Sillo F1*, Zampieri E1*, Giordano L1, Lione G1, Colpaert JV2, Balestrini R3, Gonthier P1+

Sillo F1*, Zampieri E1*, Giordano L1, Lione G1, Colpaert JV2, Balestrini R3, Gonthier P1+

Mycological progress

Identification of genes differentially expressed during the interaction between the plant symbiont Suillus luteus and two plant pathogenic allopatric Heterobasidion species

Sillo F1*, Zampieri E1*, Giordano L1, Lione G1, Colpaert JV2, Balestrini R3, Gonthier P1+

1Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini 2, I-10095 Grugliasco (TO), Italy

2HasseltUniversity, Centre for Environmental Sciences (CMK), Agoralaan gebouw D, 3590 Diepenbeek, Belgium

3Institute for Sustainable Plant Protection, CNR, Torino Unit, Viale P.A. Mattioli 25, I-10125 Torino, Italy

+Email:(for correspondence)

*: these authors contributed equally to the work

Table S1A list of the S. luteus primers used in the current work and relative Temperature of annealing (Ta)

Sequence / Name / Ta (°C)
GTGCATGTTGAAAGCGCACA / GH20_797328_f / 60
ATCAAGATGGGCGGGTCAAA / GH20_797328_r
TGGGCACAATATGCCAACGA / GH20_804096_f / 60
TTGCAACATCGGCAAGCAAT / GH20_804096_r
TCTCTCCGTGATGGCCAGTG / SluH5_808559_f / 64.6
GCTGCAGGCAAGACCAACCT / SluH5_808559_r
TCGCGTCTGTCCTTGCTGTC / SluH1_14989_f / 60
GGGGAAGACCGCGTACCATT / SluH1_14989_r
TGCGACACAGGCAACATTCA / SluH2_58198_f / 60
CAACGGAAATTGGGGAGCAG / SluH2_58198_r
TCGAATGCTCTGGCATCAGC / SluH9_810516_f / 64.6
CCGTTGCTCAGAGGACGACA / SluH9_810516_r
TGCTGCAACAACAGCACCAG / SluH10_810518_f / 60
GACGACGGCGTTCACAACTG / SluH10_810518_r
GCACTGAACATCGCCCTTGA / SluH6_808577_f / 60
CAGCAGACGGGCTCTTGGTT / SluH6_808577_r
GCCCTCCTTCCGTTTGCTCT / SluH8_804362_f / 60
TCAGGGTAGGCTCCGTTTGC / SluH8_804362_r
CGAGTCATACAGCGGCCTCA / SluH3_804369_f / 60
GCGCTCATCACTCCGTCGTA / SluH3_804369_r
TCCTTGGCGATCCTCGTTGT / SluH11_804366_f / 60
CCCAGTGCACTCGTTCGTTG / SluH11_804366_r
AGGGATTCCCGCTCTCTTCG / GH18_13153_f / 60
CCGGAGTGGTCTCTGCGAAT / GH18_13153_r
GTCGAACATCCCTGCCCAAG / GH18_79518_f / 60
CAACTTCGCCCGAGTCAGGT / GH18_79518_r
TCAAGCGTCGACCGTCTGAG / GH18_620117_f / 60
AACAGCAACATGGGCTGCAA / GH18_620117_r
TGTTGCCCTGTCCGCTGTAA / GH18_673588_f / 60
CGATGGAACGGGCGGTATTA / GH18_673588_r
TACGTGGAGCGGCTTCAACA / GH18_805786_f / 64.3
TAGCAGCAGCGACGAAGGTG / GH18_805786_r
GGGGGAGTCGAACCGTTTTC / GH18_710196_f / 60
GTCACGGTGCGAATGACAGG / GH18_710196_r
CAATAATCTCGCGGCCTTCG / GH18_8357_f / 60
GGGATGCACGGAGAACTTGG / GH18_8357_r
CAATAATCTCGCGGCCTTCG / GH18_8356_f / 60
GGGCTTTGGTGAACGTGGTC / GH18_8356_r
ACCCTCCTCGATGCTATTGACGCC / Sl_699467_EF1A_f / 64.5
CCATGCCAGCCTTGATGACACCA / Sl_699467_EF1A_r
TGGTTTGTCGAAGGCGTGAA / GH85_813330_f / 60
GTCGCGGCCACACTAAATCC / GH85_813330_r
CCCTGCGAGGAACTGGTCAT / GH85_813331_f / 60
AGGACGCGCCTGATACTCCA / GH85_813331_r

