu

sual

ly s

hort

, 5nt

exo

n; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:20

761.

2555

90_a

t

430

At2

g05

630

1.6

700

1.0

444

2.2

998

1.2

532

Put

ativ

e m

icro

tubu

le-a

ssoc

iate

d pr

otei

n; s

uppo

rted

by

full-

leng

th c

DN

A:

Cer

es:3

416.

2655

10_a

t

431

At1

g05

570

1.7

1482

1.0

844

2.2

1872

1.4

1185

Put

ativ

e gl

ucan

syn

thas

e. H

ighl

y si

mila

r to

put

ativ

e g

luca

n sy

nth

ase

GB

:AA

D1

5408

; su

ppor

ted

by

cDN

A:

gi_1

364

9387

_gb

_A

F23

773

3.1_

AF

2377

3326

3183

_at

432

At2

g17

120

2.2

2886

1.0

1286

2.2

2848

1.4

1828

Unk

now

n pr

otei

n si

mila

r to

hyp

othe

tical

pro

tein

GB

:AA

B81

674

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:6

280.

2635

82_a

t43

3A

t5g1

319

01.

517

411.

011

262.

224

811.

112

16P

utat

ive

prot

ein;

sup

port

ed

by

full-

leng

th c

DN

A: C

eres

:539

2.25

0289

_at

434

At2

g12

290

1.5

206

1.0

134

2.2

300

1.2

166

Hyp

oth

etic

al p

rote

in26

6150

_s_a

t43

5A

t5g5

254

02.

016

331.

083

02.

218

151.

412

04P

utat

ive

prot

ein

cont

ains

sim

ilarit

y to

unk

now

n pr

otei

n (d

bj B

AA

9063

7.1)

2483

09_a

t

436

At5

g12

420

2.2

191

1.0

872.

219

41.

210

7

Put

ativ

e pr

otei

n si

mila

rity

to v

ario

us p

redi

cted

pro

tein

s.C

onta

ins

AT

P s

ynth

ase

delta

(O

SC

P)

subu

nit s

igna

ture

AA

211-

230;

Pro

kary

otic

mem

bran

e lip

opro

tein

lipi

dat

tach

men

t site

AA

140-

150

2451

81_a

t

437

At5

g02

100

1.9

297

1.0

155

2.2

342

1.4

216

Put

ativ

e pr

otei

n o

xyst

erol

-bin

ding

pro

tein

--M

us m

uscu

lus,

EM

BL:

AB

0170

26;

supp

orte

d b

y cD

NA

: gi_

1529

2810

_gb

_AY

0508

39.1

_25

1037

_at

438

At5

g53

370

1.5

1551

1.0

1037

2.2

2302

1.2

1225

pect

ines

tera

se; s

uppo

rted

by

cDN

A: g

i_15

2932

86_

gb_

AY

0510

77.

1_24

8263

_at

Page 20: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 20

439

At3

g47

540

1.4

497

1.0

344

2.2

752

1.1

401

endo

chiti

nase

-lik

e pr

otei

n; b

asic

end

ochi

tinas

e ch

b4 p

recu

rsor

--B

rass

ica

napu

s,S

WIS

SP

RO

T:C

HI4

_BR

AN

A25

2421

_at

440

At1

g22

890

2.0

1072

1.0

527

2.2

1153

0.9

492

Unk

now

n pr

otei

n26

4774

_at

441

At4

g11

000

2.0

274

1.0

133

2.2

299

1.4

190

Put

ativ

e pr

otei

n va

riou

s pr

edic

ted

prot

eins

, A. t

halia

na25

4948

_at

442

At2

g39

420

1.7

240

1.0

145

2.2

317

1.3

196

Put

ativ

e ph

osph

olip

ase

2669

77_a

t

443

At3

g20

250

1.7

530

1.0

310

2.2

672

1.2

382

RN

A-b

indi

ng p

rote

in, p

utat

ive

cont

ains

Pfa

m p

rofil

e: P

F00

806

Pum

ilio-

fam

ily R

NA

bind

ing

dom

ains

(ak

a P

UM

-HD

, P

umili

o ho

mol

ogy

dom

ain)

(8

copi

es a

t C-

term

inus

)25

7122

_at

444

At2

g04

070

2.1

144

1.0

662.

214

61.

394

Hyp

oth

etic

al p

rote

in s

imila

r to

hyp

othe

tical

pro

tein

GB

:AA

C27

412

2634

01_a

t44

5A

t3g5

966

01.

876

11.

041

92.

291

31.

250

0P

utat

ive

prot

ein

othe

r h

ypot

hetic

al p

rote

ins

2514

75_a

t44

6A

t4g2

319

01.

874

0.9

392.

287

1.0

50S

erin

e/th

reon

ine

kina

se–l

ike

prot

ein;

ser

ine/

thre

onin

e ki

nase

, Bra

ssic

a ol

erac

ea25

4241

_at

447

At3

g55

470

2.4

407

1.0

169

2.2

365

1.1

192

Elic

itor

resp

onsi

ve/p

hloe

m–l

ike

prot

ein

FIE

RG

2 pr

otei

n, O

ryza

sat

iva,

PIR

:T04

363

2517

90_a

t

448

At1

g21

900

1.7

1089

1.0

628

2.2

1364

1.2

737

Tra

nsm

embr

ane

prot

ein,

put

ativ

e si

mila

r to

TR

AN

SM

EM

BR

AN

E P

RO

TE

INT

MP

21 G

B:Q

6358

4 fr

om [R

attu

s n

orve

gicu

s]26

0852

_at

449

At5

g07

770

1.4

260

1.0

179

2.2

391

1.2

223

Unk

now

n pr

otei

n25

0595

_at

450

At4

g18

880

2.0

767

1.0

380

2.2

824

1.3

511

Hea

t sho

ck tr

ansc

ript

ion

fact

or–l

ike

prot

ein;

hea

t sho

ck t

rans

crip

tion

fact

or, Z

eam

ays,

PIR

2:S

614

4825

4592

_at

451

At2

g32

800

1.6

499

1.0

306

2.2

661

1.1

334

Put

ativ

e pr

otei

n ki

nase

con

tain

s a

prot

ein

kina

se d

omai

n pr

ofile

(P

DO

C00

100)

2675

50_a

t45

2A

t3g1

955

01.

512

51.

076

2.2

167

1.4

106

Hyp

oth

etic

al p

rote

in; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

: 145

77.

2565

69_a

t

453

At3

g04

070

1.2

160

1.0

131

2.2

283

1.1

151

NA

M-l

ike

prot

ein

(no

apic

al m

eris

tem

) si

mila

r to

NA

M G

B:C

AA

631

01 [

Pet

unia

xh

ybri

da]

2588

09_a

t45

4A

t2g1

774

01.

922

41.

011

52.

225

20.

894

Unk

now

n pr

otei

n26

4616

_at

455

At1

g23

140

1.8

290

1.0

162

2.2

351

1.5

248

Unk

now

n pr

otei

n si

mila

r to

unk

now

n p

rote

in G

B:A

AD

5549

526

4893

_at

456

At2

g29

070

1.4

106

0.9

732.

216

11.

713

3P

utat

ive

ubiq

uitin

fusi

on-d

egra

datio

n pr

otei

n26

6776

_at

457

At4

g16

960

1.8

218

1.0

124

2.1

268

1.2

153

Dis

ease

res

ista

nce

RP

P5

like

prot

ein

2454

57_s

_at

458

At3

g09

010

1.7

363

1.0

213

2.1

458

1.1

231

Put

ativ

e re

cep

tor

ser/

thr

prot

ein

kina

se s

imila

r to

rec

epto

r ki

nase

GB

:S70

769

[A.

thal

iana

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

: 124

301.

2592

13_a

t45

9A

t5g0

696

01.

622

41.

013

92.

129

61.

217

8tr

ansc

ript

ion

fact

or H

BP

-1b

(gb|

AA

D24

395.

1)25

0655

_at

460

At5

g61

210

1.5

1654

1.0

1064

2.1

2267

1.1

1231

SN

AP

25A

; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:145

62.

2475

71_a

t46

1A

t3g0

949

02.

013

41.

066

2.1

149

1.2

85H

ypot

het

ical

pro

tein

pre

dict

ed b

y G

EN

SC

AN

+25

7535

_at

462

At3

g51

860

2.0

1375

1.0

676

2.1

1448

0.5

376

Ca2

+/H

+-e

xcha

ngin

g pr

otei

n-lik

e; A

. tha

liana

hig

h-af

finity

cal

cium

ant

ipor

ter

CA

X1

enco

ded

by

Gen

Ban

k A

cces

sion

Num

ber

U57

411

2463

02_a

t46

3A

t3g4

912

01.

673

521.

046

942.

110

069

1.2

5483

Per

oxi

dase

; sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:396

78.

