Here we describe the protocols to characterize the virome associated to fungi isolated from marine organisms assessed on the seagrass Posidonia oceanica and on the marine animal Holothuria poli. We provide detailed protocols for fungal isolation, fungal growth, and total RNA extraction. Ribosomal RNA depletion, cDNA library synthesis and normalization, and sequencing runs on different platforms are part of the protocols that are generally outsourced and therefore are not described in this chapter. We describe, instead, how raw reads are assembled into contigs and how to search for putative viral sequences. Furthermore, we detail qualitative checks to infer the existence of the virus as a replicative biological entity.

Different Approaches to Discover Mycovirus Associated to Marine Organisms

Nerva, Luca;Varese, Giovanna C;Turina, Massimo
2018

Abstract

Here we describe the protocols to characterize the virome associated to fungi isolated from marine organisms assessed on the seagrass Posidonia oceanica and on the marine animal Holothuria poli. We provide detailed protocols for fungal isolation, fungal growth, and total RNA extraction. Ribosomal RNA depletion, cDNA library synthesis and normalization, and sequencing runs on different platforms are part of the protocols that are generally outsourced and therefore are not described in this chapter. We describe, instead, how raw reads are assembled into contigs and how to search for putative viral sequences. Furthermore, we detail qualitative checks to infer the existence of the virus as a replicative biological entity.
Viral Metagenomics.
Vitantonio, Pantaleo, Michela, Chiumenti
Methods in Molecular Biology
1746
97
114
978-1-4939-7682-9
978-1-4939-7683-6
Holothuria poli; Mycovirus; Posidonia oceanica; RNA-Seq; Viral genome assembly
Nerva, Luca; Varese, Giovanna C; Turina, Massimo
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2318/1661558
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