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

Pirovano W, Miozzi L, Boetzer M, Pantaleo V - Front Microbiol (2015)

Bottom Line: Over the past years deep sequencing experiments have opened novel doors to reconstruct viral populations in a high-throughput and cost-effective manner.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.

View Article: PubMed Central - PubMed

Affiliation: Genome Analysis and Technology Department, BaseClear B. V. Leiden, Netherlands.

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 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.

No MeSH data available.


Related in: MedlinePlus

Alignments of contig sequences obtained using Velvet, Metavelvet, and Oases short RNA assembly tools at k = 15. Contig distribution graph for CymRSV ref_seq (A) and ToMMV ref_seq (B) REMRED = Remove redundant are displayed.
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Figure 10: Alignments of contig sequences obtained using Velvet, Metavelvet, and Oases short RNA assembly tools at k = 15. Contig distribution graph for CymRSV ref_seq (A) and ToMMV ref_seq (B) REMRED = Remove redundant are displayed.

Mentions: Obviously, a coverage value of 0,07 cannot be considered an acceptable coverage and shows the limitations of such approach for discovering novel viral entities. In Figure 10 we compare contigs which are de novo assembled using different bioinformatics tools at a k = 15 settings in the cases of CymRSV and ToMMV (Figures 10A,B respectively). Here we graphically confirm the findings revealed in Figure 7 and in Supplementary data 2 and 3. Indeed, the genome coverage of ToMMV is significantly lower compared to that of CymRSV (Figures 7A,B) and this is at least partly due to the abundance of viral-deriving siRNAs in the library (i.e., 364.590 vs. 1.909; Tables 1 and 2).


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

Pirovano W, Miozzi L, Boetzer M, Pantaleo V - Front Microbiol (2015)

Alignments of contig sequences obtained using Velvet, Metavelvet, and Oases short RNA assembly tools at k = 15. Contig distribution graph for CymRSV ref_seq (A) and ToMMV ref_seq (B) REMRED = Remove redundant are displayed.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4307218&req=5

Figure 10: Alignments of contig sequences obtained using Velvet, Metavelvet, and Oases short RNA assembly tools at k = 15. Contig distribution graph for CymRSV ref_seq (A) and ToMMV ref_seq (B) REMRED = Remove redundant are displayed.
Mentions: Obviously, a coverage value of 0,07 cannot be considered an acceptable coverage and shows the limitations of such approach for discovering novel viral entities. In Figure 10 we compare contigs which are de novo assembled using different bioinformatics tools at a k = 15 settings in the cases of CymRSV and ToMMV (Figures 10A,B respectively). Here we graphically confirm the findings revealed in Figure 7 and in Supplementary data 2 and 3. Indeed, the genome coverage of ToMMV is significantly lower compared to that of CymRSV (Figures 7A,B) and this is at least partly due to the abundance of viral-deriving siRNAs in the library (i.e., 364.590 vs. 1.909; Tables 1 and 2).

Bottom Line: Over the past years deep sequencing experiments have opened novel doors to reconstruct viral populations in a high-throughput and cost-effective manner.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.

View Article: PubMed Central - PubMed

Affiliation: Genome Analysis and Technology Department, BaseClear B. V. Leiden, Netherlands.

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 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.

No MeSH data available.


Related in: MedlinePlus