Research article
Gene expression analysis of the biocontrol fungus Trichoderma harzianum in the presence of tomato plants, chitin, or glucose using a high-density oligonucleotide microarray
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* Corresponding author: M Belén Suárez belensu@usal.es
- † Equal contributors
1 Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca. Campus de Villamayor-Parque Científico, 37185 Villamayor, Salamanca, Spain
2 Centro de Investigación Biomédica de La Rioja (CIBIR). Piqueras 98, 26006 Logroño, La Rioja, Spain
3 EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
4 Current address: Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca. Campus Miguel de Unamuno, 37007 Salamanca, Spain
BMC Microbiology 2009, 9:217 doi:10.1186/1471-2180-9-217
Published: 13 October 2009Additional files
Additional file 1:
Table S1. Identification codes of the Trichoderma sp. (EST-derived) and T. reesei (genome-derived) transcripts that were excluded from the Trichoderma HDO microarray.
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Additional file 2:
Table S2. List of 1,617 Trichoderma transcripts whose probe sets afforded a significant difference in expression levels (FDR = 0.23) in microarray experiments in at least one of the culture conditions considered: T. harzianum CECT 2413 grown for 9 hours in MS medium in the presence of tomato plants (MS-P), chitin (MS-Ch), glucose (MS-G), or MS basal medium alone.
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Additional file 3:
Table S3. List of 257 selected Trichoderma transcripts whose probe sets afforded significant up-regulation (fold-change higher that 2.0 and FDR = 0.23) in microarray experiments after hybridization with cDNA from T. harzianum CECT 2413 grown for 9 hours in MS medium in the presence of tomato plants (MS-P) in comparison with the control condition in MS medium alone. Expression values of these probe sets obtained from the fungus grown in chitin- (MS-Ch) and glucose- (MS-G) containing MS media are also shown.
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Additional file 4:
Table S4. List of 85 annotated transcript sequences of Trichoderma spp. whose probe sets showed significant up-regulation (fold-change greater than 2.0 and FDR = 0.23) in microarray experiments after hybridization with cDNA from T. harzianum CECT 2413 grown for 9 hours in interaction with tomato plants in MS medium compared with the control condition in MS medium alone. Biological processes (P), molecular functions (F) and cellular components (C) are based on Gene Ontology (GO) categories inferred from electronic annotation using the Blast2GO suite based on BLAST definitions.
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Additional file 5:
Table S5. Genes induced in T. harzianum in contact with tomato plant roots.
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Additional file 6:
Table S6. EMBL database accession numbers of the Trichoderma ESTs used in this study.
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Additional file 7:
Table S7. Trichoderma ESTs that cluster in each contig.
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