Abstract

Over the past years deep sequencing experiments have opened novel doors to ?reconstruct viral populations in a high-throughput and cost-effective manner. Currently a ?substantial number of studies have been performed which employ Next Generation Sequencing (NGS) techniques to either analyse known viruses by means of a reference-guided approach or to discover novel viruses using a de novo-based strategy. Taking ?advantage of the well-known Cymbidium ringspot virus we have carried out a comparison of ?different bioinformatics tools to reconstruct the viral genome based on 21-27 nt short (s)RNA sequencing with the aim to identify the most efficient pipeline. The same approach was ?applied to a population of plants constituting an ancient variety of Cicer arietinum with red ?seeds. Among the discovered viruses, we describe the presence of a Tobamovirus referring to the Tomato mottle mosaic virus (NC_022230), which was not yet observed on C. arietinum nor revealed in Europe and a viroid referring to Hop stunt viroid (NC_001351.1) never reported in chickpea. Notably, a reference sequence guided approach appeared the most efficient in such kind of investigation. Instead, the de novo assembly reached a non-appreciable coverage although the most prominent viral species could still be identified. ?Advantages and limitations of viral metagenomics analysis using sRNAs are discussed.

Autore Pugliese

• Pantaleo Vitantonio

Tutti gli autori

• Pirovano W.; Miozzi L.; Boetzer M.; Pantaleo V.

Titolo volume/Rivista

Frontiers in microbiology

Anno di pubblicazione

2014

ISSN

1664-302X

ISBN

Non Disponibile

Numero di citazioni Wos

Nessuna citazione

Ultimo Aggiornamento Citazioni

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Numero di citazioni Scopus

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Ultimo Aggiornamento Citazioni

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Settori ERC

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Codici ASJC

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