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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 techniques to either analyze 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.

Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population