Table S1B list of the Heterobasidion spp.primers used in the current work and relative Temperature of annealing (Ta)

Sequence / Name / Ta (°C)
GGCAGTTTGGTGCACTTAC / Het_Trypt_metF / 60
CCACCAGCCTGCGTACTT / Het_Trypt_metR
CCTCACACTGAAGTCATCTGG / Het_Gh85f / 60
AGACTGAGTAGAAACTGCGTG / Het_Gh85r
AGTGCTGCAACTCTGTCCAG / Het_Hyd46054f / 60
CAATTGATGCCAACCATGGTG / Het_Hyd46054r
TACGACCCGAAGGACAAGGA / Het_Hyd65822f / 60
GATGCCGAGGAGACCAAGAG / Het_Hyd65822r
TCTCCATACTCGCTCTTATTCC / Het_Hyd105914f / 60
GAATGTTGAGGTCTTGAACGA / Het_Hyd105914r
CGTTACAGTCGCTCCTTACC / Het_Hyd156763f / 60
ACCTTAGAATCGCATTACATCCAG / Het_Hyd156763r
ATCATGTTCGCTCGCTTCTC / Het_Hyd156764f / 60
CTTGGACTCGCTCTTGTACTC / Het_Hyd156764r
CACGCCGATCAATATCTTCCT / Het_Hyd181098f / 60
ACAGAACAAGTAGCCAAGTGAG / Het_Hyd181098r
CTTGTAGCCCTCTAAACCTCC / Het_Hyd181100f / 61.5
TTAGGACCCATAGTGCCGT / Het_Hyd181100r
GACCGATCTCCCAACCTCTC / Het_Hyd181114f / 60
CGAACTCTGACAGCATTGGAC / Het_Hyd181114r
GAAGGGCAAGAAAGTGAAACTG / Het_GH18_11431f / 60
ATCCCGTCGAGGTTGAACTG / Het_GH18_11431r
CGTATTCACCGCATTTCCATCC / Het_GH18_33306f / 60
CCTCATTTCCCTCAGCAACTC / Het_GH18_33306r
CAACTTCTTCGGCTTGGTAGAG / Het_GH18_62145f / 60
TGAATCGGCATTATCGTAGGAG / Het_GH18_62145r
GGATACATTTGACTCTTTCGGTGG / Het_GH18_109187f / 60
AGACTCCAAATGACCCTTGCT / Het_GH18_109187r
CCTACCGATAACACCACTTTCTC / Het_GH18_149771f / 61.5
CATCTGTAAACCCAACGCCT / Het_GH18_149771r
GATACCTGAACTCAATCACCCA / Het_GH18_157539f / 60
GTCCACGACAGATGTAGCAG / Het_GH18_157539r
GGCGTGACAAGAATGAATGG / Het_GH20_61259f / 60
CAACTGGATGGAGAAAGTGG / Het_GH20_61259r
GTCTCATGCCTCACAGTTCC / Het_GH20_306181f / 61.5
CCTCTCCATCAACGACAATCC / Het_GH20_306181r

Table S2 MCMC GLMMs fitted on the inhibition growth rates of S. luteus and Heterobasidion spp.in logit scale (LIGR)

For each model (M0, M1, M2, M3), the intercept, the fixed and random factors (when included) are indicated. Under the factor “species”, the coding level associated to H. irregulare and H. annosum is reported. The β and Z coefficients, for fixed and random factors respectively, with the associated 95% confidence interval (CI95%) and p-value (PMCMC) are specified. The symbol * is associated to significant coefficients (P < 0.05).

