Expression profile of non-coding small RNAs in tomato roots during Pochonia chlamydosporia endophytism.

Small RNAs play a key role in the plant-parasite interaction, regulating critical effector genes needed for infection. However, little is known about the effects of endophytes on non coding (nc)-RNAs expression in plant. To elucidate micro(mi)RNAs and other ncRNAs regulatory participation in plant-endophyte interactions, we used Illumina's NGS technology to sequence small RNAs (sRNAs) in tomato roots inoculated and not inoculated with the fungus Pochonia chlamydosporia. In both treatments, Sly-miR166a/b was the most abundant tomato miRNA, followed by sly-miR166c-3p. The two miRNAs together accounted for 81% and 74.1% of the annotated tomato miRNAs in P. chlamydosporia not inoculated or inoculated roots. Such highly expressed miRNAs are likely to have important roles in roots, considering that in epigeal parts of tomato and other plants the most abundant miRNA reported is miRNA-156. Endophytism by P. chlamydosporia affected miRNAs and other nc-sRNAs expression, with 26 miRNAs differentially expressed between the two treatments (up regulated with fold changes 2 to 9). Their 154 potential target genes involve apoptosis, primary metabolism and binding functions i.e. Squamosa promoter binding-like protein. Comparative analysis showed that 48 out of 5055 P. chlamydosporia down-regulated tomato genes, from a previous RNAseq experiment, are miRNA targets (with fold changes 2 to 16). Furthermore, five miRNAs (sly-miR9473-5p, sly-miR169c, sly-miR169a, sly-miR9476-5p and sly-miR1918) were found only in presence of the fungus. We also identified many other classes of sRNAs, including transfer RNA (tRNA)-derived sRNAs, some of which were also differentially expressed between the two treatments. Data provide valuable clues to understand the properties of sRNAs with a new insight on the role of miRNAs and other sRNAs in the host-endophyte interaction. A better understanding of ncRNA-mediated plant-endophyte interaction may sustain management of pests and diseases, and promote growth. MiRNA-based manipulations as gene suppressors, i.e. artificial miRNAs, may emerge as a new alternative approach for the improvement of crops and control of nematode pests.