2522

91_s

_at

464

At1

g77

810

1.6

432

1.0

266

2.1

565

1.2

315

Avr

9 el

icito

r re

spon

se p

rote

in, p

utat

ive

sim

ilar

to A

vr9

elic

itor

resp

onse

pro

tein

GI:4

138

265

from

[Nic

otia

na ta

bacu

m]

2621

88_a

t

465

At1

g29

240

1.7

330

1.0

195

2.1

433

1.2

246

Unk

now

n pr

otei

n si

mila

r to

unk

now

n p

rote

in G

B:A

AF

186

09 G

I:65

9841

9 fr

om [A

.th

alia

na]

2608

84_a

t

466

At5

g18

310

1.6

858

1.0

526

2.1

1113

0.9

490

Put

ativ

e pr

otei

n pr

edic

ted

prot

eins

, Dro

soph

ila m

elan

ogas

ter;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:415

25.

2499

88_a

t

467

At3

g20

590

1.4

348

1.0

233

2.1

498

1.1

261

Non

-rac

e sp

ecifi

c di

seas

e re

sist

ance

pro

tein

, put

ativ

e co

ntai

ns n

on-c

onse

nsus

CT

dono

r sp

lice

site

at e

xon

1; p

ote

ntia

l pse

udog

ene

; sim

ilar

to n

on-r

ace

spec

ific

dise

ase

resi

stan

ce p

rote

in G

B:A

AB

9520

8 [A

. th

alia

na]

2570

83_s

_at

468

At1

g03

290

1.9

499

1.0

264

2.1

556

1.2

323

Unk

now

n pr

otei

n E

ST

s gb

|H36

966,

gb|

R65

511

, gb|

T42

324

and

gb|T

2056

9 co

me

from

this

gen

e26

4362

_at

469

At4

g28

460

1.7

980.

958

2.1

126

0.6

42H

ypot

het

ical

pro

tein

2537

96_a

t

470

At5

g38

710

2.4

199

1.0

822.

117

21.

210

1P

rolin

e o

xida

se, m

itoch

ondr

ial p

recu

rsor

–lik

e pr

otei

n; P

RO

LIN

E O

XID

AS

E,

MIT

OC

HO

ND

RIA

L P

RE

CU

RS

OR

, A

. tha

liana

, S

WIS

SN

EW

:PR

OD

2495

27_a

t

Page 21: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 21

471

At4

g34

180

1.6

2418

1.0

1530

2.1

3244

1.1

1630

Put

ativ

e pr

otei

n h

ypot

het

ical

pro

tein

slr

2121

, Syn

echo

cyst

is s

p., P

IR2:

S75

497;

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:8

686.

2532

73_a

t

472

At3

g28

940

1.9

5447

1.0

2888

2.1

6122

1.4

4030

AIG

2-lik

e pr

otei

n si

mila

r to

AIG

2 pr

otei

n G

B:P

5412

1 fr

om [A

. tha

liana

]; su

ppo

rted

by

full-

leng

th c

DN

A: C

eres

:513

7.25

8000

_at

473

At1

g71

330

2.3

420

1.0

177

2.1

377

1.5

276

Put

ativ

e A

BC

tran

spor

ter

cont

ains

Pfa

m p

rofil

e: P

F00

005

AB

C tr

ansp

orte

r25

9937

_s_a

t47

4A

t4g3

854

01.

552

51.

033

82.

171

91.

345

6M

onoo

xyg

enas

e 2

(MO

2)25

2993

_at

475

At4

g37

530

1.6

331

1.0

212

2.1

455

1.1

238

Per

oxi

dase

-lik

e pr

otei

n; p

ero

xid

ase,

A. t

halia

na, g

b:X

983

1425

3099

_s_a

t

476

At5

g40

010

1.0

390.

430

2.1

831.

142

Put

ativ

e pr

otei

n B

CS

1 nu

clea

r ge

ne

enco

ding

mito

chon

dria

l pro

tein

--H

omo

sapi

ens,

EM

BL:

AF

0268

4924

9438

_at

477

At3

g50

280

1.1

581.

050

2.1

105

1.0

53

Ant

hran

ilate

N-h

ydro

xyci

nnam

oyl

/be

nzo

yltr

ansf

eras

e–lik

e pr

otei

n; a

nthr

anila

te N

-h

ydro

xyci

nnam

oyl

/ben

zoyl

tran

sfer

ase,

Dia

nth

us c

aryo

phyl

lus,

PIR

:T10

717

2522

00_a

t

478

At1

g49

050

1.7

810

1.0

463

2.1

969

1.3

630

Unk

now

n pr

otei

n co

ntai

ns s

imila

rity

to n

ucel

lin G

I:229

020

3 fr

om [H

orde

um

vulg

are]

; sup

port

ed b

y cD

NA

: gi_

1343

053

9_gb

_AF

360

182.

1_A

F36

0182

2607

72_a

t

479

At2

g11

520

1.8

705

1.0

398

2.1

841

1.2

477

Put

ativ

e pr

otei

n ki

nase

con

tain

s a

prot

ein

kina

se d

omai

n pr

ofile

(P

DO

C00

100)

;su

ppor

ted

by

cDN

A: g

i_13

6058

80_g

b_A

F36

7339

.1_A

F36

7339

2632

74_a

t

480

At3

g19

280

2.5

137

0.7

542.

111

71.

171

Fuc

osyl

tran

sfer

ase,

put

ativ

e si

mila

r to

Fuc

t c3

prot

ein

GB

:CA

B52

254

from

[Vig

nara

diat

a] (

J. B

iol.

Che

m. (

1999

) 27

4 (3

1), 2

183

0-21

839

)25

7031

_at

481

At1

g63

720

1.6

305

1.0

188

2.1

407

1.4

256

Hyp

oth

etic

al p

rote

in s

imila

r to

put

ativ

e pr

otei

n G

B:C

AA

1816

4 [A

. tha

liana

];su

ppor

ted

by

cDN

A: g

i_13

8781

44_g

b_A

F37

0335

.1_A

F37

0335

2602

43_a

t

482

At1

g67

520

2.2

213

1.0

972.

120

41.

413

5R

ecep

tor

kina

se, p

utat

ive

sim

ilar

to r

ecep

tor

kina

se 1

GI:9

2944

49 fr

om [A

.th

alia

na]

2642

23_s

_at

483

At4

g10

960

1.8

209

1.0

119

2.1

249

1.4

163

UD

P-g

alac

tose

4-e

pim

eras

e–lik

e pr

otei

n; U

DP

-gal

acto

se 4

-epi

mer

ase,

Cya

mop

sis

tetr

agon

olob

a, A

J00

5082

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

:C

eres

:156

08.

2549

52_a

t

484

At5

g38

240

1.8

239

1.0

130

2.1

273

1.3

179

Rec

epto

r se

rine

/thre

onin

e pr

otei

n ki

nase

–lik

e; r

ecep

tor

seri

ne/th

reon

ine

kina

seP

R5K

, A

. th

alia

na, E

MB

L:A

T48

698

2495

52_s

_at

485

At3

g19

010

2.0

3081

1.0

1543

2.1

3198

1.1

1739

Hyp

oth

etic

al p

rote

in c

onta

ins

sim

ilarit

y to

fla

von

ol s

ynth

ase

(FLS

) G

B:Q

4145

2fr

om [S

olan

um tu

bero

sum

], co

ntai

ns P

fam

pro

file:

PF

0067

1 Ir

on/A

scor

bate

oxi

dore

duct

ase

fam

ily; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:4

1506

.25

6922

_at

486

At1

g67

800

1.6

417

1.0

257

2.1

530

1.0

269

F12

A21

.7 h

ypot

hetic

al p

rote

in; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:345

52.

2451

97_a

t

487

At2

g35

940

1.5

735

1.0

477

2.1

987

1.2

565

Put

ativ

e ho

meo

dom

ain

tran

scri

ptio

n fa

ctor

; sup

port

ed b

y cD

NA

:gi

_138

7751

6_gb

_AF

353

094.

1_A

F35

3094

2639

56_a

t

488

At5

g06

320

1.5

5322

1.0

3488

2.1

7229

1.0

3597

Har

pin-

indu

ced

prot

ein-

like;

sup

port

ed b

y cD

NA

:gi

_950

2175

_gb_

AF

2646

99.1

_A

F26

469

925

0676

_at

489

At4

g14

400

2.0

5752

1.0

2885

2.1

6003

1.4

3968

Hyp

oth

etic

al p

rote

in; s

uppo

rted

by

cDN

A: g

i_15

8102

32_

gb_A

Y05

6155

.1_

2452

65_a

t

490

At3

g11

820

1.8

1089

1.0

608

2.1

1255

1.4

876

Put

ativ

e sy

nta

xin

con

tain

s P

fam

pro

file:

PF

0080

4 s

ynta

xin;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:3

8899

.25

8786

_at

491

At5

g55

170

2.0

276

1.0

134

2.1

278

1.6

219

ubiq

uitin

-like

pro

tein

2480

92_a

t

492

At1

g68

570

1.7

842

1.0

504

2.1

1044

1.3

645

pept

ide

tran

spor

ter,

pu

tativ

e si

mila

r to

PE

PT

IDE

TR

AN

SP

OR

TE

R P

TR

2-B

GB

:P46

032

GI:1

1727

04 f

rom

[A. t

halia

na]

2622

81_a

t49

3A

t4g2

326

01.

449

51.

032

62.

168

51.

