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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

Number of contigs (log scale) obtained using Velvet, Metavelvet, and Oases short (s)RNA assembly tools with different k-mer settings. REMRED = Remove redundant.
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Figure 4: Number of contigs (log scale) obtained using Velvet, Metavelvet, and Oases short (s)RNA assembly tools with different k-mer settings. REMRED = Remove redundant.

Mentions: We observe that Velvet and Metavelvet constructed the largest number of consensus sequences at all k-mer setting (hereafter “k”) used. Surprisingly, for all tools the maximum number of consensus sequences was obtained at setting k = 15 (Figure 4; Supplementary Data 1A). More specifically, Velvet is able to provide a higher number of consensus sequences at k = 15 when using a non-redundant sRNA dataset, i.e., 16.604 sequences using Velvet versus 23.251 using Velvet REDREM (Supplementary Data 1A,B, respectively). Accordingly, the total number of assembled nucleotides was higher when using Velvet and Metavelvet compared to Oases (Figure 5; Supplementary Data 1).


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)

Number of contigs (log scale) obtained using Velvet, Metavelvet, and Oases short (s)RNA assembly tools with different k-mer settings. REMRED = Remove redundant.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Number of contigs (log scale) obtained using Velvet, Metavelvet, and Oases short (s)RNA assembly tools with different k-mer settings. REMRED = Remove redundant.
Mentions: We observe that Velvet and Metavelvet constructed the largest number of consensus sequences at all k-mer setting (hereafter “k”) used. Surprisingly, for all tools the maximum number of consensus sequences was obtained at setting k = 15 (Figure 4; Supplementary Data 1A). More specifically, Velvet is able to provide a higher number of consensus sequences at k = 15 when using a non-redundant sRNA dataset, i.e., 16.604 sequences using Velvet versus 23.251 using Velvet REDREM (Supplementary Data 1A,B, respectively). Accordingly, the total number of assembled nucleotides was higher when using Velvet and Metavelvet compared to Oases (Figure 5; Supplementary Data 1).

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