harzianum CECT 2413 in its early interactions with tomato plant roots using microarray technology. We report the construction of a Trichoderma HDO microarray composed of 384,659 25-mer probes designed against 14,081 EST-derived transcripts from twelve strains belonging to the eight Trichoderma species cited above, and 9,121 genome-derived transcripts from T. reseei [20], since it was the only entire Trichoderma genome available when the microarray was designed.
As far as we know, this is the first time that an oligonucleotide microarray has been used to study gene expression changes of a Trichoderma strain in the presence of a plant host. RNAs from T. harzianum CECT 2413 mycelia cultured in the presence and absence of tomato plants and also in
glucose- or chitin-containing media were hybridized to Selleck TSA HDAC the Trichoderma selleck screening library HDO microarray proposed in this work. Results Trichoderma HDO microarray design The probe selection process conducted as described in Methods yielded a total of 384,659 different probes [GEO accession number: GPL7702] that were included on our custom-designed Trichoderma HDO microarray. After mapping these individual probes to the initial collections of EST-derived transcripts of twelve Trichoderma strains and genome-derived transcripts of T. reesei, from which the probes were designed, it was found that approximately 35% of the probes on the chip matched transcripts from Trichoderma spp. and about 65% matched transcripts from T. reesei, which was consistent with the size in base-pairs of each of the two sequence collections (7.1 and 13.9 Mbp, respectively). Moreover, 1.5% of the probes on the chip could be mapped to sequences from both databases. The the number of probes associated with each particular transcript sequence (probe set size) ranged from 1 to 94 for Trichoderma spp. transcripts, and from 1 to 1,245 for T. reesei transcripts, with a median
value of 16 and 22, respectively, and a maximum of approximately 40 nt between adjacent probes (data not shown). The final composition of the microarray in terms of the number of transcript sequences of each Trichoderma strain represented by a probe set is shown in Figure 1. In all, of the original 14,237 EST-derived sequences of Trichoderma spp. and 9,129 genome-derived sequences of T. reesei, only 156 (1,1%) and 8 (0.1%), respectively, were not represented on the microarray since no probe passed the selection procedure (the identification codes of the excluded sequences are available as supplementary material in additional file 1). Figure 1 Trichoderma HDO microarray composition. Number of gene transcripts of Trichoderma spp. (EST-derived) and T. reesei (genome-derived) represented on the Trichoderma HDO microarray generated in the present work. Overview of expression data in T. harzianum from microarray analysis Trichoderma HDO microarrays were hybridized with cDNA obtained from T.