240

0P

utat

ive

prot

ein;

rec

epto

r pr

otei

n ki

nase

, Ip

omoe

a tr

ifida

2542

47_a

t49

4A

t5g2

376

01.

727

61.

015

92.

135

51.

322

0U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:257

23.

2498

11_a

t

495

At3

g46

440

1.8

1113

1.0

619

2.1

1291

1.2

732

dTD

P-g

luco

se 4

-6-d

ehyd

rata

ses-

like

prot

ein;

dT

DP

-glu

cose

4-6

-deh

ydra

tase

sho

mol

og--

A. t

halia

na,P

IR:S

5828

2; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:319

01.

2525

27_a

t

496

At3

g03

640

1.4

714

1.0

517

2.1

1063

1.1

591

β-G

luco

sida

se id

entic

al to

β-g

luco

sida

se G

B:A

AC

319

62 [

A. t

halia

na];

supp

orte

db

y cD

NA

: gi_

342

093

4_gb

_AF

082

157.

1_A

F08

2157

2591

73_a

t

497

At1

g56

120

2.0

472

1.0

238

2.1

508

1.4

331

Wal

l-ass

ocia

ted

kina

se 2

, put

ativ

e si

mila

r to

rec

epto

r-lik

e se

rine

/thre

onin

e ki

nase

GB

:AA

C5

0043

GI:2

4659

23 fr

om [A

. th

alia

na]

2620

82_s

_at

Page 22: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 22

498

At4

g26

060

1.5

320

0.9

213

2.1

439

0.9

194

Put

ativ

e pr

otei

n; s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

5410

.25

3992

_at

499

At2

g47

470

1.6

4085

1.0

2504

2.1

5147

1.1

2713

Put

ativ

e pr

otei

n di

sulfi

de-i

som

eras

e24

5175

_at

500

At2

g39

710

1.9

552

1.0

281

2.0

603

1.3

380

Unk

now

n pr

otei

n si

mila

r to

GP

224

5012

|gnl

|PID

|e32

7000

|Z97

341

; sup

port

ed

bycD

NA

: gi_

1529

323

0_g

b_A

Y05

104

9.1

_26

7592

_at

501

At1

g70

810

1.7

1094

1.0

625

2.0

1280

1.2

783

Unk

now

n pr

otei

n co

ntai

ns s

imila

rity

to z

inc

finge

r an

d C

2 do

mai

n pr

otei

nG

I:99

5723

8 fr

om [A

. tha

liana

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:233

22.

2623

14_a

t50

2A

t4g2

388

51.

621

41.

013

22.

027

91.

216

2E

xpre

ssed

pro

tein

; sup

por

ted

by

full-

leng

th c

DN

A: C

eres

: 28

506.

2541

90_a

t50

3A

t2g4

551

01.

966

41.

035

12.

073

81.

555

2P

utat

ive

cyto

chro

me

P-4

5026

7500

_s_a

t50

4A

t5g0

736

01.

428

01.

020

22.

042

41.

226

0P

utat

ive

amid

ase

2506

27_a

t50

5A

t4g2

138

02.

193

91.

044

12.

089

81.

461

8R

ecep

tor-

like

seri

ne/th

reon

ine

prot

ein

kina

se A

RK

325

4416

_at

506

At2

g15

390

1.9

294

0.9

153

2.0

318

1.2

198

Unk

now

n pr

otei

n26

3565

_at

507

At1

g51

790

2.0

247

1.0

119

2.0

241

1.6

202

Rec

epto

r pr

otei

n ki

nase

, put

ativ

e co

nta

ins

Pfa

m p

rofil

es: P

F00

069:

Euk

aryo

ticpr

otei

n ki

nase

dom

ain,

mul

tiple

PF

0056

0: le

ucin

e-ri

ch r

epea

t25

6170

_at

508

At2

g17

720

2.0

1185

1.0

599

2.0

1214

1.2

719

Put

ativ

e pr

olyl

4-h

ydro

xyla

se, a

lpha

sub

unit;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

:C

eres

:360

54.

2645

92_a

t50

9A

t1g2

293

01.

134

91.

031

82.

066

30.

931

0U

nkno

wn

prot

ein

loca

tion

of E

ST

gb|

H36

530,

gb|

AA

395

402

, and

gb|

T43

793

2647

72_a

t

510

At1

g52

770

2.4

316

1.0

131

2.0

264

1.4

196

Put

ativ

e no

n-ph

oto

trop

ic h

ypoc

otyl

sim

ilar

to n

on-p

hoto

trop

ic h

ypoc

otyl

3G

B:A

AF

0591

4 fr

om [A

. tha

liana

]26

0146

_at

511

At4

g01

720

2.0

405

1.0

201

2.0

415

1.1

224

Put

ativ

e D

NA

-bin

ding

pro

tein

sim

ilar

to w

ild o

at D

NA

-bin

ding

pro

tein

AB

F2,

Gen

Ban

k ac

cess

ion

num

ber

Z48

431

2555

96_a

t

512

At3

g19

930

1.9

1601

1.0

833

2.0

1686

1.0

877

Mon

osac

char

ide

tran

spor

t pro

tein

, ST

P4

iden

tical

to G

B:S

2500

9 fr

om [A

.th

alia

na];

supp

orte

d b

y cD

NA

: gi

_136

059

05_

gb_

AF

3673

52.

1_A

F36

7352

2579

39_a

t

513

At4

g21

400

1.6

182

1.0

111

2.0

224

1.1

128

Ser

ine/

thre

onin

e pr

otei

n ki

nase

–lik

e pr

otei

n re

cept

or p

rote

in k

inas

e (I

RK

1),

Ipom

oea

trifi

da, g

b:U

209

4825

4409

_at

514

At5

g35

735

1.8

3219

1.0

1830

2.0

3697

1.2

2264

Exp

ress

ed p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 3

245

0.24

9719

_at

515

At2

g37

970

1.3

710

1.0

549

2.0

1136

1.2

673

Unk

now

n pr

otei

n; s

upp

orte

d b

y cD

NA

: gi_

1545

1063

_gb

_AY

0546

12.1

_26

6097

_at

516

At1

g74

210

1.8

905

1.0

499

2.0

1009

1.3

662

Put

ativ

e gl

ycer

opho

spho

dies

ter

phos

phod

iest

eras

e si

mila

r to

gly

cero

phos

phor

yldi

este

r ph

osph

odie

ster

ase

GB

:AA

F1

2f49

from

[Dei

noco

ccus

rad

iodu

rans

];su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:241

82.

2602

54_a

t51

7A

t4g1

165

00.

748

0.9

702.

014

92.

618

5O

smot

in p

recu

rsor

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

379

6.25

4889

_at

518

At5

g52

640

2.3

203

1.0

861.

916

41.

513

0H

eat s

hock

pro

tein

; sup

port

ed b

y cD

NA

: gi

_166

769_

gb_

M62

984

.1_

AT

HH

SP

8324

8332

_at

519

At5

g17

990

2.1

3356

1.0

1589

1.8

3017

1.3

2059

Ant

hran

ilate

pho

sph

orib

osyl

tran

sfer

ase,

chl

orop

last

pre

curs

or (

sp|Q

0216

6);

supp

orte

d b

y cD

NA

: gi_

1545

0851

_gb

_AY

0545

06.1

_25

0014

_at

520

At1

g51

660

2.2

400

1.0

179

1.8

325

1.2

212

MA

P k

inas

e ki

nase

4 (

AT

MK

K4)

; ide

ntic

al to

MA

P k

inas

e ki

nase

4 [A

. th

alia

na];

supp

orte

d b

y cD

NA

: gi_

1326

5419

_gb

_AF

3246

67.2

_AF

3246

6725

6183

_at

521

At5

g36

930

2.1

403

1.0

188

1.8

339

1.5

278

Dis

ease

res

ista

nce

like

prot

ein

TM

V r

esis

tanc

e pr

otei

n N

, Nic

otia

na g

lutin

osa,

PIR

:A5

4810

2496

39_a

t

522

At2

g24

600

2.3

681

1.0

296

1.7

514

1.2

370

Hyp

oth

etic

al p

rote

in p

redi

cted

by

GE

NS

CA

N ;

sup

port

ed b

y cD

NA

:gi

_158

1033

0_gb

_AY

0562

04.1

_26

3800

_at

523

At4

g23

280

2.1

193

1.0

941.

716

01.

211

2S

erin

e /th

reon

ine

kina

se–l

ike

prot

ein;

ser

ine

/thre

onin

e ki

nase

, Bra

ssic

a ol

erac

ea25

4249

_at

524

At4

g16

260

2.3

785

1.0

347

1.6

571

0.7

265

β-1,

3-G

luca

nase

cla

ss I

prec

urso

r; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:317

6.24

5393

_at

525

At1

g18

380

2.1

212

1.0

941.

615

61.

211

3H

ypot

het

ical

pro

tein

sim

ilar

to h

ypot

hetic

al p

rote

in G

B:A

AF

2599

6 G

I:671

4300

from

[A. t

halia

na]

2617

19_a

t52

6A

t1g2

301

02.

193

0.9

431.

