Tomato root miRNA dynamics in response to Potato Cyst Nematode (Globodera rostochiensis) infection

To understand in detail plant nematode interactions, we studied in depth the micro RNA (miRNA) dynamics in the feeding structure (syncytium) induced by Globodera rostochiensis in tomato roots. The microtranscriptomes were obtained from samples covering the early and intermediate developmental stages of feeding structures. The expression of 1,235 miRNAs was examined. Down- and up-regulated species, including their isomiRs, were further used to identify their potential targets. The fold change (log2FC) ranged from -7.36 to 8.38, indicating that this transcriptome fraction was very variable. Moreover, we showed that DE miRNAs do not fully overlap between the selected time points, suggesting infection stage specific regulation by miRNA. The accuracy of RNA-seq expression profiling was confirmed by qRT-PCR for seven miRNA species. Differentially expressed miRNAs have a number of potential target transcripts with rather typical miRNA functional category distribution, including a large number of transcription factors regulating different aspects of plant development. Target cleavage was proven in total for 29 miRNAs using three alternative methods: 5’ RACE, tasiRNA analysis, and tomato degradome data mining GEO databases. Eight target transcripts showed a negative correlation with their respective miRNAs at two or three time points. The target sequences detected in our research belong to gene families such as APETALA2(AP2), SQUAMOSA (MADS-box), MYB, GRAS, and AUXIN RESPONSE FACTOR (ARF), and thus indicate the involvement of miRNA mediated regulation of the plant defense response, cell wall maintenance, and developmental processes. Target sequences of these transcription factors (TFs) are known to regulate root development (AP2, SQUAMOSA, GRAS) or play crucial roles in the metabolic feedback and fine tuning of the phytohormonal response to the nematode infection (MYB, ARF).