The number of reported mycoviruses is increasing exponentially due to the current ability to detect mycoviruses using next-generation sequencing (NGS) approaches, with a large number of viral genomes built in-silico using data from fungal transcriptome projects. We decided to screen a collection of fungi originating from a specific marine environment (associated with the seagrass Posidonia oceanica) for the presence of mycoviruses: our findings reveal a wealth of diversity among these symbionts and this complexity will require further studies to address their specific role in this ecological niche. In specific, we identified twelve new virus species belonging to nine distinct lineages: they are members of megabirnavirus, totivirus, chrysovirus, partitivirus and five still undefined clades. We showed evidence of an endogenized virus ORF, and evidence of accumulation of dsRNA from metaviridae retroviral elements. We applied different techniques for detecting the presence of mycoviruses including (i) dsRNA extraction and cDNA cloning, (ii) small and total RNA sequencing through NGS techniques, (iii) rolling circle amplification (RCA) and total DNA extraction analyses, (iv) virus purifications and electron microscopy. We tried also to critically evaluate the intrinsic value and limitations of each of these techniques. Based on the samples we could compare directly, RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses. To our knowledge this is the first report on the virome of fungi isolated from marine environment.

Multiple approaches for the detection and characterization of viral and plasmid symbionts from a collection of marine fungi

NERVA, LUCA;CIUFFO, MARINA;VALLINO, MARTA;VARESE, Giovanna, Cristina;GNAVI, Giorgio;TURINA, MASSIMO
2016

Abstract

The number of reported mycoviruses is increasing exponentially due to the current ability to detect mycoviruses using next-generation sequencing (NGS) approaches, with a large number of viral genomes built in-silico using data from fungal transcriptome projects. We decided to screen a collection of fungi originating from a specific marine environment (associated with the seagrass Posidonia oceanica) for the presence of mycoviruses: our findings reveal a wealth of diversity among these symbionts and this complexity will require further studies to address their specific role in this ecological niche. In specific, we identified twelve new virus species belonging to nine distinct lineages: they are members of megabirnavirus, totivirus, chrysovirus, partitivirus and five still undefined clades. We showed evidence of an endogenized virus ORF, and evidence of accumulation of dsRNA from metaviridae retroviral elements. We applied different techniques for detecting the presence of mycoviruses including (i) dsRNA extraction and cDNA cloning, (ii) small and total RNA sequencing through NGS techniques, (iii) rolling circle amplification (RCA) and total DNA extraction analyses, (iv) virus purifications and electron microscopy. We tried also to critically evaluate the intrinsic value and limitations of each of these techniques. Based on the samples we could compare directly, RNAseq analysis is superior to sRNA for de novo assembly of mycoviruses. To our knowledge this is the first report on the virome of fungi isolated from marine environment.
219
22
38
Mycovirus; Taxonomy; Posidonia oceanica
Luca, Nerva; Marina, Ciuffo; Marta, Vallino; Paolo, Margaria; Giovanna C, Varese; Giorgio, Gnavi; Massimo, Turina
File in questo prodotto:
File Dimensione Formato  
Multiple approaches_4aperto.pdf

accesso aperto

Descrizione: Multiple approaches_Articolo completo con figure e tabelle
Tipo di file: POSTPRINT (VERSIONE FINALE DELL’AUTORE)
Dimensione 1.42 MB
Formato Adobe PDF
1.42 MB Adobe PDF Visualizza/Apri
1-s2.0-S0168170215301076-main.pdf

non disponibili

Tipo di file: PDF EDITORIALE
Dimensione 3.96 MB
Formato Adobe PDF
3.96 MB Adobe PDF   Visualizza/Apri   Richiedi una copia

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2318/1527617
Citazioni
  • ???jsp.display-item.citation.pmc??? 48
  • Scopus 94
  • ???jsp.display-item.citation.isi??? 88
social impact