ArticleStandards in genomic sciences2013
Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects.
Article in Standards in genomic sciences, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed.
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- A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?Journal of clinical microbiology · 2016Review
- Taxonomy, Physiology, and Natural Products of Actinobacteria.Microbiology and molecular biology reviews : MMBR · 2016Review
- Genome-Based Taxonomic Classification ofFrontiers in microbiology · 2016Article
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- High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2(T) (DSM 21788(T)), a valuable source of polysaccharide decomposing enzymes.Standards in genomic sciences · 2015Article
- Draft genome sequence of Halomonas lutea strain YIM 91125(T) (DSM 23508(T)) isolated from the alkaline Lake Ebinur in Northwest China.Standards in genomic sciences · 2015Article
- High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India.Standards in genomic sciences · 2015Article
- Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.Standards in genomic sciences · 2015Article
- High quality draft genome sequence of Meganema perideroedes str. Gr1(T) and a proposal for its reclassification to the family Meganemaceae fam. nov.Standards in genomic sciences · 2015Article
- High quality draft genome sequence of Leucobacter chironomi strain MM2LB(T) (DSM 19883(T)) isolated from a Chironomus sp. egg mass.Standards in genomic sciences · 2015Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Despite the steadily decreasing costs of genome sequencing, prioritizing organisms for sequencing remains important in large-scale projects. Phylogeny-based selection is of interest to identify those organisms whose genomes can be expected to differ most from those that have already been sequenced. Here, we describe a method that infers a phylogenetic scoring independent of which set of organisms has previously been targeted, which is computationally simple and easy to apply in practice. The scoring itself, as well as pre- and post-processing of the data, is illustrated using two real-world examples in which the method has already been applied for selecting targets for genome sequencing. These projects are the JGI CSP Genomic Encyclopedia of Bacteria and Archaea phase I, targeting 1,000 type strains, and, on a smaller-scale, the phylogenomics of the Roseobacter clade. Potential artifacts of the method are discussed and compared to a selection approach based on the taxonomic classification.
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