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

Type

• Articolo in rivista (Classe)
• Prodotto della ricerca (Classe)

Label

• Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population. (Articolo in rivista) (literal)

Anno

• 2014-01-01T00:00:00+01:00 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi

• 10.3389/fmicb.2014.00790 (literal)

Alternative label

• Pirovano W., Miozzi L., Boetzer M., Pantaleo V. (2014)
  Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population.
  in Frontiers in microbiology
  (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori

• Pirovano W., Miozzi L., Boetzer M., Pantaleo V. (literal)

Pagina inizio

• 790 (literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume

• 5 (literal)

Rivista

• Frontiers in microbiology (Rivista)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni

• Institute for Sustainable Plant Protection of CNR, Strada delle Cacce 73, Turin (2) and Research Unit of Bari (3), Italy. Genome Analysis and Technology Department, BaseClear B. V., Leiden, Netherlands (1) (literal)

Titolo

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

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. (literal)

Prodotto di

• Interazioni biologiche e molecolari delle piante con virus e agenti patogeni virus-simili (AG.P01.010.001) (Modulo)

Autore CNR

• VITANTONIO PANTALEO (Persona)
• LAURA MIOZZI (Unità di personale interno)

Insieme di parole chiave

• Keywords of "Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population." (Insieme di parole chiave)

Incoming links:

Autore CNR di

• VITANTONIO PANTALEO (Persona)
• LAURA MIOZZI (Unità di personale interno)

Prodotto

• Interazioni biologiche e molecolari delle piante con virus e agenti patogeni virus-simili (AG.P01.010.001) (Modulo)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#rivistaDi

• Frontiers in microbiology (Rivista)

Insieme di parole chiave di

• Keywords of "Bioinformatics approaches for viral metagenomics in plants using short RNAs: model case of study and application to a Cicer arietinum population." (Insieme di parole chiave)