Suillus luteus inhibition growth rate / Heterobasidion species inhibition growth rate
Fixed and random factors / M0 / M1 / M2 / M3 / M0 / M1 / M2 / M3
Intercept /  = 0.858*
CI95% = (0.704; 1.019) PMCMC = 0.001 /  = 0.610*
CI95% = (0.401; 0.815)
PMCMC = 0.001 /  = 0.854*
CI95% = (0.429; 1.297) PMCMC = 0.004 /  = 0.612
CI95% = (-0.025; 1.329)
PMCMC = 0.054 /  = -1.047*
CI95% = (-1.190; -0.896) PMCMC = 0.001 /  = -0.963*
CI95% = (-1.175; -0.755) PMCMC = 0.001 /  = -1.050*
CI95% = (-1.474; -0.617) PMCMC = 0.001 /  = -0.957*
CI95% = (-1.648; -0.036)
PMCMC = 0.032
Species
(H. irregulare = 1;
H. annosum = 0) / - /  = 0.493*
CI95% = (0.220; 0.775) PMCMC = 0.001 / - /  = 0.489
CI95% = (-0.461; 1.312) PMCMC = 0.216 / - /  = -0.170
CI95% = (-0.446; 0.116) PMCMC = 0.232 / - /  = -0.182
CI95% = (-1.298; 0.846)
PMCMC = 0.700
1 / - / - / Z = 0.160
CI95% = (-0.282; 0.674) PMCMC = 0.502 / Z = -0.056
CI95% = (-0.774; 0.612) PMCMC = 0.840 / - / - / Z = -0.163
CI95% = (-0.602; 0.320) PMCMC = 0.476 / Z = -0.077
CI95% = (-0.788; 0.826)
PMCMC = 0.796
2 / - / - / Z = 0.088
CI95% = (-0.388; 0.575) PMCMC = 0.690 / Z = -0.140
CI95% = (-0.818; 0.548) PMCMC = 0.626 / - / - / Z = 0.454*
CI95% = (0.026; 0.929) PMCMC = 0.038 / Z = 0.540
CI95% = (-0.332; 1.257)
PMCMC = 0.150
3 / - / - / Z = 0.437
CI95% = (-0.067; 0.946) PMCMC = 0.072 / Z = 0.208
CI95% = (-0.403; 0.996) PMCMC = 0.480 / - / - / Z = -0.507*
CI95% = (-0.983; -0.027) PMCMC = 0.034 / Z = -0.435
CI95% = (-1.139; 0.436)
PMCMC = 0.210
4 / - / - / Z = -0.818*
CI95% = (-1.282; -0.269) PMCMC = 0.002 / Z = -0.586
CI95% = (-1.394; 0.021) PMCMC = 0.052 / - / - / Z = 0.556*
CI95% = (0.051; 1.015) PMCMC = 0.028 / Z = 0.483
CI95% = (-0.328; 1.227)
PMCMC = 0.180
5 / - / - / Z = 0.027
CI95% = (-0.460; 0.530) PMCMC = 0.868 / Z = 0.240
CI95% = (-0.438; 0.967) PMCMC = 0.398 / - / - / Z = -0.151
CI95% = (-0.634; 0.319) PMCMC = 0.434 / Z = -0.241
CI95% = (-1.068; 0.595)
PMCMC = 0.444
6 / - / - / Z = 0.135
CI95% = (-0.406; 0.634) PMCMC = 0.532 / Z = 0.341
CI95% = (-0.314; 1.054) PMCMC = 0.266 / - / - / Z = -0.160
CI95% = (-0.647; 0.335) PMCMC = 0.456 / Z = -0.256
CI95% = (-1.146; 0.438)
PMCMC = 0.438
DIC / 112.547 / 103.355 / 79.043 / 79.128 / 104.371 / 104.876 / 67.469 / 67.402

The Heterobasidion isolates used in dual culture with S. luteus were: 1: H. irregulare MUT00001193, 2: H. irregulare MUT00001151, 3: H. irregulare MUT00003560, 4: H. annosum 137OC-142OH, 5: H. annosum MUT00001143, 6: H. annosum MUT00001204.

