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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

Alignment statistics of contig sequences constructed using Velvet, Metavelvet, and Oases short RNA assembly tools with different k-mer settings. The graph and table display the number of contig sequence aligning with CymRSV ref_seq (A) and fraction of CymRSV ref_seq covered by the consensus sequence (B). REMRED = Remove redundant.
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Figure 7: Alignment statistics of contig sequences constructed using Velvet, Metavelvet, and Oases short RNA assembly tools with different k-mer settings. The graph and table display the number of contig sequence aligning with CymRSV ref_seq (A) and fraction of CymRSV ref_seq covered by the consensus sequence (B). REMRED = Remove redundant.

Mentions: All contig sequences obtained by different tools and settings were aligned against the CymRSV ref_seq. First Velvet REMRED and second Metavelvet and Velvet showed to be the most efficient tools by generating, respectively, 45 and 41 consensus sequences at k = 15 (Figure 7A). For these approaches an increase or a decrease of k values resulted in a sensible decrease of contig sequences aligning with the CymRSV ref_seq: e.g., in the case of Velvet REMRED the use k = 13 or k = 17 reduces the number of contigs to 30 and 39, respectively, whereas for k = 15 in total 45 contigs were assembled (Figure 7A). Moreover, when applying k = 15 to both Velvet methods and MetaVelvet the coverage of the CymRSV genome was the highest, i.e., 0,69% (3.247 nt out of 4.733 nt of the CymRSV genome). Again a setting of k = 13 or k = 17 sensibly reduces the efficiency of the method (Figure 7B).


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)

Alignment statistics of contig sequences constructed using Velvet, Metavelvet, and Oases short RNA assembly tools with different k-mer settings. The graph and table display the number of contig sequence aligning with CymRSV ref_seq (A) and fraction of CymRSV ref_seq covered by the consensus sequence (B). REMRED = Remove redundant.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Alignment statistics of contig sequences constructed using Velvet, Metavelvet, and Oases short RNA assembly tools with different k-mer settings. The graph and table display the number of contig sequence aligning with CymRSV ref_seq (A) and fraction of CymRSV ref_seq covered by the consensus sequence (B). REMRED = Remove redundant.
Mentions: All contig sequences obtained by different tools and settings were aligned against the CymRSV ref_seq. First Velvet REMRED and second Metavelvet and Velvet showed to be the most efficient tools by generating, respectively, 45 and 41 consensus sequences at k = 15 (Figure 7A). For these approaches an increase or a decrease of k values resulted in a sensible decrease of contig sequences aligning with the CymRSV ref_seq: e.g., in the case of Velvet REMRED the use k = 13 or k = 17 reduces the number of contigs to 30 and 39, respectively, whereas for k = 15 in total 45 contigs were assembled (Figure 7A). Moreover, when applying k = 15 to both Velvet methods and MetaVelvet the coverage of the CymRSV genome was the highest, i.e., 0,69% (3.247 nt out of 4.733 nt of the CymRSV genome). Again a setting of k = 13 or k = 17 sensibly reduces the efficiency of the method (Figure 7B).

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