a

Poplar ID b c d e f
Band Poplar genome accession number Public ID AGI match Protein description References
[Poptrdraft_]
826290 estExt_fgenesh4_pg.C_LG_XIX0853 EEF00423 AT3G54420 GHF 19; class IV chitinase; PR-3 3; 4; 5; 6; 17
1
292112 gw1.619.1.1 EEE75453 AT1G29670 GDSL lipase like 11; 12; 15
2 593152 eugene3.04780002 EEE74715 AT4G18970 GDSL lipase like 11; 12; 15
581173 eugene3.127820001 EEF08209 AT1G29670 GDSL lipase like 11; 12; 15
3
586261 eugene3.192750001 EEF11997 AT1G29670 GDSL lipase like 11; 12; 15
290846 gw1.5405.1.1 EEE74968 AT4G16260 GHF 17; beta-1,3-glucanase; PR-2 4; 5; 9; 16; 17; 19; 22
4
717157 estExt_Genewise1_v1.C_LG_VI1054 EEE92847 AT4G19810 GHF 18; class V chitinase; PR-3 3; 4; 5; 6; 17
826290 estExt_fgenesh4_pg.C_LG_XIX0853 EEF00423 AT3G54420 GHF 19; class IV chitinase; PR-3 3; 4; 5; 6; 17
5
827727 estExt_fgenesh4_pg.C_1210040 EEF07674 AT5G45670 GDSL lipase like 11; 12; 15
826290 estExt_fgenesh4_pg.C_LG_XIX0853 EEF00423 AT3G54420 GHF 19; class IV chitinase; PR-3 3; 6; 17
6
652688 grail3.0024032801 EEE91541 AT3G57270 GHF 17; beta-1,3-glucanase; PR-2 4; 5; 9; 16; 17; 19; 22
7 746640 estExt_Genewise1_v1.C_1970084 EEF12198 AT5G24090 GHF 18; class III chitinase; PR-8 3; 4; 5; 6; 17, 21
571046 eugene3.00130410 EEE95000 AT3G04720 hevein-like protein; PR-4 17
8
763978 fgenesh4_pg.C_LG_VII000323 EEE90334 AT1G73260 kunitz-type trypsin inhibitor; PR-6 7; 13; 17; 20
9 669475 grail3.0020019002 EEF03642 AT4G11650 thaumatin like; PR-5 2; 4; 5; 8; 10; 14; 17; 18
550049 eugene3.00012490 EEE85099 AT2G14580 SCP PR-1 like protein; PR-1 4; 5; 13; 17
10
590536 eugene3.03190002 EEE72843 AT1G70890 bet v I like protein; PR-10 1; 17

Supplemental Table 1: Populus trichocarpa extrafloral nectar proteins. All peptides detected in the nectar origin from defense or
pathogen related proteins. Band numbers correspond to Figure 1. PR = pathogenesis-related. a Accession number of corresponding
sequence at JGI (http://genome.jgi-psf.org/cgi-bin/searchGM?db=Poptr1_1). b Poplar genome name according to a.c Accession
number of the corresponding sequence at (www.ncbi.nlm.nih.gov) according to the poplar gene model ID. d AGI code of the closest
Arabidopsis homolog according to b. e Annotation according to NCBI Blast (http://www.ncbi.nlm.nih.gov/) and a. f additional information
to the respective protein class.
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 Ident.
found Mascot
Public IDa peptide mol. peptide1 peptide2 peptide3 peptide4 peptide5 peptide6 peptide7 peptide8
peptides score
weight
GSNIEVVLGV IYDPNRDTLEAL AAGIEQHFGLFL RSGQAIETYLFA NGNNLPSDQEV LQSLTDASAATT AGAPDLNIVVSE
EEE74968 34,805 7 522 PNDK R PNK MFDENLK VSLFQTNVIGR WVQDNVVAYSS SGWPSEGGTAA
NVK TADNAGTFYR
QAAENYLNK VLIDQYSQQIK DILVGVNYASGA GRDILVGVNYAS TEYVFWDAIHPT
EEE75453 39,532 5 785
AGIR GAAGIR EALNQFTAR
HYTQVVWR YDYNSNSCVGG LVHSGGPYGEN CSNGGTVISCN
EEE85099 17,601 5 1114 ECR LAGGSGDLTGS YSPPGNYVGQR
AAVK PY
VTNTGTGAQV SSGSGGGTGG IVDQCSNGGLDL
EEE95000 21,646 3 491
TVR GGESASNVR DAGVFR
VVDVGCCPAR SDGQCIQDSTP SYNAFLPSDAYP TEYVFWDAIHPT
EEF08209 8587 4 576
CQNR TDISHLIS EALNQFTAR
TEYVFWDAIH SYSAFLPSDAYP
EEF11997 9094 2 121 PTESSNQFTA YDISHLVNMQI
R
LEVSDDNIAR VKDEVETVDDP
EEE72843 16,399 2 107
TK
LTQLLGTK QAAENYLNK VLIDQYSQQIK DILVGVNYASGA GRDILVGVNYAS ISLNEQLQNHAA
EEE74715 17,012 6 495
AGIR GAAGIR TLSR
NALDSAGLGSI LYDPDQDALR
EEE91541 31,697 2 166
K
CPDAYSYPK ASGGCNNPCTV CAADINGQCPN
EEF03642 25,702 3 195
FK PLR
SWIQAGMSAK KSFIDSSITLAR LVLGLPFYGWS TLLSIGGGGSDV LTNSNNNGLFA
EEE92847 40,351 5 352 WR NTFASMASQSS PANGQGLAGDG
SR SIGYNQIK
ALNGFSQQR YGGVMLWSK QYDNGYSAAIK KVYLAAAPQCIF
EEF12198 31,306 4 397
PDANLDTAIK
LLVLDGPAFPF YILAETDPNPSS
EEE90334 20,639 2 116
IFR NAWHFNIVK
DAVVSFK TALWFWMNR VRPVVSQGFGA DAFLSAVNSYP SNNFDGLNNPDI GPLQLSWNYNY AINGIECNGGNP DYCSQLGVST
EEF00423 30,195 8 2612
TIR QFGK VAR GPAGR GAVQAR ENNLTC
VNYLPYGIDFP IFNSLLQTMLEE
EEF07674 30,344 2 175
LGATGR LNEK