Table S3A expression values in qRT-PCR of S. luteus genes

Name_Protein ID / Description
(length) / Heterobasidion irregulare / Suillus luteus / Heterobasidion annosum/ Suillus luteus
1 / 2 / 3 / 4 / 5 / 6
Outside / Interface / Outside / Interface / Outside / Interface / Outside / Interface / Outside / Interface / Outside / Interface
SlGH18_8356 / Glycoside Hydrolase Family 18 protein(322) / 0.40 / 0.80* / 0.47 / 0.23 / 0.34 / 1.10* / 0.83* / 0.22 / 0.96* / 0.20 / 2.18* / 0.55*
SlGH18_8357 / Glycoside Hydrolase Family 18 protein(316) / 1.05* / 2.17 / 1.12* / 1.16* / 1.74 / 3.37 / 1.14* / 0.64* / 1.30 / 1.48* / 12.71 / 5.88
SlGH18_620117 / Glycoside Hydrolase Family 18 protein(410) / 0.77 / 1.56* / 1.27* / 0.63 / 1.29 / 0.67 / 1.23* / 0.31 / 0.74* / 0.41 / 2.33* / 0.61
SlGH18_673588 / Glycoside Hydrolase Family 18 protein(432) / 3.06 / 11.71 / 1.57 / 1.46* / 15.95 / 3.54 / 3.54 / 0.25 / 2.35 / 2.98 / 3.74 / 2.89
SlGH18_13153 / Glycoside Hydrolase Family 18 protein(421) / 0.83* / 1.59* / 1.23* / 1.14* / 1.32 / 1.26 / 1.31* / 0.84* / 0.72* / 1.14* / 5.95 / 3.76
SlGH18_710196 / Glycoside Hydrolase Family 18 protein(336) / 0.97* / 2.05 / 1.08* / 0.99* / 1.85 / 1.49* / 1.13* / 0.73* / 1.19* / 0.88* / 7.48 / 3.49
SlGH18_79518 / Glycoside Hydrolase Family 18 protein(489) / 0.83* / 3.10 / 1.28* / 1.37* / 3.09 / 1.85* / 1.40* / 1.25* / 0.94* / 0.99* / 21.94 / 11.06
SlGH18_805786 / Glycoside Hydrolase Family 18 protein(440) / 0.52 / 0.60* / 0.90* / 0.23 / 0.59 / 0.34 / 0.80* / 0.22 / 0.85* / 0.23 / 0.96* / 0.18
SlGH85_813330 / Glycoside Hydrolase Family 85 protein(654) / 0.63 / 1.60 / 0.81* / 1.10* / 0.70 / 1.23* / 1.24* / 1.54 / 0.97* / 1.11* / 3.02* / 1.24
