Plant virus diversity in invasive weeds and crop plant varying between plant species and management systems

We conducted field surveys to detect the population density of the most important invasive weed species and their associated virus vectoring aphids in crops grown under high input (HIF) vs low-input (LIF) field conditions, with and without fertilizers and pesticides. The most frequent invasive weed species were Stenactis annua, Erigeron canadensis and Solidago canadensis. These species were hosts predominantly for the aphids Brachycaudus helichrysi and Aulacorthum solani in both management systems. The 13% higher coverage of S. annua under LIF conditions resulted in a 30% higher B. helichrysi abundance and ~85% higher A. solani abundance compared with HIF conditions. To reveal virus infection in crop plants and invasive weeds high-throughput sequencing of small RNAs were carried out. Bioinformatics analysis of the results detected the presence of 16 important plant viruses, but not resulting strikingly different pattern under LIF and HIF. This could suggest that invasive weeds serves as a virus reservoir both under low and high input management systems. The lake of any management increases virus vector aphids abundances, their presence has a great impact on the viromes of the crops. Overall design: Leaf samples were collected from Tusnad and from Segesvar from three different crops: Solanum tuberosum, Medicago sativa and Zea mays and from two weeds species from each place. RNA was extracted by a phenol-chloroform method. RNA pools were prepared mixing equal amounts of RNA originating from different individuals, collection times (in case of the weeds) and from different species (in case of the crops). These pools were used for small RNA library preparation (6 libraries in total) using Truseq Small RNA Library Preparation Kit (Illumina, USA) and our modified protocol. Samples were sequenced using single index on a HiScan2000 by UD Genomed (Debrecen, Hungary) 50 bp, single end.