672

1.3

57U

nkno

wn

prot

ein

sim

ilar

to B

acill

us s

pore

coa

t pro

tein

, Cot

A, G

B:B

AA

2277

426

4752

_at

527

At1

g47

400

1.6

296

0.9

184

1.2

235

2.4

463

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

2616

84_a

t52

8A

t5g0

525

01.

676

10.

947

61.

258

82.

311

18U

nkno

wn

prot

ein;

sup

por

ted

by

cDN

A: g

i_15

8100

44_g

b_A

Y05

4291

.1_

2508

28_a

t

529

At1

g57

660

0.7

2709

0.9

3191

1.1

3949

0.5

1692

60S

rib

osom

al p

rote

in L

21, p

utat

ive;

sim

ilar

to 6

0S r

ibos

omal

pro

tein

L21

GB

:Q43

291

GI:2

851

508

from

[A. t

halia

na];

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:

2463

79_s

_at

Page 23: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 23

2854

5.

530

At2

g19

830

0.5

328

1.0

665

1.0

635

0.7

464

Cop

ia-l

ike

retr

oele

men

t pol

pol

ypro

tein

; sup

port

ed b

y cD

NA

:gi

_150

2817

6_gb

_AY

0459

11.1

_26

6698

_at

531

At5

g50

310

0.4

296

1.0

560

0.8

478

0.8

460

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to u

nkno

wn

prot

ein

(gb|

AA

F49

898.

1);

supp

orte

d b

y cD

NA

: gi_

1572

4227

_gb

_AF

4120

54.1

_AF

4120

5424

8549

_at

532

At5

g60

840

0.5

188

1.0

381

0.8

354

0.5

189

Put

ativ

e pr

otei

n pr

edic

ted

prot

ein,

Dro

soph

ila m

elan

oga

ster

2475

96_a

t53

3A

t5g0

160

00.

593

81.

019

330.

714

320.

593

5F

erri

tin 1

pre

curs

or; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:110

0.25

1109

_at

534

At5

g44

670

0.4

120

1.0

282

0.7

204

0.8

225

Put

ativ

e pr

otei

n st

rong

sim

ilari

ty to

un

know

n pr

otei

n (p

ir||T

0532

5); s

uppo

rted

by

cDN

A: g

i_13

605

502_

gb_

AF

361

577

.1_A

F3

6157

724

9011

_at

535

At3

g58

120

0.5

268

1.0

509

0.7

365

0.9

453

Put

ativ

e pr

otei

n; b

asic

leuc

ine

zipp

er tr

ansc

ript

ion

activ

ator

sho

ot-f

orm

ing

PK

SF

1--P

aulo

wni

a ka

wa

kam

ii, E

MB

L:A

F04

6934

; sup

port

ed

by

full-

leng

th c

DN

A:

Cer

es:3

4553

.25

1575

_at

536

At5

g33

300

0.6

731.

012

70.

791

0.8

104

Put

ativ

e pr

otei

n; c

hrom

okin

esin

KIF

4--H

omo

sapi

ens,

EM

BL:

AF

1793

08

2466

83_a

t53

7A

t5g3

548

00.

583

1.0

155

0.7

126

0.4

72U

nkno

wn

prot

ein

2497

26_a

t53

8A

t5g2

457

00.

467

61.

016

310.

711

300.

699

0U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:141

953

.24

9750

_at

539

At4

g30

440

0.4

1426

1.0

2889

0.7

2037

0.6

1973

Nuc

leot

ide

suga

r ep

imer

ase-

like

prot

ein;

nuc

leot

ide

suga

r ep

imer

ase-

-Vib

riovu

lnifi

cus,

PID

:g30

9397

5; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:154

741.

2536

31_a

t

540

At3

g07

360

0.5

294

1.0

575

0.7

398

0.8

468

Hyp

oth

etic

al p

rote

in s

imila

r to

hyp

othe

tical

pro

tein

GB

:AA

B7

2157

[A

. th

alia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

132.

2590

12_a

t54

1A

t4g2

327

00.

437

71.

079

00.

759

30.

651

0S

erin

e/th

reon

ine

kina

se; s

erin

e/th

reon

ine

kina

se,

Bra

ssic

a ol

erac

ea25

4248

_at

542

At4

g28

240

0.5

1444

1.0

2662

0.7

1864

0.6

1691

Put

ativ

e w

ound

indu

ced

prot

ein;

wo

und-

indu

ced

prot

ein-

-tom

ato

(fra

gmen

t),

PIR

2:S

1977

3; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:201

61.

2538

12_a

t

543

At2

g01

850

0.5

1111

1.0

2242

0.7

1548

0.8

1803

Put

ativ

e xy

logl

ucan

-spe

cific

glu

cana

se id

entic

al to

GB

:D63

509;

su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:188

76.

2635

98_a

t54

4A

t5g5

865

00.

513

51.

026

90.

718

20.

923

5P

utat

ive

prot

ein;

sup

port

ed

by

cDN

A: g

i_15

529

263_

gb_

AY

0522

56.

1_24

7793

_at

545

At2

g28

190

0.8

4736

1.0

5613

0.7

3897

0.4

2150

Put

ativ

e co

ppe

r/zi

nc s

uper

oxi

de d

ism

utas

e id

entic

al to

GP

:327

3753

:AF

061

519;

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:3

979

6.26

6165

_at

546

At4

g35

470

0.5

641

1.0

1285

0.7

867

1.0

1240

Put

ativ

e pr

otei

n le

ucin

e-ri

ch p

rote

in--

Hel

iant

hus

annu

us (

com

mon

sunf

low

er),

PIR

:T12

704

2531

36_a

t54

7A

t5g6

564

00.

314

01.

037

90.

726

00.

726

2U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:132

67.

2471

51_a

t

548

At1

g73

330

0.3

183

0.9

538

0.6

398

0.6

347

Dr4

(pr

otea

se in

hibi

tor)

iden

tical

to D

r4 G

I:469

114

from

[A.

thal

iana

]; su

ppor

ted

by

cDN

A: g

i_13

877

842_

gb_

AF

370

184

.1_A

F3

7018

424

5736

_at

549

At3

g62

700

0.6

1228

1.0

1980

0.6

1394

0.7

1524

AB

C tr

ansp

orte

r-lik

e pr

otei

n; g

luta

thio

ne-c

onju

gate

tran

spor

ter

AtM

RP

4--A

.th

alia

na, E

MB

L:A

J00

2584

2512

27_a

t

550

At3

g54

260

0.5

304

1.0

565

0.6

370

0.9

538

Put

ativ

e pr

otei

n; v

ario

us p

redi

cted

pro

tein

s, A

. tha

liana

; sup

port

ed

by

cDN

A:

gi_1

5451

107_

gb_A

Y05

4634

.1_

2518

86_a

t

551

At1

g04

240

0.6

229

0.9

392

0.6

262

0.7

276

Put

ativ

e au

xin-

indu

ced

prot

ein

AU

X2-

11.

Ma

tch

to A

rabi

dops

is IA

A3

(gb|

U18

406)

.E

ST

gb|

T04

296

com

es fr

om th

is g

ene;

sup

port

ed b

y cD

NA

:gi

_972

910_

gb_U

184

06.1

_AT

U18

406

2636

56_a

t55

2A

t1g1

672

00.

518

091.

037

540.

623

570.

727

24U

nkno

wn

prot

ein

2557

64_a

t

553

At3

g61

890

0.5

941.

020

00.

612

40.

817

7H

omeo

box-

leuc

ine

zipp

er p

rote

in A

TH

B-1

2; s

uppo

rted

by

full-

leng

th c

DN

A:

Cer

es:3

2615

.25

1272

_at

554

At1

g21

920

0.5

1050

1.0

2110

0.6

1315

0.7

1541

Pho

spha

tidyl

inos

itol-

4-ph

osph

ate

5-ki

nase

, put

ativ

e si

mila

r to

phos

phat

idyl

inos

itol-

4-ph

osph

ate

5-ki

nase

GB

:CA

B53

377

GI:5

7773

66

from

[A.

thal

iana

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:37

462.

2608

55_a

t55

5A

t3g5

732

00.

516

31.

033

30.

619

90.

725

0H

ypot

het

ical

pro

tein

2516

76_a

t55

6m

itoch

ondr

ia.1

0.7

300

1.0

418

0.6

247

0.5

200

AT

P s

ynth

ase

subu

nit 9

2573

39_s

_at

557

At2

g21

650

1.1

487

1.0

459

0.6

276

0.5

237

Unk

now

n pr

otei

n26

3549

_at

Page 24: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 24

558

At4

g20

070

0.5

172

1.0

375

0.6

220

0.7

282

hyu

C-l

ike

prot

ein

5-su

bstit

uted

hyd

anto

ins

to th

e co

rres

pond

ing

L-am

ino

acid

s,P

seud

omo

nas

sp.,P

IR2:

D42

594

2544

96_a

t55

9A

t2g3

945

00.

556

01.

011

010.

664

70.

776

9U

nkno

wn

prot

ein

2669

63_a

t56

0A

t2g4

408

00.

524

31.

048

60.

628

20.