SlGH85_813331 / Glycoside Hydrolase Family 85 protein(72) / 0.72 / 1.35* / 0.71* / 0.90* / 0.75 / 1.26* / 1.05* / 1.12* / 0.83* / 0.67 / 2.37 / 1.28*
SlGH20_797328 / Glycoside Hydrolase Family 20 protein(563) / 0.60* / 1.75* / 0.82* / 1.63 / 0.67* / 1.27* / 1.12* / 1.05* / 0.79* / 1.15* / 6.36 / 2.81
SlGH20_804096 / Glycoside Hydrolase Family 20 protein(563) / 0.70 / 1.72 / 0.92* / 1.52 / 0.79* / 1.29* / 1.32* / 1.30* / 0.95* / 1.08* / 1.14* / 0.79*
SlHyd_808559 / Class 1 hydrophobin(110) / 0.80* / 0.79* / 1.00* / 0.56 / 0.97* / 0.72* / 0.74* / 0.51 / 0.68* / 0.68* / 1.81 / 0.80
SlHyd_805078 / Class 1 hydrophobin(110) / 0.85* / 2.52 / 0.84* / 1.53* / 0.57* / 1.64* / 0.57* / 1.12* / 0.68* / 0.89* / 11.70 / 2.61
SlHyd_14989 / Class 1 hydrophobin(136) / 1.22* / 4.65 / 1.00* / 2.58 / 4.33 / 6.17 / 1.94 / 0.59 / 0.76* / 1.66 / 264.69 / 29.73
SlHyd_810516 / Class 1 hydrophobin(106) / 0.59 / 1.32* / 0.43 / 1.30* / 0.97* / 2.04 / 0.60* / 0.97* / 0.55 / 1.39* / 2.34* / 2.19
SlHyd_810518 / Class 1 hydrophobin(105) / 0.73 / 1.32* / 0.76 / 1.51 / 0.81* / 1.15* / 0.96* / 1.16* / 0.96* / 1.01* / 6.51* / 0.63*
SlHyd_808577 / Class 1 hydrophobin(121) / 0.51 / 0.52 / 0.61* / 0.71* / 0.83* / 0.29* / 0.72* / 0.55 / 0.35 / 0.51 / 0.38* / 0.20
SlHyd_804362 / Class 1 hydrophobin(103) / 0.87* / 1.41 / 0.91* / 0.82* / 1.47 / 0.66* / 1.81 / 0.71 / 1.04* / 0.94* / 3.60* / 0.31
SlHyd_804369 / Class 1 hydrophobin(110) / 0.27 / 0.25 / 0.34 / 0.21 / 0.52 / 0.15 / 0.41 / 0.34 / 0.20 / 0.27 / 0.14 / 0.09
SlHyd_804366 / Class 1 hydrophobin(132) / 0.56 / 0.73 / 0.59 / 0.61 / 0.52 / 0.52 / 0.61* / 0.60 / 0.41 / 0.62 / 0.90* / 0.62