a
Supplemental Table 2: Detail information about proteins identified in Populus trichocarpa extrafloral nectar. Accession
number of the corresponding sequence at (www.ncbi.nlm.nih.gov) (cf. Supplemental Table 1).
 Protein IDa Ptr qPCRc Ptt arrays
Descriptionb
[Poptrdraft_] nectary leaf FCd adj.P-Vae
827727 GDSL lipase like, na 41814 ± 13912 8±6 - -
586261 GDSL lipase like, na 4±1 nd - -
593152 GDSL lipase like, na 0.12 ± 0.04 nd - -
581173 GDSL lipase like, na 7±4 nd - -
292112 GDSL lipase like, na 8905 ± 2224 nd - -
590536 bet v I like protein; PR-10, na 1 ± 0.5 nd - -
290846 GHF 17; beta-1,3-glucanase; PR-2 8241 ± 2286 1565 ± 543 2 1,0E-02
652688 GHF 17; beta-1,3-glucanase; PR-2 2422 ± 698 17 ± 2 0,9 5,2E-01
746640 GHF 18; class III chitinase; PR-8 39949 ± 17514 471 ± 38 2,2 1,7E-02
717157 GHF 18; class V chitinase; PR-3 262 ± 85 nd 0,9 5,9E-01
826290 GHF 19; class IV chitinase; PR-3 0.06 ± 0,01 nd 2,4 1,1E-02
550049 SCP PR-1 like protein; PR-1 66 ± 1 0.02 2,9 6,8E-04
571046 hevein-like protein; PR-4 61461 ± 13160 94 ± 24 1,5 2,5E-02
763978 kunitz-type trypsin inhibitor; PR-6 1300 ± 189 1.9 ± 0.2 1,2 4,2E-01
669475 thaumatin like; PR-5 2048 ± 559 6±1 12,5 3,3E-05

Supplemental Table 3: Populus trichocarpa nectar proteins compared to Populus tremula x P. tremuloides nectary array
a b
analyses. accession number of corresponding sequence at JGI (http://genome.jgi-psf.org/cgi-bin/searchGM?db=Poptr1_1).
Annotation according to NCBI Blast (http://www.ncbi.nlm.nih.gov) and a, GHF = glycosyl hydrolase family, na, not present on Ptt
c d
arrays. Molecules per 10000 molecules of actin (mean values of three replicates ± SE), nd = not detectable, FC, fold change
nectary/leaf. e adj.P-Va, adjusted P-value.
Material and Methods

Plant material and growing conditions

Populus tremula × P. tremuloides (clone T89) and Populus trichocarpa (clone 93-
968) plants were grown in the field under ambient light regime and in growth
chambers under long day conditions, with 16 h light (22oC) and 8 h darkness (17oC)
periods, exposed to TLD 58 W/840 Super 80 (Philips), and 58 W L58/77 (Osram)
lamps.

