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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

Average size of contigs obtained using Velvet, Metavelvet, and Oases short (s)RNA assembly tools with different k-mer settings. REMRED = Remove redundant.
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Figure 6: Average size of contigs obtained using Velvet, Metavelvet, and Oases short (s)RNA assembly tools with different k-mer settings. REMRED = Remove redundant.

Mentions: On the other hand, when comparing the average size of the contig sequences obtained by the different methods at different k-mers’s, Oases appears to be the best method. Indeed, except in the case of k = 11, Oases appears to provide the longest consensus sequences on average for all settings (Figure 6). Regarding the consensus sequences generated with Velvet and Metavelvet, the average length increased from k = 11 (the lowest) to k = 21 (the highest; Figure 6). The longest consensus sequence was obtained by Oases at k = 17 (i.e., 919 nt in length, Supplementary Data 1). Other tools obtained their maximum length (between 400 to 600 nt) at k-values ranging from 15 to 21 (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)

Average size of contigs 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 6: Average size of contigs obtained using Velvet, Metavelvet, and Oases short (s)RNA assembly tools with different k-mer settings. REMRED = Remove redundant.
Mentions: On the other hand, when comparing the average size of the contig sequences obtained by the different methods at different k-mers’s, Oases appears to be the best method. Indeed, except in the case of k = 11, Oases appears to provide the longest consensus sequences on average for all settings (Figure 6). Regarding the consensus sequences generated with Velvet and Metavelvet, the average length increased from k = 11 (the lowest) to k = 21 (the highest; Figure 6). The longest consensus sequence was obtained by Oases at k = 17 (i.e., 919 nt in length, Supplementary Data 1). Other tools obtained their maximum length (between 400 to 600 nt) at k-values ranging from 15 to 21 (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