Recent research work, concened a transcriptomics study aimed to acquire informations about the hostantagonist interactions among plants and other organims. In particular, RNA libraries and smallRNAs were produced and processed, from RNA extracted by the antagonist fungus Pochonia chlamydosporia in artificial medium, or from inoculated tomato plants, developing bioinformatic analyses of high-throughput molecular data, generated using “next generation sequencing” techniques and “Illumina” technology. The data analyses allowed the production of a “de novo” transcriptome assembling of P. chlamydosporia, essential for gene expression studies aimed to assess the fungus genes expressed during host plant (endophytism) or nematode (parasitism) interactions.
Moreover, NGS data processing showed that P. chlamydosporia causes intense reprogramming of transcriptional profile in the roots. The expression analyses identified 9112 differentially expressed genes of tomato in the two conditions (non-inoculated /inoculated roots) of which 5,055 transcripts, involved in primary metabolism, were down-regulated during endophytism and 4057, related to defense mechanisms and plant growth promotion, were up-regulated with high levels of expression. The undertaken transcriptome analysis is the first step towards a more complete understanding of the plant-endophyte relationships, with important practical implications on the potential of P. chlamydosporia as a rhizosphere management tool.