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mpp12006-sup-0001-FigS1.tif90K

Fig. S1 Bar chart of categories of significantly differentially expressed genes from the experiment; 1906 genes were sorted into 17 different categories of biological function. Sequences showing no homology to previously described genes were classified into the ‘No hits’ category, sequences with homology to predicted proteins of unknown function were classified into the ‘Unknown’ category, and sequences showing homology with several functions were classified into the ‘Miscellaneous’ category.

mpp12006-sup-0002-FigS2.tif114K

Fig. S2 Functional categorization of common toxin-induced genes in all three genotypes (total of 405 genes, Table S5A). Genes were sorted into 16 different categories of biological function. Sequences showing no homology to previously described genes were classified into the ‘No hits’ category, sequences with homology to predicted proteins of unknown function were classified into the ‘Unknown’ category, and sequences showing homology with several functions were classified into the ‘Miscellaneous’ category.

mpp12006-sup-0003-FigS3.tif113K

Fig. S3 Functional categorization of common toxin-repressed genes in all three varieties (total of 93 genes, Table S5B). Genes were sorted into 13 different categories of biological function. Sequences showing no homology to previously described genes were classified into the ‘No hits’ category, sequences with homology to predicted proteins of unknown function were classified into the ‘Unknown’ category, and sequences showing homology with several functions were classified into the ‘Miscellaneous’ category.

mpp12006-sup-0004-FigS4.tif430K

Fig. S4 Hierarchical cluster analysis of the differential expression profiles of the genes expressed at a higher level in PI567.734 than in the other two varieties. Sixty-six genes were expressed at a higher level in PI567.734 than in Williams 82 and Essex, and were clustered among a total of 19 experiments. Nod, nodulation when inoculated with Bradyrhizobium japonicum; VIR and HR, compatible and incompatible Pseudomonas syringae inoculations; PIVEI, PIVWI, WIVEI, PIVPIU, WIVWU, EIVEU, PIUVWU, WUVEU and PIUVEU, PI–EI, PI–WI, WI–EI, PI–PU, WI–WU, EI–EU, PU–WU, WU–EU and PU–EU, respectively; AW, atrazine versus water treatment, 1,2,4 and 8 h post application. A, Cluster A; B, Cluster B. P, PI567.374; W, Williams 82; E, Essex; V, versus; I, plant treated by Fusarium virguliforme phytotoxin (Fv toxin); U, mock.

mpp12006-sup-0005-FigS5.tif388K

Fig. S5 Hierarchical cluster analysis of shared genes between PI–EI and WI–EI. (A) Fifteen of the 16 genes that were induced in Williams 82 and PI567.374 on Fusarium virguliforme phytotoxin (Fv toxin) treatment were clustered with the 19 treatments as defined in the legend of Fig. S4. (B) Hierarchical clustering of shared genes between PI–PU and WI–WU. Four of the 44 genes were identified as commonly induced in PI567.374 and Williams 82, and were clustered with the 19 treatments as defined in the legend of Fig. S4. P, PI567374; W, Williams 82; E, Essex, I, plant treated by Fv toxin; U, mock.

mpp12006-sup-0006-TableS1.xls2199K

Table S1 Significantly differentially expressed genes from the whole experiment. A gene is considered to be significantly differentially expressed if it has both significance [false discovery rate (FDR) P value of ≤0.05] and a fold-change ratio of ≥1.5 or ≤0.667. P, PI567374; W, Williams 82; E, Essex; I, plant treated with Fusarium virguliforme phytotoxin (Fv toxin); U, mock; v, versus. Genes with increased and decreased transcripts are highlighted in red and blue, respectively.

mpp12006-sup-0007-TableS2.xlsx11K

Table S2 Primer name, gene annotation, GenBank ID and matching soybean gene, primer sequence, estimated melting temperature for each primer pair, TM (°C) and amplicon size (bp) of primers used in quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). For, forward primer; Rev, reverse primer.