736

8U

nkno

wn

prot

ein

2672

30_a

t

561

At5

g49

450

0.5

149

1.0

280

0.6

172

0.9

246

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to b

ZIP

tran

scri

ptio

n fa

ctor

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:4

3004

.24

8606

_at

562

At1

g29

500

0.5

178

1.0

388

0.6

221

1.0

395

Au

xin-

indu

ced

prot

ein,

put

ativ

e s

imila

r to

SP

:P33

083

from

[Gly

cine

max

]25

9773

_at

563

At1

g12

520

0.6

373

1.0

589

0.6

334

0.5

293

Unk

now

n pr

otei

n co

ntai

ns s

imila

rity

to c

oppe

r zi

nc s

uper

oxi

de d

ism

utas

eG

I:56

8961

1 fr

om (

A. t

halia

na);

sup

port

ed b

y cD

NA

:gi

_152

1565

7_gb

_AY

0503

57.1

_25

9511

_at

564

At4

g10

770

0.5

462

1.0

975

0.6

549

0.8

788

Put

ativ

e ol

igop

eptid

e tr

ansp

orte

r si

mila

r to

C. a

lbic

ans

Opt

1, G

enB

ank

acce

ssio

nnu

mbe

r U

6097

3 fu

nctio

nal c

atal

og ID

=07

.99

; sup

port

ed b

y cD

NA

:gi

_150

1073

3_gb

_AY

0456

68.1

_25

4938

_at

565

At5

g35

970

0.5

2290

1.0

4555

0.6

2554

0.7

3096

DN

A h

elic

ase-

like

2496

77_a

t

566

At1

g52

190

0.5

1547

1.0

3365

0.6

1910

0.7

2439

Pep

tide

tran

spor

ter,

put

ativ

e si

mila

r to

pep

tide

tran

spor

ter

PT

R2-

B S

P:P

4603

2 [A

.th

alia

na (

mou

se-e

ar c

ress

)]; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

: 113

723

and

gi:1

6648

852

2598

39_a

t56

7A

t2g3

622

00.

521

41.

044

10.

624

40.

629

1U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:122

51.

2639

31_a

t

568

At4

g30

020

0.4

855

1.0

1764

0.6

969

0.8

1399

ES

T G

B:N

3737

7 sp

ans

last

intr

on a

nd 3

end

of g

ene

con

tain

s si

mila

rity

to m

eiot

icse

rine

pro

tein

ase

TM

P G

I:646

8325

from

[Lyc

oper

sico

n es

cule

ntum

]25

3650

_at

569

At1

g20

440

0.5

1779

1.0

3810

0.5

2048

0.6

2168

Hyp

oth

etic

al p

rote

in25

9570

_at

570

At5

g18

060

0.5

240

1.0

497

0.5

267

0.8

412

Au

xin-

indu

ced

prot

ein-

like

2500

12_

x_at

571

At1

g78

070

0.4

370

1.0

973

0.5

527

0.6

596

Unk

now

n pr

otei

n; s

upp

orte

d b

y cD

NA

: gi_

1393

7194

_gb

_AF

3729

51.1

_AF

3729

5126

2164

_at

572

At1

g68

190

0.5

349

1.0

737

0.5

395

0.7

507

Put

ativ

e zi

nc fi

nger

pro

tein

sim

ilar

to z

inc

finge

r pr

otei

n G

B:B

AA

3320

6 fr

om[O

ryza

sat

iva]

2604

31_a

t57

3A

t5g5

908

00.

558

71.

011

430.

560

40.

779

6P

utat

ive

prot

ein

2477

54_a

t

574

At4

g38

690

0.5

323

1.0

668

0.5

348

0.7

458

Put

ativ

e pr

otei

n ph

osph

olip

ase

C (

EC

3.1

.4.3

) pr

ecur

sor,

phos

phat

idyl

inos

itol-

spec

ific-

-Lis

teria

mon

ocyt

ogen

es, P

IR2:

A3

7204

2529

50_a

t

575

At1

g29

510

0.4

302

1.0

676

0.5

348

0.8

573

Au

xin-

indu

ced

prot

ein,

put

ativ

e s

imila

r to

SP

:P33

083

from

[Gly

cine

max

];su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:931

1.25

9783

_at

576

At2

g05

540

0.4

381

1.0

865

0.5

447

0.4

382

Put

ativ

e gl

ycin

e-ri

ch p

rote

in; s

uppo

rted

by

cDN

A:

gi_1

5215

617_

gb_A

Y05

0337

.1_

2655

11_a

t

577

At5

g01

520

0.4

226

1.0

542

0.5

277

0.8

414

Put

ativ

e pr

otei

n pu

tativ

e pr

otei

ns--

A. t

halia

na; s

upp

orte

d b

y cD

NA

:gi

_152

9280

2_gb

_AY

0508

35.1

_25

1084

_at

578

At2

g27

060

0.4

324

1.0

722

0.5

367

0.7

510

Put

ativ

e re

cep

tor-

like

prot

ein

kina

se26

6303

_at

579

At5

g45

840

0.7

107

1.0

157

0.5

820.

610

3R

ecep

tor

prot

ein

kina

se-l

ike

prot

ein

pred

icte

d b

y G

ene

Mar

k.hm

m a

nd G

EN

SC

AN

+24

8916

_at

580

At2

g43

535

0.7

371

1.0

537

0.5

273

0.7

400

Exp

ress

ed p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 9

170

4.26

0549

_at

581

At2

g34

620

0.7

1030

1.0

1562

0.5

783

0.8

1279

Hyp

oth

etic

al p

rote

in p

redi

cted

by

gen

efin

der

2668

99_a

t58

2A

t5g2

535

00.

459

01.

013

820.

568

80.

810

87le

ucin

e-ric

h re

peat

s co

ntai

ning

pro

tein

grr

1--G

lyci

ne m

ax. E

MB

L:A

F01

9910

2469

35_a

t58

3A

t1g7

488

00.

688

51.

013

820.

573

80.

811

73U

nkno

wn

prot

ein;

sup

por

ted

by

cDN

A: g

i_15

2941

95_g

b_A

F41

0289

.1_A

F41

0289

2621

75_a

t

584

At5

g44

130

0.7

1492

1.0

2017

0.5

1030

0.7

1433

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to s

urfa

ce p

rote

in; s

uppo

rted

by

cDN

A:

gi_1

6648

846_

gb_A

Y05

8201

.1_

2490

37_a

t58

5A

t1g6

952

30.

726

71.

039

50.

519

60.

833

6E

xpre

ssed

pro

tein

; sup

por

ted

by

cDN

A:

gi_1

5450

408_

gb_

AY

052

305.

1_

2563

04_a

t

586

At1

g14

700

0.7

312

1.0

450

0.5

237

0.9

407

Pur

ple

acid

pho

spha

tase

, put

ativ

e co

nta

ins

Pfa

m p

rofil

e: P

F02

227

Pur

ple

acid

phos

phat

ase

2628

30_a

t58

7A

t1g6

618

00.

742

21.

057

80.

533

50.

849

1U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:996

25.

2565

25_a

t

588

At5

g48

490

0.4

1550

1.0

4121

0.5

2041

0.8

3350

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (p

ir||S

7253

0); s

uppo

rted

by

full-

leng

thcD

NA

: Cer

es:3

2925

.24

8683

_at

589

At1

g32

520

0.4

190

1.0

410

0.5

216

0.8

326

Unk

now

n pr

otei

n26

0696

_at

Page 25: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 25

590

At1

g68

840

0.4

813

0.9

1686

0.5

888

0.7

1246

Put

ativ

e D

NA

-bin

ding

pro

tein

(R

AV

2-lik

e) id

entic

al to

res

idue

s 34

-352

of R

AV

2G

B:B

AA

3425

1 (A

. th

alia

na);

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

9561

.26

0037

_at

591

At4

g13

800

0.8

235

1.0

303

0.5

153

0.8

258

Hyp

oth

etic

al p

rote

in; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:405

89.

2546

83_a

t59

2A

t5g4

973

00.

548

831.

097

200.

548

710.

882

28F

RO

2-lik

e pr

otei

n; N

AD

PH

oxi

das

e-lik

e24

8566

_s_a

t

593

At1

g51

090

0.5

260

1.0

488

0.5

244

0.8

404

prol

ine-

rich

prot

ein,

put

ativ

e si

mila

r to

pro

line-

rich

prot

ein

GI:3

2420

79 fr

om[C

apsi

cum

ann

uum

]; su

ppor

ted

by

cDN

A: g

i_14

3348

47_

gb_

AY

0350

97.1

_24

5749

_at

594

At5

g62

430

0.5

282

1.0

551

0.5

287

1.0

538

H-p

rote

in p

rom

oter

bin

ding

fact

or-l

ike

prot

ein

2474

52_a

t59

5A

t5g6

539

00.

534

81.

065

00.

532

70.

748

2U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:108

595

.24

7189

_at

596

At5

g67

390

0.6

166

1.0

293

0.5

146

0.9

273

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (g

b|A

AF

6776

6.1)

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:5

12.