Nectar proteome analysis

P. trichocarpa nectar samples were collected from field-grown cultures between May
and June, and stored for further analyses at -20ºC. For protein analysis, 100μl
aliquots with 10-fold diluted nectar were resuspended in LDS-sample buffer
(Invitrogen), heated to 90°C for 10 min and separated in a 4%-12% gradient 1D-Bis-
Tris-SDS-Gel (Novex NuPAGE, Invitrogen). Gels were stained as described (Neuhoff
et al., 1990) and visible bands were excised. Gel slices were washed twice
alternating with washing buffer A (50 mM ammonium bicarbonate) and washing
buffer B (25 mM ammonium bicarbonate in 50% v/v acetonitrile).
Carbamidomethylation was carried out using 10 mM DTT at 56 °C for 30 minutes and
5 mM IAA at RT in the dark for 30 minutes followed by two subsequent washes with
the washing buffers A & B. Gel slices were vacuum dried and subjected to tryptic
over-night digestion using 5 µL trypsin solution (12.5 ng/µl in buffer A). The obtained
peptide mixture was eluted from the gel pieces using 20 µl 5% formic acid and
separated by nano-RP-HPLC using an ultimate 3000 nano-HPLC system (Dionex)
coupled to an LCQ Deca XP Plus iontrap mass spectrometer (ThermoElectron). The
nano-LC-system was equipped with precolumn concentration (100 µm inner
diameter, 2 cm length, 5 µm particle size, C18 column (nanoseparations, Nieuwkoop,
Netherlands); flow rate 8µl 0.1% trifluoroacetic acid) and used a 1 h binary gradient
from 5 to 50% solvent B (solvent A: 0.1% FA; solvent B: 0.1% FA, 84% acetonitrile)
with a flow rate of 300 nl/min. The mass spectrometer acquired repeatedly one full-
MS and three tandem-MS spectra of the three most intensive ions in the previous full-
MS-scan. Obtained MS/MS spectra were analyzed using the Mascot algorithm
(version 2.1, Matrixscience) which searched against the JGI Populus trichocarpa v1.1
database using the following parameter settings: trypsin as protease, max. one
missed cleavage, carbamidomethylation as fixed modification and oxidized
methionine and pyroglutamic acid (pyro-Glu at N-term. Q) as variable modifications;
peptide and fragment mass tolerance were set to 1.5 Da. At least two significantly
scored peptide spectra were necessary for protein identification; peptide spectra with
Mascot scores below 38 were discarded.

Anti-microbial test
The effect of nectar on fungal growth was monitored by halo assays (Becker et al.,
1996). A lawn of fungal cells was plated on Petri dishes (100 x 15mm) containing
10ml YEP agar media supplemented with 50μg/ml ampicillin to avoid bacterial
growth. To study fungal growth inhibition, sterile blank paper disks (Sample Discs
SS-033 Wescor) were placed on the agar surface before the mycelium developed. A
10µl aliquot of pure or diluted nectar samples as well as nystatin (50mg/ml) controls
were applied to the disk. The plates were incubated at room temperature for about 72
hours until microbial growth inhibition became visible as dark halo around the filter
disk. To exclude osmotic effects on fungal growth, a solution containing sucrose of
the same osmolality as the nectar were used. In an additional test nectar samples
were boiled for 15 minutes to probe if fungal growth inhibition is lost when nectar
proteins denature.

Identification of Fusarium solani

Older leaves of field-grown Ptt, producing no extrafloral nectar anymore, revealed
dark spots (Figure 1B). These fungal infestations accumulated predominately around
dry nectaries, and were cultivated by pressing the infected leaves on Sabouraud agar
plates. After 48h of incubation at 30°C small mould colonies became visible that later
showed a pale aerial mycelium and a shady vinaceous color at the reverse. Species
identification was performed in an accredited diagnostic mycology lab (Institute of
Hygiene and Microbiology, University of Wuerzburg). Microscopic analysis revealed
thin hyphae with laterally arising conidiophores producing abundant elongated
microconidia and 3-5 septate macroconidia with a typical “banana-like” shape as well
as abundant formation of chlamydospores, allowing initial identification as Fusarium
spp. For unequivocal species identification DNA was isolated from the culture using a
bead disruption based protocol (de Hoog et al., 2000). Internal transcribed spacer
regions were amplified from genomic DNA using primers ITS1 (5’-
TCCGTAGGTGAACCTGCGG-3’) and ITS4 (5’-TCCTCCGCTTATTGATATGC-3’)
and analyzed by double-strand sequencing with the same primers (White et al.,
1990). Sequence analysis placed the fungus in the Fusarium solani complex with a
99%homology over ITS1 and ITS2 to reference strain CBS490.63 (Genbank
accession number AY677295.1). Identification was confirmed using the CBS
Fusarium MLST database (http://www.cbs.knaw.nl/fusarium/BioloMICS.aspx).

