| Naslov: | Next generation sequencing for detection and discovery of plant viruses and viroids : comparison of two approaches |
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| Avtorji: | ID Pecman, Anja (Avtor)
ID Kutnjak, Denis (Avtor)
ID Gutiérrez-Aguirre, Ion (Avtor)
ID Adams, Ian (Avtor)
ID Fox, Adrian (Avtor)
ID Boonham, Neil (Avtor)
ID Ravnikar, Maja (Avtor) |
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| Datoteke: |  URL - Izvorni URL, za dostop obiščite https://dx.doi.org/10.3389/fmicb.2017.01998
 PDF - Predstavitvena datoteka, prenos (1,32 MB)
MD5: A69764026D1F6EA718A38E507466DD58
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| Jezik: | Angleški jezik |
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| Tipologija: | 1.01 - Izvirni znanstveni članek |
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| Organizacija: |  NIB - Nacionalni inštitut za biologijo
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| Povzetek: | 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). |
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| Ključne besede: | next generation sequencing, small RNA, ribosomal RNA depleted total RNA, detection, plant viruses, plant viroids |
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| Status publikacije: | Objavljeno |
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| Verzija publikacije: | Objavljena publikacija |
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| Datum objave: | 13.10.2017 |
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| Leto izida: | 2017 |
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| Št. strani: | str. 1-10 |
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| Številčenje: | Vol. 8 |
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| UDK: | 577.21 |
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| ISSN pri članku: | 1664-302X |
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| DOI: | 10.3389/fmicb.2017.01998  |
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| COBISS.SI-ID: | 4476495 |
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| Opomba: | Nasl. z nasl. zaslona;
Opis vira z dne 16. 10. 2017;
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| Datum objave v DiRROS: | 25.07.2024 |
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| Število ogledov: | 7 |
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| Število prenosov: | 3 |
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| Metapodatki: |     |
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