2469

97_a

t

597

At1

g66

100

0.5

2815

1.0

5495

0.5

2689

0.8

4251

Thi

onin

, put

ativ

e si

mila

r to

thio

nin

[A. t

halia

na] G

I:11

8153

3; s

uppo

rted

by

cDN

A:

gi_1

4190

504_

gb_A

F38

065

2.1

_AF

3806

5225

6527

_at

598

At1

g23

080

0.6

807

1.0

1444

0.5

704

0.9

1337

Put

ativ

e au

xin

tra

nspo

rt p

rote

in s

tron

gly

sim

ilar

to a

uxi

n tr

ansp

ort p

rote

inG

B:A

AD

526

97; s

upp

orte

d b

y cD

NA

: gi

_154

505

08_

gb_

AY

0523

56.1

_26

4900

_at

599

At1

g18

330

0.7

711

1.0

1083

0.5

528

0.8

920

Hyp

oth

etic

al p

rote

in s

imila

r to

hyp

othe

tical

pro

tein

GB

:AA

F25

987

GI:6

7142

91fr

om [A

. tha

liana

]26

1663

_at

600

At3

g13

750

0.6

1745

1.0

3126

0.5

1522

0.8

2664

Gal

acto

sida

se, p

utat

ive

sim

ilar

to β

-GA

LAC

TO

SID

AS

E P

RE

CU

RS

OR

(LA

CT

AS

E)

GB

:P4

8980

from

[Lyc

oper

sico

n es

cule

ntum

]25

6772

_at

601

At2

g43

200

0.7

137

1.0

186

0.5

900.

815

1H

ypot

het

ical

pro

tein

pre

dict

ed b

y gr

ail

2664

39_s

_at

602

At5

g48

900

0.6

1021

1.0

1826

0.5

879

0.8

1397

Pec

tate

lyas

e n

on-c

onse

nsus

AG

don

or s

plic

e si

te a

t exo

n 2;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es: 2

131

1.24

8681

_at

603

At5

g02

540

0.6

222

1.0

358

0.5

173

0.8

303

Put

ativ

e pr

otei

n va

riou

s pr

edic

ted

prot

eins

, Bra

ssic

a ra

pa, A

. th

alia

na; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:265

38.

2510

13_a

t60

4A

t4g0

484

00.

611

951.

021

200.

510

320.

612

85P

utat

ive

prot

ein

sim

ilar

to tr

ansc

riptio

nal r

egul

ator

2552

98_a

t

605

At1

g21

910

0.5

113

1.0

223

0.5

107

0.7

159

TIN

Y-l

ike

prot

ein

sim

ilar

to T

INY

GB

:CA

A64

359

GI:1

2464

03 f

rom

[A. t

halia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

972

1.26

0856

_at

606

At3

g19

850

0.5

425

1.0

808

0.5

386

0.8

644

Hyp

oth

etic

al p

rote

in s

imila

r to

hyp

othe

tical

pro

tein

GB

:AA

D50

054

from

[A.

thal

iana

]25

7964

_at

607

At3

g05

640

0.5

186

1.0

356

0.5

169

0.7

250

Put

ativ

e pr

otei

n ph

osph

atas

e-2C

sim

ilar

to p

rote

in p

hosp

hata

se-2

CG

B:A

AC

366

99 fr

om [M

ese

mbr

yant

hem

um c

ryst

allin

um];

supp

orte

d b

y cD

NA

:gi

_152

1571

8_gb

_AY

0503

88.1

_25

8901

_at

608

At5

g65

730

0.5

1182

1.0

2419

0.5

1190

0.7

1692

Xyl

oglu

can

end

o-tr

ansg

lyco

syla

se-l

ike

prot

ein;

sup

port

ed

by

full-

leng

th c

DN

A:

Cer

es:1

2301

.24

7162

_at

609

At2

g25

900

0.4

1509

1.0

3304

0.5

1657

0.6

2109

Put

ativ

e C

CC

H-t

ype

zinc

fing

er p

rote

in id

entic

al to

GB

:U81

238

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:3

9893

.26

6656

_at

610

At5

g44

190

0.6

839

1.0

1514

0.5

719

0.8

1240

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to u

nkno

wn

prot

ein

(gb|

AA

D2

1709

.1);

supp

orte

d b

y cD

NA

: gi_

1521

5714

_gb

_AY

0503

86.1

_24

9035

_at

611

At1

g64

390

0.7

2277

1.0

3060

0.5

1473

0.8

2333

End

o-β-

1,4-

gluc

anas

e, p

utat

ive

sim

ilar

to G

I:497

2236

fro

m [F

raga

ria

x an

anas

sa]

(Pla

nt M

ol. B

iol.

40, 3

23-

332

(199

9));

sup

port

ed b

y cD

NA

:gi

_139

3717

2_gb

_AF

372

940.

1_A

F37

2940

2597

36_a

t61

2A

t1g2

374

00.

621

041.

033

850.

515

871.

032

91P

utat

ive

auxi

n-in

duce

d pr

otei

n; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:155

143.

2651

82_a

t61

3A

t3g6

108

00.

665

01.

011

540.

554

70.

910

68P

utat

ive

prot

ein

hyp

oth

etic

al p

rote

in--

Syn

echo

cyst

is s

p., P

IR:S

767

9025

1353

_at

614

At4

g32

770

0.5

293

1.0

555

0.5

263

0.7

409

Put

ativ

e pr

otei

n pr

edic

ted

prot

ein,

Syn

echo

cyst

is s

p., P

IR2:

S7

4814

; sup

port

ed b

ycD

NA

: gi_

1433

401

1_g

b_A

F3

0218

8.1

_AF

302

188

2533

94_a

t

615

At1

g25

230

0.6

623

1.0

1129

0.5

544

0.9

1021

Hyp

oth

etic

al p

rote

in s

imila

r to

put

ativ

e pu

rple

aci

d ph

osph

atas

e pr

ecur

sor

GI:7

331

195

from

[Gly

cine

max

]24

5637

_at

616

At5

g02

230

0.5

166

1.0

305

0.5

147

1.0

306

Put

ativ

e pr

otei

n pu

tativ

e h

ydro

lase

At2

g321

50-

-A. t

halia

na, E

MB

L:A

C0

0622

3;su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:367

24.

2510

28_a

t

Page 26: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 26

617

At4

g25

480

0.5

234

1.0

445

0.5

219

0.7

326

tran

scri

ptio

nal a

ctiv

ator

CB

F1-

like

prot

ein

stro

ng s

imila

rity

to t

rans

crip

tiona

lac

tivat

or C

BF

1, A

. tha

liana

0025

4066

_at

618

ndhG

0.5

851

1.0

1540

0.5

721

0.7

1054

NA

DH

deh

ydro

gen

ase

ND

624

4934

_at

619

At5

g60

860

0.4

243

1.0

561

0.5

260

0.6

345

GT

P-b

indi

ng p

rote

in–l

ike;

GT

P-b

indi

ng p

rote

in, g

arde

n p

ea,

PIR

:T06

447

2475

97_a

t62

0A

t2g4

061

00.

523

451.

044

380.

520

400.

732

68P

utat

ive

exp

ansi

n; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:27

553.

2558

22_a

t

621

At5

g16

030

0.6

2438

1.0

4049

0.5

1866

0.9

3512

Put

ativ

e pr

otei

n w

ith p

oly

glut

amic

aci

d st

retc

h hy

poth

etic

al p

rote

in F

16B

3.1

3--A

.th

alia

na, E

MB

L:A

C02

164

0; s

uppo

rte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 2

974

5.24

6487

_at

622

At3

g15

450

0.4

3147

1.0

7892

0.5

3882

0.6

5118

Unk

now

n pr

otei

n ve

ry s

imila

r to

unk

now

n pr

otei

n G

B:A

AC

394

68 f

rom

[A.

thal

iana

]; su

ppor

ted

by

cDN

A:

gi_1

433

5087

_gb

_A

Y03

7223

.1_

2584

02_a

t

623

At1

g70

610

0.5

378

1.0

713

0.5

327

0.8

579

Put

ativ

e A

BC

tran

spor

ter

cont

ains

Pfa

m p

rofil

e: P

F00

005

AB

C tr

ansp

orte

rs;

sim

ilar

to T

AP

1 pr

otei

n (t

rans

port

er o

f pro

cess

ed a

ntig

en)

GB

:AA

D53

033

(Onc

orhy

nchu

s m

ykis

s)26

0308

_at

624

At3

g47

340

0.4

194

1.0

554

0.5

252

0.6

334

Glu

tam

ine-

depe

nden

t as

para

gine

syn

thet

ase;

sup

por

ted

by

cDN

A:

gi_1

6930

406_

gb_A

F41

955

7.1

_AF

4195

5725

2415

_at

625

At5

g41

140

0.5

162

1.0

300

0.5

137

0.6

209

Put

ativ

e pr

otei

n co

ntai

ns s

imila

rity

to m

yosi

n he

avy

cha

in24

9340

_at

626

At3

g61

060

0.4

578

1.0

1420

0.5

659

0.7

1011

Put

ativ

e pr

otei

n h

ypot

het

ical

pro

tein

s--A

. tha

liana

; sup

port

ed b

y cD

NA

:gi

_143

3458

7_gb

_AY

0349

67.1

_25

1356

_at

627

At1

g79

460

0.7

292

1.0

416

0.4

191

0.8

351

ent-

Kau

ren

e sy

nth

ase,

put

ativ

e si

mila

r to

ent

-kau

rene

syn

thas

e G

I:30

5672

5 fr

om[A

. tha

liana

]; su

ppor

ted

by

cDN

A:

gi_3

0567

24_g

b_A

F03

4774

.1_A

F03

4774

2628

91_a

t62

8A

t4g1

566

00.

