Role and activity of miRNAs in the interaction of tomato roots with endophytic Pochonia chlamydosporia.

MicroRNAs (miRNAs) are endogenous small-RNAs transcribed from non-coding DNA, matching a target messenger RNA to repress translation or induce cleavage. They act in almost every biological plant activity e.g. development, abiotic stress tolerance, signal transduction, and in defense from pathogens or parasites. To elucidate miRNAs role in plant-endophyte interactions, we constructed libraries from roots of Solanum lycopersicum endophytically colonized (Pmi) or not (Pm) by the hyphomycete Pochonia chlamydosporia. This fungus shows endophytic behaviour with growth promotion or nematode biocontrol effects. No data are available on tomato miRNAs role and targets in the endophytic interaction. Illumina(TM) NGS of small-RNAs yielded 9 o 106 (Pmi) and 12 o 106 (Pm) reads per library. CLC Genomics Workbench was used for trimming, counting, annotation and data analysis. Non-redundant, unique small-RNAs (869178 in Pmi, 958026 in Pm), were produced. MiRNAs expression was affected by endophytism. Analyses of tomato miRNAs (miRBase, rel.21), revealed miR156 and miR168 (conserved across higher plants), as most abundant in roots. Four further miRNAs (miR169a, miR169c, miR9473 and miR9476), out of 75 known in tomato, were expressed only in Pmi, with seven further (miR169d, miR1917, miR169e, miR394, miR167a, miR5300 and miR9475) over-expressed and 27 down-regulated (fold change range: 1.2-4.8). 37 remaining miRNAs were equally expressed in both conditions. A Pmi comparative analysis showed that 1732 out of 5055 Pmi down-regulated genes were miRNA targets, involved in structural protein, metabolism, transcription factor, growth and development, stress-related, signaling pathways, storage and other processes.