Open Access Research article

Downy mildew resistance induced by Trichoderma harzianum T39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes

Michele Perazzolli1*, Marco Moretto1, Paolo Fontana1, Alberto Ferrarini2, Riccardo Velasco1, Claudio Moser1, Massimo Delledonne2 and Ilaria Pertot1

Author Affiliations

1 IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all’Adige (TN), Italy

2 Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, 37134, Verona, Italy

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BMC Genomics 2012, 13:660  doi:10.1186/1471-2164-13-660

Published: 22 November 2012

Additional files

Additional file 1:

RNA-Seq sequencing and read mapping of each sequencing replicate. Numbers of RNA-Seq reads passing the quality check and mapping to the grapevine genome are reported for each sequencing replicate (named A and B) of each biological replicate (numbered from 1 to 3) for control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants.

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Additional file 2:

RNA-Seq sequencing and coverage of the grapevine transcriptome for each biological and sequencing replicate. Total bases (Mbp) sequenced by RNA-Seq analysis and coverage of the grapevine transcriptome are reported for each sequencing replicate (named A and B) of each biological replicate (numbered from 1 to 3) for control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants.

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Additional file 3:

Distribution of RNA-Seq sequences within the grapevine genome. (A) Proportions of reads mapping to unique locations (unique reads, yellow), reads mapping to multiple locations with 2–100 matches (multi-reads, red), and reads not mapping or ambiguously mapping to more than 100 locations (unused reads, white) to the grapevine genome. The mean number of sequenced reads and standard errors for three biological replicates are presented for each treatment. Percentages (%) are calculated with respect to the total filtered reads. Unique reads and multi-reads were used for evaluating gene expression. (B) Proportions of reads mapping to grapevine genes (green) and to intergenic regions (red) of the grapevine genome. The mean number of sequenced reads and standard errors for three biological replicates are presented for each treatment. Percentages (%) are calculated with respect to the total mapping reads. Grapevine treatments: control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v) plants.

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Additional file 4:

RNA-Seq reads mapping to grapevine genes. Numbers of RNA-Seq reads mapping to grapevine genes are reported for each sequencing replicate (named A and B) of each biological replicate (numbered from 1 to 3) for control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants.

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Additional file 5:

Expressed grapevine genes and novel genes identified by RNA-Seq analysis. Numbers of expressed grapevine genes and novel genes with respect to the grapevine annotation are reported for each sequencing replicate (named A and B) of each biological replicate (numbered from 1 to 3) for control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants

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Additional file 6:

Expression levels of grapevine genes. Gene expression values (FPKM) and standard errors are reported for all (33,514) Pinot Noir grapevine predicated genes [77] Release 3 [78] in control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants. Expression values in each biological replicate (numbered from 1 to 3) and each sequencing replicate (named A and B) are also listed.

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Additional file 7:

Correlations between sequencing replicates of RNA-Seq analysis. Comparison of the expression levels of all grapevine genes, expressed as fragments per kilobase of transcript per million fragments mapped (FPKM), in the two sequencing replicates (named A and B) of (A) control (C) biological replicate no. 1; (B) C biological replicate no. 2 (B); (C) C biological replicate no. 3; (D) Trichoderma harzianum T39-treated (T39) biological replicate no. 1; (E) T39-treated biological replicate no. 2; (F) T39-treated biological replicate no. 3; (G) Plasmopara viticola-inoculated control (C+P.v.) biological replicate no. 1; (H) C+P.v. biological replicate no. 2; (I) C+P.v. biological replicate no. 3; (J) P. viticola-inoculated T39-treated plants (T39+P.v) biological replicate no. 1; (K) T39+P.v biological replicate no. 2; and (L) T39+P.v biological replicate no. 3.

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Additional file 8:

Principal component analysis of grapevine treatments. Principal component analysis (PCA) is based on the expression values (FPKM) of all grapevine genes for each sequencing replicate (named A and B) of each biological replicate (numbered from 1 to 3) for control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants.

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Additional file 9:

Pearson’s correlation coefficients between sequencing and biological replicates of RNA-Seq analysis. Pearson’s correlation coefficients are based on the gene expression values (FPKM) of all grapevine genes in two sequencing replicates (A and B) of each biological replicate (numbered from 1 to 3) for control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants.

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Additional file 10:

Expression levels, clustering, and annotation results of differentially expressed genes. Gene expression values (FPKM) and standard errors are reported for differentially expressed (7,024) genes in control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v.) plants. Differentially expressed genes were identified by the DESeq package with a false discovery rate (FDR) of 5% and a fold-change greater than two in at least one pairwise comparison. Fold-changes, clustering results, and functional annotation are reported for each gene.

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Additional file 11:

Primer sequences of the grapevine genes analysed by real-time RT-PCR. Forward and reverse primer sequences of real-time RT-PCR analysis are reported for 24 selected grapevine genes. Grapevine Actin (TC81781) [4, 52] and VATP16 (XM_002269086.1) [94] were used as constitutive genes for normalising the real-time RT-PCR data.

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Additional file 12:

Expression levels of grapevine genes that are members of the actin gene family. Gene expression values (FPKM) and standard errors are reported for grapevine genes belonging to the Actin gene family in control (C), Trichoderma harzianum T39-treated (T39), Plasmopara viticola-inoculated control (C+P.v.), and P. viticola-inoculated T39-treated (T39+P.v) plants.

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