The DNA probes were
P32-labelled using Ready to go DNA labelling beads (Amersham Biosciences, Freiburg, Germany) and radioactive signals were visualized with a PhosphorImager System (Bio-Rad, Hercules, CA, USA), using QuantityOne software. Acknowledgements This research was supported by grants (SA038A06 and GR67) from the Junta de Castilla and León (Spain). The authors wish to thank Francisco J. González for his help in managing the Trichoderma EST database. Electronic supplementary material 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. (XLS 17 KB) Additional file 2: Table S2. List of 1,617 Trichoderma transcripts VX-765 datasheet whose probe sets afforded a significant difference in expression levels (FDR = 0.23) in microarray experiments in at least one of the culture LY2157299 order 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. (XLS 442 KB) 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. (XLS 77 KB) 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 VEGFR inhibitor 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. (PDF 92 KB) Additional file 5: Table S5. Genes induced in T. harzianum in contact with tomato plant roots. (PDF 80 KB) Additional file 6: Table S6. EMBL database accession numbers of the Trichoderma ESTs used in this study. (XLS 2 MB) Additional file 7: Table S7. Trichoderma ESTs that cluster in each contig. (XLS 596 KB) References 1. Benítez T, Rincón AM, Limón MC, Codón AC: Biocontrol mechanisms of Trichoderma strains. Int Microbiol 2004, 7:249–60.PubMed 2. Howell CR: Mechanisms employed by Trichoderma species in the biological control of plant diseases: the hystory and evolution of current concepts. Plant Disease 2003, 87:4–10.