Plant parasitic cyst nematodes respond to viral infection through RNA interference

Plant-parasitic nematodes (PPN) cause yield losses to multiple important crop species and counteractive measures are only partially successful. Recently the first viruses that infect PPN were discovered, presenting new research opportunities to understand and halt PPN. A critical step in this process is to identify how PPN respond to viruses. Here, two PPN species, the potato cyst nematode Globodera rostochiensis and the beet cyst nematode Heterodera schachtii, were used to study PPN-virus interactions. Viral discovery based on bioinformatic analyses indicated three putative viral genomes present in G. rostochiensis (a Toti-like, Xinzhou-like, and Picorna-like virus) and five putative viral genomes in H. schachtii (a Bunya-like, Tobamo-like, Picorna-like, and two Nyami-like viruses). A genome composition analysis and RT-PCR data confirmed that these viruses infect the nematodes and not their host plants. Subsequently, antiviral RNAi activity was detected in both H. schachtii and G. rostochiensis using small RNA sequencing. For G. rostochiensis two distinct genotypes were investigated. These strongly differed in their RNAi response: Ro5-line 22 produced roughly 40 times more antiviral viRNAs than Ro1-line 19. Our measurement of an active antiviral response represents the first indication of antiviral activity in PPN. Author summary Plant-parasitic nematodes (PPN) are key agricultural pests and although some PPN viruses have been discovered recently, it is still unknown if and how PPN respond to viral infection. Here we find three viruses in the potato cyst nematode ( Globodera rostochiensis ) and five viruses in the beet cyst nematode ( Heterodera schachtii ). Of these viruses, six are newly discovered. Genome and molecular analyses confirm that all found viruses specifically infect nematodes and not their host plants. By measuring small RNA profiles, it was confirmed that PPN react to viral infection by means of RNAi, except for a weak response against two negatively stranded Nyami-like viruses. Moreover, distinct RNAi profiles were found for two potato cyst nematode lines, giving the first insight into which genes might be involved in RNAi in PPN. Together, this research provides the first proof of an active antiviral response in PPN. Thereby this finding opens new opportunities for biological control and gene editing tools.