Tomato Root Small-RNA Transcriptome Dynamics in Response to Potato Cyst Nematode Infection

Plant-parasitic cyst nematodes infect roots and induce formation of multinuclear syncytium, a specialized structure becoming a sole food source for developing larvae and adults. The formation of syncytium is accompanied with active suppression of defense response as well as substantial reprogramming of development and metabolism of incorporated cells. Such processes are likely to engage different mechanisms of gene expression regulation including those mediated by small RNAs. Since down-regulation of genes upon plant parasitic nematode infection is a common phenomenon concerning a third part of regulated genes we decided to purify and sequence the sRNA fraction of infected and uninfected root transcriptome.

The results show many changes in composition of sRNA transcriptomes. Within the fraction of miRNA, 71 known sequences have been found with 16 of them manifesting over 2-fold induction/suppression as compared to control samples. Their predicted target genes in tomato genome are encoding transcription factors (GRAS, MYB, NAM), proteins involved in signal transduction (glucose/ribitol dehydrogenase, phosphatidate cytidyltransferase) and other defense related proteins such as LRR receptor-like serine/threonine-protein kinases or ACRE proteins. Several miRNA homologues identified, such as mir1446, mir164 and mir399 are up-regulated in infected tissues showing the potential mechanism of defense suppression by cyst nematodes.