mpp12006-sup-0008-TableS3.xlsx15K

Table S3 Cross comparison of gene expression profiles between microarrays and quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR). The expression profiles of these genes were determined by qRT-PCR at 6, 8 and 24 h post-treatment (hpt). Expression levels are given as the log2-transformed fold change of Fusarium virguliforme (Fv) filtrate-treated soybeans compared with mock treatment. SE, standard error.

mpp12006-sup-0009-TableS4.xls649K

Table S4 Significantly differentially expressed genes from the three genotypes treated with Fusarium virguliforme phytotoxin (Fv toxin). Expression levels are calculated as the ratio of Fv toxin-treated genotype to the same mock-treated genotype. PI, PI567.374 plants treated by Fv toxin; PU, PI567.374 mock-treated plants; WI, Williams 82 plants treated by Fv toxin; WU, Williams 82 mock-treated plants; EI, Essex plants treated by Fv toxin; EU, Essex mock-treated plants. Genes with increased and decreased transcripts are highlighted in red and blue, respectively.

mpp12006-sup-0010-TableS5.xls160K

Table S5 Up- and down-regulated genes shared among the three genotypes treated by Fusarium virguliforme phytotoxin (Fv toxin). Expression levels are calculated as the ratio of filtrate-treated genotype to the same mock-treated variety. PI, PI567.374 plants treated by Fv toxin; PU, PI567.374 mock-treated plants; WI, Williams 82 plants treated by Fv toxin; WU, Williams 82 mock-treated plants; EI, Essex plants treated by Fv toxin; EU, Essex mock-treated plants.

mpp12006-sup-0011-TableS6.xls33K

Table S6 Toxin-induced and repressed genes in resistant genotypes (shared only between PI–PU and WI–WU). Expression levels are calculated as the ratio of Fusarium virguliforme phytotoxin (Fv toxin)-treated genotype to the same mock-treated genotype. P, PI567374; W, Williams 82; I, plant treated by Fv toxin; U, mock.

mpp12006-sup-0012-TableS7.xlsx14K

Table S7 Toxin-induced and repressed genes unique to resistant PI567.374 (the most resistant genotype) on treatment with Fusarium virguliforme phytotoxin (Fv toxin).

mpp12006-sup-0013-TableS8.xlsx344K

Table S8 Gene expression comparison between soybean roots infected by Fusarium virguliforme (Fv) (Radwan et al., 2011) at 7 days post-inoculation (dpi) and soybean leaves treated by Fv toxin at 8 h post-treatment (hpt) (current study). PI, PI567.374; E, Essex. Genes with increased and decreased transcripts are highlighted in red and blue, respectively.

mpp12006-sup-0014-TableS9.xls27K

Table S9 Up-regulated genes in the three genotypes without Fusarium virguliforme phytotoxin (Fv toxin) treatment. P, PI567374; W, Williams 82; E, Essex; U, mock.

mpp12006-sup-0015-TableS10.xls41K

Table S10 Resistance-related genes (up-regulated genes shared between PI–WI and PI–EI and between PI–EI and WI–EI). Expression levels were calculated as the ratio of Fusarium virguliforme phytotoxin (Fv toxin)-treated genotype to another different Fv toxin-treated genotype. P, PI567374; W, Williams 82; E, Essex; I, plant treated by Fv toxin.

mpp12006-sup-0016-TableS11.xls25K

Table S11 Physical mapping of simple sequence repeat (SSR) markers linked to Fusarium virguliforme (Fv) resistance and cDNA arrays with differential abundance [false discovery rate (FDR) P value of <0.05]. cDNA sequences mapping <550 kbp away from SSR markers are presented. P, PI567374; W, Williams 82; E, Essex; I, plant treated by Fv toxin; U, mock; v, versus. Genes with increased and decreased transcripts are highlighted in red and blue, respectively.

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