Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves
| Autor: | Frank Rabenstein, Victor Golyaev, Mikhail Pooggin, Thierry Candresse |
|---|---|
| Přispěvatelé: | Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Julius Kühn-Institut (JKI), INRA SPE department, European Project: 232250,EC:FP7:SME,FP7-SME-2008-1,DIVAS(2009), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB) |
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
0106 biological sciences
0301 basic medicine Molecular biology Virologie lcsh:Medicine 01 natural sciences Deep sequencing Article Plant Viruses 03 medical and health sciences RNA interference Plant virus Virology Human virome RNA-Seq Desiccation RNA Small Interfering lcsh:Science pathologie végétale Illumina dye sequencing Furovirus Genetics Multidisciplinary biology lcsh:R fungi RNA food and beverages Hordeum Argonaute biology.organism_classification antiviral Plant Leaves 030104 developmental biology RNA Plant maladie virale [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology lcsh:Q Plant sciences 010606 plant biology & botany |
| Zdroj: | Scientific Reports Scientific Reports, Nature Publishing Group, 2019, 9, ⟨10.1038/s41598-019-55547-3⟩ Scientific Reports, 2019, 9, ⟨10.1038/s41598-019-55547-3⟩ Scientific Reports (9), . (2019) Scientific Reports, Vol 9, Iss 1, Pp 1-10 (2019) |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-019-55547-3⟩ |
| Popis: | In plants, RNA interference (RNAi) generates small interfering (si)RNAs from entire genomes of viruses, satellites and viroids. Therefore, deep small (s)RNA sequencing is a universal approach for virome reconstruction and RNAi characterization. We tested this approach on dried barley leaves from field surveys. Illumina sequencing of sRNAs from 2 plant samples identified in both plants Hordeum vulgare endornavirus (HvEV) and barley yellow mosaic bymovirus (BaYMV) and, additionally in one plant, a novel strain of Japanese soil-borne wheat mosaic furovirus (JSBWMV). De novo and reference-based sRNA assembly yielded complete or near-complete genomic RNAs of these viruses. While plant sRNAs showed broad size distribution, viral sRNAs were predominantly 21 and 22 nucleotides long with 5′-terminal uridine or adenine, and were derived from both genomic strands. These bona fide siRNAs are presumably processed from double-stranded RNA precursors by Dicer-like (DCL) 4 and DCL2, respectively, and associated with Argonaute 1 and 2 proteins. For BaYMV (but not HvEV, or JSBWMV), 24-nucleotide sRNAs represented the third most abundant class, suggesting DCL3 contribution to anti-bymovirus defence. Thus, viral siRNAs are well preserved in dried leaf tissues and not contaminated by non-RNAi degradation products, enabling both complete virome reconstruction and inference of RNAi components mediating antiviral defense. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|