Gene expression analyses

Microarray analyses and biostatistics were conducted as described (Escalante Pérez
et al., 2012). Annotation of Affymetrix probe set IDs was done by using
BarleyBase/PLEXdb (Wise et al., 2007). Microarray data have been uploaded to
GEO. Data are accessible at:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=pzehnqawcmikqxw&acc=GSE2
3897

Quantitative real time PCR (qPCR)

For qPCR potential DNA contamination was removed from total RNA by treatment
with RNase-Free DNase (Fermentas) according to the manufacturer’s protocol. First-
strand cDNA was prepared using 2.5 µg RNA with the M-MLV-RT kit (Promega,
Mannheim, Germany). First-strand cDNA samples were 20-fold diluted and sobjected
to qPCR using a Mastercycler® ep Realplex2S (Eppendorf) with the ABsolute QPCR
SYBR Green Capillary Mix (ABgene, Hamburg, Germany). Primers used (TIB
MOLBIOL, Germany) have been designed according to the poplar protein IDs and
their corresponding cDNA-sequences (JGI, Joint Genome Institute, http://genome.jgi-
psf.org/pages/search-for-genes.jsf?organism=Poptr1_1). The resulting primers were
validated prior to real time PCR analysis. Transcript numbers were quantified by
normalization to actin cDNA amplified by PtACT2fwd and PtACT2rev. These poplar
actin fragments were homologous to actins 2 and 8 constitutively expressed in
Arabidopsis (for details see An et al., 1996; Szyroki et al., 2001). Each transcript was
quantified using individual standards. To enable detection of contaminating genomic
DNA, PCR was performed with the same RNA as template that was used for cDNA
synthesis. All kits were used according to the manufacturer’s protocols. The following
primers were used: PtAct2 fwd (5´-CCC AGA AGT CCT CTT-3´), PtAct2 rev (5´-ACT
GAG CAC AAT GTT AC-3´), 827727 fwd (5´-ATC TGC CTT ATG GAA TAG-3´),
827727 rev (5´-CTT AGC AAC GTC ATC G-3´), 586261 fwd (5´-AAC TAC CGG GTT
TAG G-3´), 586261 rev (5´-TCG TAT GGA TAA GCA TCA-3´), 593152 fwd (5´-CAA
CTG GGT GAT AGA AT-3´), 593152 rev (5´-CGA AAC GGA TAG GAA T-3´),
581173 fwd (5´-TGC ATA ACA GGG TTT AG-3´), 581173 rev (5´-GGT TGG ATA
AGC ATC AGA-3´), 292112 fwd (5´-TTG GAG CAA TAG GCA G-3´), 292112 rev (5´-
CTT ACC GAG CAC AGA A-3´), 590536 fwd (5´-TGA TAT TGT GAA CGA CAT-3´),
590536 rev (5´-CTG CGT CTG TAT AAG C-3´), 290846 fwd (5´-ACT TGA AGC CCT
TAG A-3´), 290846 rev (5´-CTG TCA CTA AAG GAC C-3´), 652688 fwd (5´-ATT CTT
GGT ATT CTA AAT CC-3´), 652688 rev (5´-ATC AAT AGC GGT TGA AA-3´),
746640 fwd (5´-TCA ATT TGT GAA CGT AGC-3´), 746640 rev (5´-GCC CTG CAT
CGT C-3´), 717157 fwd (5´-AAC ATA TCA AGT TAC AAT CT-3´), 717157 rev (5´-
TTG CTA ACG TGA TGG A-3´), 826290 fwd (5´-TAC GCC TAC TAC TCC C-3´),
826290 rev (5´-TTG ACC GGA AGC A-3´), 550049 fwd (5´-TTG TCT GGG ACA CTA
ATG-3´), 550049 rev (5´-GGC CAA CGT AGT TGC-3´), 571046 fwd (5´-GAC GAT
CAT TGT AAT CC-3´), 571046 rev (5´-AGT CCA GCC GTA TTT C-3´), 763978 fwd
(5´-CAT GGA TGG TAG GTG A-3´), 763978 rev (5´-CAA AGG CCT AGG ACA-3´),
669475 fwd (5´-GCT GAA TAT GCC TTG AAC-3´), 669475 rev (5´-ACA GTA TTG
ATC TGT CTT-3´).

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