Title |
Assembly of viral genomes from metagenomes
|
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Published in |
Frontiers in Microbiology, December 2014
|
DOI | 10.3389/fmicb.2014.00714 |
Pubmed ID | |
Authors |
Saskia L. Smits, Rogier Bodewes, Aritz Ruiz-Gonzalez, Wolfgang Baumgärtner, Marion P. Koopmans, Albert D. M. E. Osterhaus, Anita C. Schürch |
Abstract |
Viral infections remain a serious global health issue. Metagenomic approaches are increasingly used in the detection of novel viral pathogens but also to generate complete genomes of uncultivated viruses. In silico identification of complete viral genomes from sequence data would allow rapid phylogenetic characterization of these new viruses. Often, however, complete viral genomes are not recovered, but rather several distinct contigs derived from a single entity are, some of which have no sequence homology to any known proteins. De novo assembly of single viruses from a metagenome is challenging, not only because of the lack of a reference genome, but also because of intrapopulation variation and uneven or insufficient coverage. Here we explored different assembly algorithms, remote homology searches, genome-specific sequence motifs, k-mer frequency ranking, and coverage profile binning to detect and obtain viral target genomes from metagenomes. All methods were tested on 454-generated sequencing datasets containing three recently described RNA viruses with a relatively large genome which were divergent to previously known viruses from the viral families Rhabdoviridae and Coronaviridae. Depending on specific characteristics of the target virus and the metagenomic community, different assembly and in silico gap closure strategies were successful in obtaining near complete viral genomes. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 2 | 15% |
Germany | 1 | 8% |
Switzerland | 1 | 8% |
Austria | 1 | 8% |
Canada | 1 | 8% |
India | 1 | 8% |
Norway | 1 | 8% |
Unknown | 5 | 38% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Scientists | 6 | 46% |
Members of the public | 6 | 46% |
Science communicators (journalists, bloggers, editors) | 1 | 8% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Brazil | 7 | 3% |
United States | 4 | 2% |
United Kingdom | 2 | <1% |
Switzerland | 1 | <1% |
Sweden | 1 | <1% |
Egypt | 1 | <1% |
Germany | 1 | <1% |
Belgium | 1 | <1% |
Slovenia | 1 | <1% |
Other | 0 | 0% |
Unknown | 206 | 92% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 62 | 28% |
Researcher | 62 | 28% |
Student > Master | 29 | 13% |
Student > Bachelor | 13 | 6% |
Professor > Associate Professor | 9 | 4% |
Other | 20 | 9% |
Unknown | 30 | 13% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 96 | 43% |
Biochemistry, Genetics and Molecular Biology | 41 | 18% |
Immunology and Microbiology | 17 | 8% |
Medicine and Dentistry | 15 | 7% |
Engineering | 8 | 4% |
Other | 12 | 5% |
Unknown | 36 | 16% |