627

91.

042

70.

419

50.

833

7gl

utar

edo

xin

2455

04_a

t

629

At5

g39

610

0.3

831.

023

60.

410

40.

922

1

NA

M/U

C2–

like

prot

ein;

CU

C2,

A. t

halia

na,

EM

BL:

AT

AB

2560

; sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:113

779.

2494

67_a

t63

0A

t1g1

862

00.

551

71.

010

270.

446

00.

988

7U

nkno

wn

prot

ein

2557

74_a

t

631

At5

g55

620

0.6

2071

1.0

3223

0.4

1487

1.0

3353

Put

ativ

e pr

otei

n si

mila

r to

unk

now

n pr

otei

n (g

b|A

AF

0442

8.1)

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:2

7668

.24

8028

_at

632

At3

g57

040

0.5

361

1.0

676

0.4

299

0.6

441

Res

pons

e re

acto

r 4;

sup

port

ed b

y cD

NA

:gi

_327

3201

_dbj

_AB

010

918.

1_A

B01

0918

2516

65_a

t

633

At3

g16

770

0.5

3338

1.0

6852

0.4

3232

0.7

4668

AP

2 d

omai

n co

ntai

ning

pro

tein

RA

P2

.3 id

entic

al to

GB

:AA

C49

769

from

[A.

thal

iana

]; su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:35

981.

2584

34_a

t63

4A

t2g3

812

00.

513

471.

025

410.

411

090.

820

15U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:315

86.

2670

92_a

t

635

At1

g19

450

0.6

1738

1.0

2715

0.4

1144

0.9

2388

Inte

gral

mem

bran

e pr

otei

n, p

utat

ive

sim

ilar

to G

B:U

4362

9 fr

om [B

eta

vulg

aris

][P

lant

Phy

siol

. 110

(2)

, 511

-52

0 (1

996)

]; su

ppor

ted

by

cDN

A:

gi_1

6648

956_

gb_A

Y05

9848

.1_

2606

76_a

t63

6A

t5g0

698

00.

537

21.

081

50.

433

80.

760

7U

nkno

wn

prot

ein;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:262

293

.25

0665

_at

637

At2

g37

640

0.5

581

1.0

1117

0.4

476

0.8

931

Put

ativ

e e

xpan

sin

2671

58_a

t

638

At5

g12

050

0.4

241

1.0

597

0.4

245

0.7

425

Put

ativ

e se

rine

ric

h pr

otei

n pr

edic

ted

prot

eins

, A. t

hal

iana

; sup

port

ed b

y fu

ll-le

ngth

cDN

A: C

eres

:369

58.

2503

27_a

t63

9A

t4g3

366

60.

410

931.

025

870.

410

870.

718

14E

xpre

ssed

pro

tein

; sup

por

ted

by

full-

leng

th c

DN

A: C

eres

: 38

416.

2533

05_a

t

640

At1

g71

030

0.4

2336

1.0

5242

0.4

2210

0.6

3326

Put

ativ

e tr

ansc

ript

ion

fact

or s

imila

r to

Myb

-rel

ated

tra

nscr

iptio

n fa

ctor

24

GB

:S71

287

; sup

port

ed

by

full-

leng

th c

DN

A: C

eres

:315

92.

2597

51_a

t

641

At4

g15

550

0.4

201

1.0

463

0.4

196

0.7

330

Glu

cosy

ltran

sfer

ase

like

prot

ein;

sup

port

ed b

y cD

NA

:gi

_214

9126

_gb_

U81

293

.1_A

TU

8129

324

5277

_at

642

At4

g03

550

1.1

941

1.0

818

0.4

334

0.3

294

Put

ativ

e gl

ucan

syn

thas

e co

mpo

nent

sim

ilar

to 1

,3-β

-glu

can

synt

hase

2553

78_a

t

643

At2

g31

380

0.6

484

1.0

781

0.4

321

0.9

691

Put

ativ

e C

ON

ST

AN

S-l

ike

B-b

ox

zinc

fing

er p

rote

in; s

uppo

rted

by

cDN

A:

gi_1

2698

721_

gb_A

F32

366

6.1

_AF

3236

6626

3252

_at

644

At5

g58

310

0.8

165

1.0

213

0.4

891.

123

8P

olyn

euri

dine

ald

ehyd

e es

tera

se-l

ike;

als

o si

mila

r to

alp

ha-h

ydro

xyni

trile

lyas

e;su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:123

228

.24

7814

_at

645

At2

g46

790

0.3

941.

028

90.

412

10.

721

5H

ypot

het

ical

pro

tein

pre

dict

ed b

y ge

nef

inde

r; s

uppo

rte

d b

y cD

NA

:gi

_102

8099

9_db

j_A

B04

6953

.1_A

B04

695

326

6720

_s_a

t

Page 27: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 27

646

At4

g24

340

0.8

1043

1.0

1226

0.4

518

1.0

1187

Put

ativ

e pr

otei

n st

orag

e pr

otei

n--P

opul

us d

elto

ides

, PIR

2:S

3158

0; s

uppo

rte

d by

full-

leng

th c

DN

A: C

eres

:877

2.25

4163

_s_a

t64

7A

t3g0

590

00.

525

51.

055

50.

422

90.

845

1U

nkno

wn

prot

ein

2587

36_a

t

648

At5

g25

190

0.3

192

1.0

584

0.4

235

0.5

313

Eth

ylen

e-re

spon

sive

ele

men

t–lik

e pr

otei

n; e

thyl

ene

-res

pons

ive

elem

ent b

indi

ngpr

otei

n ho

mol

og, S

tylo

sant

hes

ham

ata,

EM

BL:

U91

857;

sup

port

ed b

y cD

NA

:gi

_150

1071

5_gb

_AY

0456

59.1

_24

6932

_at

649

At1

g04

250

0.5

502

1.0

1012

0.4

409

0.7

769

Put

ativ

e au

xin-

indu

ced

prot

ein,

IAA

17/A

XR

3-1.

Ide

ntic

al to

Ara

bido

psis

gb|A

F04

063

2 an

d gb

|U49

073

IAA

17/A

XR

3 g

ene

. ES

Ts

gb|H

3678

2 an

dgb

|F14

074

com

e fr

om th

is g

ene;

sup

port

ed b

y fu

ll-le

ngth

cD

NA

: Cer

es:3

361

3.26

3664

_at

650

At1

g10

370

0.5

348

1.0

723

0.4

287

0.8

609

Put

ativ

e gl

utat

hion

e S

-tra

nsfe

rase

TS

I-1

sim

ilar

to g

luta

thio

ne S

-tra

nsfe

rase

TS

I-1

(gi|2

1909

92);

sim

ilar

to E

ST

s gb

|R29

860,

em

b|Z

2975

7, a

nd e

mb|

Z29

758;

supp

orte

d b

y cD

NA

: gi_

1109

6015

_gb

_AF

2881

91.1

_AF

2881

9126

4436

_at

651

At4

g12

980

0.5

1372

1.0

3003

0.4

1187

0.6

1975

Put

ativ

e pr

otei

n h

ypot

het

ical

pro

tein

--A

. tha

liana

,PIR

2:H

7144

1; s

uppo

rted

by

full-

leng

th c

DN

A: C

eres

:464

2.25

4746

_at

652

At3

g23

080

0.6

1031

1.0

1635

0.4

681

0.7

1165

Unk

now

n pr

otei

n C

-ter

m s

imila

r to

pho

spha

tidyl

chol

ine

tran

sfer

pro

tein

GB

:AA

F08

345

[Hom

o sa

pien

s]; s

uppo

rte

d b

y cD

NA

:gi

_158

1025

6_gb

_AY

0561

67.1

_25

7772

_at

653

At1

g29

395

0.4

1312

1.0

3182

0.4

1280

0.6

1848

Exp

ress

ed p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 3

060

2.25

9789

_at

654

At3

g45

970

0.2

651.

028

80.

411

80.

413

5

Put

ativ

e pr

otei

n; c

im1

indu

ced

alle

rgen

, Gly

cine

max

, EM

BL:

U03

860;

sup

por

ted

by

full-

leng

th c

DN

A: C

eres

:275

34.

2525

63_a

t

655

At5

g39

860

0.4

165

1.0

418

0.4

163

0.6

272

Put

ativ

e pr

otei

n; p

utat

ive

DN

A-b

indi

ng p

rote

in--

A. t

halia

na,

EM

BL:

AC

011

765

;su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:473

4.24

9383

_at

656

At2

g26

020

0.8

2049

0.9

2172

0.4

876

0.4

922

Put

ativ

e an

tifun

gal p

rote

in25

7365

_x_

at

657

At2

g40

670

0.5

268

1.0

542

0.4

212

0.7

405

Put

ativ

e tw

o-co

mpo

nent

res

pons

e re

gula

tor

prot

ein;

sup

port

ed b

y cD

NA

:gi

_118

7006

7_gb

_AF

305

721.

