GSE106240
NGS of virus derived small RNAs as a diagnostics method used to determine viromes of Hungarian vineyards
As virus diseases cannot be controlled by traditional plant protection methods the risk of their spread have to be minimized on vegetatively propagated plants, such as grapevine. Metagenomics approaches used for virus diagnostics, offer a unique opportunity to reveal the presence of all viral pathogens in the investigated plant, why their usage can reduce the risk of using infected material for a new plantation. Here we used a special field, deep sequencing of virus derived small RNAs, of this high throughput method for virus diagnostics and determined viromes of vineyards in Hungary. With NGS of virus derived small RNAs we could detect not only the viruses tested routinely, but also new ones, which have never been described in Hungary before. Virus presence didn't correlated with the age of the plantation, moreover phylogenetic analysis of the identified virus isolates suggests that infections mostly caused by the usage of infected propagating material. Our results, validated by other molecular methods, highlighted further questions to be answered before these method can be introduced as a routine, reliable test for grapevine virus diagnostics. Overall design: Samples were collected from 14 vineyards representing 18 different varieties and 9 wine growing-regions at different locations of Hungary. Shoots of 1-10 randomly chosen individual plants per plantation were collected on the field or from forced canes. RNA was extracted from different organs: shoot tips, young leaves (until the 3rd internodes from the soot apex), older leaves (lower than the 3rd internodes), tendrils and flowers by CTAB method (Gambino, 2008). RNA pools representing each plant were generated mixing equal content of RNA originated from different organs. This individual plant RNA pools (library 14-18) or a plantation pool generated by the same strategy, representing all of the sampled plant from the same plantation (library 1-13), was used for small RNA library preparation (18 libraries in total