Regulatory factors in Pochonia chlamydosporia-induced gene expression

Soil microorganisms respond to and release signals in the rhizosphere, affecting root growth and their interactions with parasites. Understanding the gene expression patterns that are active in roots is fundamental for successful exploitation of beneficial associations. Pochonia chlamydosporia is a facultative parasite of nematode eggs and a growth-promoting endophyte. Next generation sequencing of transcripts from tomato roots colonized by P. chlamydosporia showed several differentially regulated genes. They included transcription factors and microRNAs, differentially expressed during root endophytism. Both are transcriptional regulators and form integral parts of signaling webs, modulating many biological processes. The Transcription factors involved in defense, resistance and plant growth included WRKY genes expressed either in P. chlamydosporia colonized or control roots. Endophytism also showed differential expression of 26 miRNAs, with 154 potential target genes involved in apoptosis, metabolism and binding, including Transcription factors. The differential gene expression induced by P. chlamydosporia in presence of nematodes or other pathogens may disclose novel pests and disease management strategies. Next generation sequencing analyses also support the production of industrial and commercial bioformulations for plant protection through the exploitation of endogenous defense mechanisms.