GSE130859
VIROME OF PEACH TREES IDENTIFIED BY SMALL RNA HTS IN HUNGARY
Virus elimination is indispensable for the maintenance of stone fruit plantations, because these pathogens can cause serious crop damage and crop losses. Currently we do not possess efficient plant protection methods against viruses therefore prevention has a prominent role. In order to prevent infections, pathogen-free propagation material production and application of effective diagnostic methods have essential role. Our examined peach samples derived from isolator houses and stock nurseries of Fruitculture Research Institute of NARIC. With the help of highly sensitive metagenomic diagnostic methods: such as next generation sequencing of small RNAs, we are able to detect all of the presenting pathogens within our samples. During preparation steps, total RNA was isolated from leaf samples, RNA pools were made from the varieties, and then small RNA libraries were prepared. Sequencing was performed on Illumina platform and we used CLC Genomics Workbench for the bioinformatics evaluation. Results were verified by RT-PCR and Northern-blot. PCR products were cloned into pJET vector and Sanger sequenced. As a result, we detected nectarine stem pitting-associated virus (NSPaV), peach associated luteovirus (PaLV) and also peach latent mosaic viroid (PLMVd) which presence has to be checked regularly. Moreover we proved the incidence of PLMVd and PaLV first time in Hungary. We suspect, that the source of the viral infection might be the propagation material, which was used as a base for the variety collection in this isolator house. Overall design: Virus diagnostics of 2 peach varieties in isolator house (2 libraries), open air stock nurseries (2 libraries) and 10 different peach variety in isolator house (1 library) by Illumina sequencing of the small RNAs