20.500.12556/DiRROS-19717 Next generation sequencing for detection and discovery of plant viruses and viroids comparison of two approaches Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families. The results demonstrate the ability for detection and identification of a wide array of known plant viruses/viroids in the tested samples by both approaches. In general, yield of viral sequences was dependent on viral genome organization and the amount of viral reads in the data. A putative novel Cytorhabdovirus, discovered in this study, was only detected by analysing the data generated from ribosomal RNA depleted total RNA and not from the small RNA dataset, due to the low number of short reads in the latter. On the other hand, for the viruses/viroids under study, the results showed higher yields of viral sequences in small RNA pool for viroids and viruses with no RNA replicative intermediates (single stranded DNA viruses). next generation sequencing small RNA ribosomal RNA depleted total RNA detection plant viruses plant viroids true false true Angleški jezik Ni določen Neznano 2024-07-24 03:47:08 2024-07-25 09:55:46 2024-09-10 13:58:47 0000-00-00 00:00:00 2017 0 0 Nasl. z nasl. zaslona; Opis vira z dne 16. 10. 2017; str. 1-10 Vol. 8 2017 0000-00-00 Zaloznikova Objavljeno NiDoloceno 0000-00-00 0000-00-00 2017-10-13 577.21 1664-302X 10.3389/fmicb.2017.01998 4476495 https://dx.doi.org/10.3389/fmicb.2017.01998 1 f6964be7-494d-11ef-b487-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=27238 RAZ_Pecman_Anja_2017.pdf RAZ_Pecman_Anja_2017.pdf 1 A69764026D1F6EA718A38E507466DD58 1685aaafaa239987676c98de1d1119e8f574d10ad19209cacc0d81c60683f023 ca5ec8a7-4a4a-11ef-b487-001a4af901a5 https://dirros.openscience.si/Dokument.php?lang=slv&id=27451 Nacionalni inštitut za biologijo 0 0 0