The genes whose differences have no statistical significance are indicated with *.

The Heterobasidion isolates used in dual culture with S. luteus were: 1: H. irregulare MUT00001193, 2: H. irregulare MUT00001151, 3: H. irregulare MUT00003560, 4: H. annosum 137OC-142OH, 5: H. annosum MUT00001143, 6: H. annosum MUT00001204.

Table S3B expression values in qRT-PCR of Heterobasidion spp. genes

Name_Protein ID / Description
(length) / Heterobasidion irregulare / Suillus luteus / Heterobasidion annosum/ Suillus luteus
1 / 2 / 3 / 4 / 5 / 6
Outside / Interface / Outside / Interface / Outside / Interface / Outside / Interface / Outside / Interface / Outside / Interface
HiGH18_62145 / Glycoside Hydrolase Family 18 protein (423) / 1.25* / 0.00 / 0.33 / 0.37 / 1.06* / 0.44 / 0.96* / 0.32 / 1.09* / 0.44 / 4.40 / 3.78*
HiGH18_109187 / Glycoside Hydrolase Family 18 protein (355) / 0.53* / 0.86 / 0.20* / 0.16 / 0.71 / 0.18 / 2.18* / 0.55* / 0.88* / 0.08 / 5.94 / 2.13
HiGH18_157539 / Glycoside Hydrolase Family 18 protein (560) / 0.52* / 0.00 / 0.33 / 0.20 / 1.18* / 0.17* / 4.16* / 0.75* / 1.21* / 0.17 / 2.18 / 0.00
HiGH18_149771 / Glycoside Hydrolase Family 18 protein (537) / 0.32* / 0.00 / 0.13 / 0.07 / 0.91* / 0.17 / 2.24* / 0.63* / 0.63 / 0.02 / 1.60 / 0.00
HiGH18_11431 / Glycoside Hydrolase Family 18 protein (378) / 0.30 / 0.00 / 0.12 / 0.34 / 0.30 / 0.08 / 1.04* / 1.24* / 0.54 / 0.35 / 5.22* / 0.00
HiGH18_33306 / Glycoside Hydrolase Family 18 protein (399) / 0.47 / 0.00 / 0.33 / 0.37* / 0.78* / 0.28 / 0.96* / 0.32 / 0.66* / 0.76* / 3.00 / 0.00
HiGH85_47693 / Glycoside Hydrolase Family 85 protein (673) / 1.03* / 1.60 / 1.25* / 2.55 / 1.71 / 3.83 / 1.61* / 0.65* / 0.60* / 0.01 / 0.36* / 0.55*
HiGH20_306181 / Glycoside Hydrolase Family 20 protein (720) / 0.82* / 0.72 / 0.10 / 0.11 / 0.66 / 0.20 / 22.79 / 10.73 / 4.31* / 0.24* / 6.12 / 0.69*
HiGH20_61259 / Glycoside Hydrolase Family 20 protein(557) / 0.10 / 1.29* / 0.08 / 0.20 / 0.42 / 0.15 / 1.00* / 0.45* / 0.28 / 0.55 / 1.96 / 2.27*
HiHyd_46054 / Hydrophobin-like protein(121) / 0.31* / 1.76* / 0.20 / 0.11 / 0.60* / 0.06 / 0.97 / 0.32 / 0.56 / 0.05 / 0.60* / 0.21*
HiHyd_105914 / Hydrophobin-like protein (114) / 1.81 / 0.35 / 0.25 / 0.00 / 1.25* / 0.04* / 9.44 / 2.18* / 3.29 / 0.00 / 2.64 / 0.15*
HiHyd_156763 / Hydrophobin-like protein (116) / 0.20 / 1.25* / 0.07 / 0.10 / 1.14* / 0.41 / 6.43* / 11.68* / 1.07* / 0.40* / 0.86* / 0.78*
HiHyd_156764 / Hydrophobin-like protein (145) / 0.30* / 0.07* / 0.56 / 0.89 / 0.16* / 0.11 / 3.88* / 11.41* / 0.44* / 0.15 / 1.59* / 0.02
HiHyd_181098 / Hydrophobin-like protein (140) / 0.09* / 0.00 / 0.27 / 0.08 / 0.62* / 0.13 / 1.66* / 0.84* / 0.90* / 0.04 / 1.18* / 0.00*
HiHyd_65822 / Hydrophobin-like protein (300) / 0.04* / 0.00* / 0.04 / 0.11* / 0.12* / 0.00* / 0.03* / 2.82* / 0.76 / 0.08* / 1.38* / 0.45*
HiHyd_181114 / Hydrophobin-like protein (220) / 0.11* / 0.01* / 0.08* / 0.01* / 0.12* / 0.32* / 0.08* / 0.04 / 0.11* / 0.23* / 0.13* / 0.12*
HiHyd_181100 / Hydrophobin-like protein (114) / 0.50 / 0.07 / 0.08 / 0.10* / 3.92* / 0.18 / 0.48* / 0.49* / 3.14* / 0.31 / 0.83* / 0.01

The genes whose differences have no statistical significance are indicated with *.

The Heterobasidion isolates used in dual culture with S. luteus were: 1: H. irregulare MUT00001193, 2: H. irregulare MUT00001151, 3: H. irregulare MUT00003560, 4: H. annosum 137OC-142OH, 5: H. annosum MUT00001143, 6: H. annosum MUT00001204.