Going underground to improve Capsicum annuum resilience: exploring root gene expression in the interaction with the endophytic and nematophagous fungus Pochonia chlamydosporia

RNA-seq analyses were conducted on pepper plants inoculated with Pochonia chlamydosporia, a root endophytic fungus, parasitic of root-knot nematodes (RKN). The transcriptome of pepper cv Quadrato d'Asti colonized in vitro by P. chlamydosporia DSM_26985 was sequenced. Data showed that differentially expressed genes (DEGs) in endophytized roots (n = 48, FC > 10, FDR < 0.01) included aquaporins (7/48 transcripts), ethylene and MYB transcription factors (4/48), with expansins and other enzymes. Further transcriptome data from pot-grown pepper cv. Crusco di Senise, inoculated with RKN and/or DSM_26985, showed hydrolase and biosynthetic processes differentially upregulated only after 24 hrs in the fungus-RKN treatment. At two weeks, DEGs of RKNinoculated plants were related to transport, homeostasis, lignin and cell wall pathways, whereas DSM_26985 induced processes related to cell wall recognition and response to fungus, also upregulated with RKN. Field data showed increased performance of Crusco di Senise plants treated with the fungus. The potential of P. chlamydosporia in promoting pepper resilience and growth after RKN attacks is consistent with the complex role played by the fungus in the tri-trophic host-plant interactions. Study partially funded by PSR BASILICATA 2014-2020 TINNOGEPRA, and EUROSTARS E-7364.