Generation, annotation, and analysis of ESTs from four different Trichoderma strains grown under conditions related to biocontrol

Abstract

The functional genomics project "TrichoEST" was developed focused on different taxonomic groups of Trichoderma with biocontrol potential. Four cDNA libraries were constructed, using similar growth conditions, from four different Trichoderma strains: Trichoderma longibrachiatum T52, Trichoderma asperellum T53, Trichoderma virens T59, and Trichoderma sp. T78. In this study, we present the analysis of the 8,160 expressed sequence tags (ESTs) generated. Each EST library was independently assembled and 1,000-1,300 unique sequences were identified in each strain. First, we queried our collection of ESTs against the NCBI nonredundant database using the BLASTX algorithm. Moreover, using the Gene Ontology hierarchy, we performed the annotation of 40.9% of the unique sequences. Later, based on the EST abundance, we examined the highly expressed genes in the four strains. A hydrophobin was found as the gene expressed at the highest level in two of the strains, but we also found that other unique sequences similar to the HEX1, QID3, and NMT1 proteins were highly represented in at least two of the Trichoderma strains.

Comparative study of Trichoderma gene expression in interactions with tomato plants using high-density oligonucleotide microarrays

“…The 12 662 Trichoderma unique sequences came from 14 237 Trichoderma spp. EST-derived transcripts obtained from 12 strains of eight different Trichoderma spp., including 991 ESTs from T. virens T59 (Vizcaíno et al, 2006(Vizcaíno et al, , 2007. The microarray contained 374 824 probes, corresponding to 34 138 transcripts: 11 probes for 34 026 transcripts and less than 11 probes for 112 that had passed the previous filters.…”

“…More global studies have applied 'omics to the understanding of the general aspects of biocontrol by Trichoderma spp. (Carpenter et al, 2005;Liu & Yang, 2005;Scherm et al, 2009;Vizcaíno et al, 2006Vizcaíno et al, , 2007. Several researchers have explored the responses of plants to the presence of a root-colonizing Trichoderma strain (Alfano et al, 2007;Marra et al, 2006;Segarra et al, 2007;Shoresh & Harman, 2008), but the fungal component of this association has been less studied.…”

“…In the present study, an HDO microarray composed of 374 824 60-mer probes was constructed by adding 11 643 genes of the annotated genome of the biocontrol strain Trichoderma virens (Hypocrea virens) Gv29-8 to the previously described Trichoderma HDO microarray that encompassed 12 662 unique sequences derived from a Trichoderma expressed sequence tag (EST) collection obtained from 12 strains belonging to eight species (Vizcaíno et al, 2006(Vizcaíno et al, , 2007, and 9129 genes of Trichoderma reesei (Samolski et al, 2009), and was used to compare the transcriptional responses of Trichoderma hamatum IMI 224801 and T. harzianum CECT 2413, which both promote tomato growth, and T. virens Gv29-8, which showed detrimental effects in our study, during the early stages of their interactions with tomato roots.…”

Identification of potential marker genes for Trichoderma harzianum strains with high antagonistic potential against Rhizoctonia solani by a rapid subtraction hybridization approach

“…Despite the widespread use of this principle with industrially applied and plant pathogenic fungi, it has not yet yielded unambiguous results with respect to genes required for the physiological changes accompanying mycoparasitism and biocontrol. While this study was completed, three papers were published, two of which dealt with the collection of ESTs (Vizcaino et al 2006(Vizcaino et al , 2007, whereas a third one used subtractive hybridization in T. hamatum (Carpenter et al 2005). However, in the Wrst two cases mRNAs were isolated from Trichoderma spp.…”

“…In fact, both approaches have recently been applied to T. harzianum (Liu and Yang 2005;Vizcaino et al 2006), T. hamatum (Carpenter et al 2005) and T. asperellum, T. longibrachiatum, T. cf. viride and T. virens (Vizcaino et al 2007), but the obtained clones were not thoroughly characterized. In addition, in the majority of these studies, the fungi were grown in submerged culture on cell wall of potential plant pathogens as carbon source, and the physiological relevance of this approach to biocontrol is debatable.…”