Project description:Plant-beneficial fungi from the genus Trichoderma (Hypocreales, Ascomycota) can control oomyceteous plant-pathogenic Pythium myriotylum (Peronosporales, Oomycota) and thus serve as bioeffectors for the eco-friendly products of crop protection. However, the underlying mechanisms of microbe-microbe interactions have yet to be fully understood. In this study, we focused on the role of the Trichoderma secretome induced by P. myriotylum mycelia. For this purpose, we selected strains showing strong (T. asperellum, T. atroviride, T. virens), moderate (T. cf. guizhouense, T. reesei), and weak (T. parepimyces) activities, respectively, and cultured with the sterilized P. myriotylum mycelia. Secreted proteins were analyzed using label-free LC-MS/MS, bioinformatic localization prediction, gene ontology (GO) annotation, and ortholog analysis. The exoproteomic analysis quantified proteins in the six Trichoderma spp., suggesting unequal antagonistic mechanisms among the strong and weak strains, respectively, with different proportions of putative cellulases, proteases, redox enzymes, and extracellular proteins of unknown function. Notably, proteolysis-related proteins were abundant, while the abundant proteases tended not to be conserved across the species (i.e., non-orthologous). Putative cellobiohydrolases were detected abundantly in all Trichoderma species except for the weak antagonist T. parepimyces, even though its genome encodes for these proteins. Notably, secretomes of the most potent anti-Pythium bioeffectors tended to have higher endo-cellulase activity. Cellulose and other glucans are major components of the oomycete cell wall, which was partly reflected in the cellulases produced by the Trichoderma species. The varying abundances of orthologous proteins suggested the evolution of differing transcription regulation mechanisms across the Trichoderma genus in response to the ubiquitous presence of Oomycota.
Project description:Annotation of small RNAs from 11 Drosophila species for the purpose of non-coding RNA annotation and comparative genomics assessment.
Project description:A self-designed Trichoderma high density oligonuclotide (HDO) microarray (Roche-NimbleGen, Inc., Madison, WI, USA) was constructed in a similar way than a previous Trichoderma HDO microarray (Samolski et al., 2009). The microarray was composed of 392,779 60-mer probes designed against 14,081 EST-derived transcripts (Trichochip-1) and the genomes of T. reesei (9,129 genes) and T. virens (11,643 genes). The Trichochip-1 ESTs were obtained from 28 cDNA libraries from eight different species (representing the biodiversity of this genus: T. harzianum, T. atroviride, T. asperellum, T. viride, T. longibrachiatum, T. virens, T. stromaticum and T. aggresivum), under a wide range of growth conditions, including biocontrol-related conditions and different nutritional situations (Vizcaíno et al., 2006). This HDO microarray was used to analyze Trichoderma spp. transcriptomes after 20 h incubation in the presence of tomato plants. The Trichochip1 EST database was generated in the TrichoEST project funded by the EU (QLK3-CT-2002-02032).