1_A

F30

5721

2660

78_a

t

658

At4

g32

280

0.3

175

1.0

520

0.4

205

0.6

324

Exp

ress

ed p

rote

in; s

upp

orte

d b

y cD

NA

:gi

_141

9049

2_gb

_AF

380

646.

1_A

F38

0646

2534

23_a

t

659

At1

g74

670

0.5

2551

1.0

5261

0.4

2081

0.7

3826

GA

ST

1-lik

e pr

otei

n si

mila

r to

GA

ST

1 pr

otei

n pr

ecur

sor

GB

:P27

057

[Lyc

oper

sico

nes

cule

ntum

] (in

duce

d b

y gi

bber

ellin

s, in

hibi

ted

by A

BA

[P

lant

J.

Mar

; 2(2

):15

3-9

(199

2)]

2602

21_a

t66

0A

t3g6

029

00.

421

91.

050

60.

420

60.

736

5S

RG

1-lik

e pr

otei

n; S

RG

1 pr

otei

n, A

. tha

liana

, P

IR:S

4426

125

1402

_at

661

At1

g73

830

0.3

150

1.0

447

0.4

176

0.6

276

Put

ativ

e he

lix-l

oop-

helix

DN

A-b

indi

ng p

rote

in c

onta

ins

Pfa

m p

rofil

e: P

F00

010

Hel

ix-l

oop-

helix

DN

A-b

indi

ng d

omai

n26

0070

_at

662

At1

g06

080

0.4

172

1.0

428

0.4

166

0.6

279

Del

ta 9

des

atur

ase;

iden

tical

to d

elta

9 d

esat

uras

e G

B:B

AA

251

80 G

I:297

0034

from

[A. t

halia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 1

0052

5.26

0957

_at

663

At3

g28

220

0.4

310

1.0

822

0.4

324

0.7

603

Unk

now

n pr

otei

n25

6577

_at

664

At1

g20

070

0.6

332

1.0

588

0.4

224

0.7

425

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

2612

47_a

t66

5A

t2g1

583

00.

310

11.

035

10.

417

40.

620

9U

nkno

wn

prot

ein

2655

39_a

t66

6A

t2g2

929

00.

411

171.

025

070.

491

70.

821

33P

utat

ive

trop

inon

e re

duc

tase

2662

79_a

t

667

At5

g02

760

0.2

436

1.0

1867

0.4

677

0.7

1255

Pro

tein

pho

spha

tase

–lik

e pr

otei

n; p

rote

in p

hosp

hata

se 2

C h

omol

og,

Mes

embr

yant

hem

um c

ryst

allin

um, E

MB

L:A

F09

7667

2510

17_a

t66

8A

t3g4

916

00.

364

1.0

186

0.4

710.

364

Pyr

uva

te k

inas

e–lik

e pr

otei

n; v

ario

us p

yru

vate

kin

ases

from

pro

cary

otes

2523

00_a

t66

9A

t5g4

442

01.

120

830.

817

880.

462

80.

595

0A

ntifu

ngal

pro

tein

-lik

e (P

DF

1.2)

2490

52_a

t

670

At1

g53

870

0.5

469

1.0

1019

0.3

360

0.7

716

Hyp

oth

etic

al p

rote

in p

redi

cted

by

Gen

eM

ark.

hmm

; sup

port

ed b

y fu

ll-le

ngth

cD

NA

:C

eres

:109

4.26

2259

_s_a

t67

1A

t4g2

329

00.

553

31.

010

780.

337

30.

994

4S

erin

e/th

reon

ine

kina

se–l

ike

prot

ein;

ser

ine/

thre

onin

e ki

nase

, Bra

ssic

a ol

erac

eae

2542

50_a

t

672

At4

g23

600

0.6

1152

1.0

1940

0.3

665

0.8

1641

Tyr

osin

e tr

ansa

min

ase

like

prot

ein;

tyr

osin

e tr

ansa

min

ase

(EC

2.6

.1.5

)--r

at,

EM

BL

:X02

741;

sup

por

ted

by

cDN

A:

gi_1

5076

852_

gb_

AF

268

090

.1_A

F2

6809

025

4232

_at

673

At3

g30

720

0.4

157

1.0

349

0.3

119

0.4

130

Unk

now

n pr

otei

n25

6940

_at

Page 28: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Scie

nce

Supp

ortin

g O

nlin

e M

ater

ial

doi 1

0.11

26/s

cien

ce.1

0867

16, p

. 28

674

At5

g51

720

0.5

1403

1.0

2793

0.3

906

0.4

1182

Unk

now

n pr

otei

n; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 2

6674

4.24

8377

_at

675

At5

g57

340

0.2

156

1.0

619

0.3

197

0.6

401

Unk

now

n pr

otei

n; s

upp

orte

d b

y cD

NA

: gi_

1622

6274

_gb

_AF

4282

89.1

_AF

4282

8924

7903

_at

676

At5

g45

820

0.5

1070

1.0

1998

0.3

627

0.8

1650

Ser

ine

thre

onin

e pr

otei

n ki

nase

; sup

port

ed

by

cDN

A:

gi_1

4486

383_

gb_A

Y03

5225

.1_

2489

10_a

t

677

At1

g14

280

0.5

477

1.0

1055

0.3

342

0.8

878

Ph

ytoc

hrom

e ki

nase

sub

stra

te 1

, put

ativ

e si

mila

r to

ph

ytoc

hrom

e ki

nase

sub

stra

te1

GI:5

0201

68 fr

om [A

. th

alia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:9

7569

.26

1480

_at

678

At3

g21

670

0.3

559

1.0

1639

0.3

529

0.7

1233

Nitr

ate

tran

spor

ter

iden

tical

to n

itrat

e tr

ansp

orte

r G

B:C

AB

387

06 [

A. t

hal

iana

];su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:111

089

.25

8181

_at

679

At2

g42

540

0.3

1034

1.0

3068

0.3

907

0.6

1783

Col

d-re

gula

ted

prot

ein;

cor

15a

prec

urso

r; s

uppo

rted

by

cDN

A:

gi_1

4532

457_

gb_A

Y03

9853

.1_

2634

97_a

t

680

At5

g62

920

0.5

198

1.0

410

0.3

120

0.5

217

Res

pons

e re

gula

tor

6 (A

RR

6); s

uppo

rted

by

cDN

A:

gi_3

9536

00_d

bj_A

B00

848

9.1

_AB

0084

8924

7406

_at

681

At1

g13

650

0.5

490

1.0

1021

0.3

284

0.5

523

Unk

now

n pr

otei

n25

6096

_at

682

At5

g50

335

0.2

561.

032

40.

270

0.4

158

Exp

ress

ed p

rote

in; s

upp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es: 1

552

7.24

8509

_at

683

At1

g20

190

0.3

757

1.0

2638

0.2

551

0.5

1257

Exp

ans

in S

2 pr

ecur

sor,

put

ativ

e si

mila

r to

GB

:U30

460

from

[Cuc

umis

sat

ivus

];su

ppor

ted

by

full-

leng

th c

DN

A: C

eres

:110

11.

2612

26_a

t

684

At4

g35

770

0.2

213

1.0

1120

0.2

215

0.4

445

Sen

esce

nce-

asso

ciat

ed p

rote

in s

en1

iden

tical

to s

enes

cenc

e-as

soci

ated

pro

tein

GI:1

046

270

from

[A. t

halia

na];

supp

orte

d b

y fu

ll-le

ngth

cD

NA

: Cer

es:1

3699

.25

3161

_at

685

At3

g44

990

0.5

603

1.0

1295

0.1

147

0.7

920

Xyl

oglu

can

end

o-tr

ansg

lyco

syla

se; s

upp

orte

d b

y cD

NA

:gi

_158

1024

8_gb

_AY

0561

63.1

_25

2607

_at

Page 29: Supporting Online Material for Nishimura et al., 1086716Supporting Online Material for Nishimura et al., 1086716 Materials and Methods Table S1. Alleles of PMR4 Table S2. Ratio and

Science Supporting Online Materialdoi 10.1126/science.1086716, p. 29

Table S3. Genotyping primers.Mutant ortransgene

Primer name Primer sequence (5′ ��′)

coi1-1-XcmI-F GGTTCTCTTTAGTCTTTACcoi1-1

coi1-1-XcmI-R CAGACAACTATTTCGTTACC

pmr4-1-NheI-F TTACCAGCCCAACCAATTTCpmr4-1

pmr4-1-NheI-R AGATCAGGGACATGGGACAG

Etr1-1-ApaI-F AAGTTAATAAGATGAGTTGGTGCAEtr1-1

Etr1-1-ApaI-R AGAAATCAGCCGTGTTTCCG

pad4-1-PflmI-F ATGAGTCGCATAAGACTAGCCAAGpad4-1

pad4-1-PflmI-R CCATTTCTTTCCTAAATGAAAATCA

NahG-F GGCTTGCGCATCGGTATCGTCGGCNahG

NahG-R GCCATGGGCCCGATAGGCTTCTCG

npr1-1-NlaIII-F AGGCACTTGACTCGGATGATnpr1-1

npr1-1-NlaIII-R ATGCACTTGCACCTTTTTCC