ArticleMolecular biology and evolution2008
Signature genes as a phylogenomic tool.
Article in Molecular biology and evolution, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Alternative characterizations of Fitch's xenology relation.Journal of mathematical biology · 2019Article
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- Inferring phylogenetic trees from the knowledge of rare evolutionary events.Journal of mathematical biology · 2018Article
- Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms.PloS one · 2018Article
- Phylogenomics and Comparative Genomic Studies Robustly Support Division of the GenusFrontiers in microbiology · 2018Article
- Article
- The composition of the global and feature specific cyanobacterial core-genomes.Frontiers in microbiology · 2015Article
- A New Comparative-Genomics Approach for Defining Phenotype-Specific Indicators Reveals Specific Genetic Markers in Predatory Bacteria.PloS one · 2015Article
- Whole genome phylogenies for multiple Drosophila species.BMC research notes · 2012Article
- Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.BMC genomics · 2012Article
- Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.Microbiology and molecular biology reviews : MMBR · 2012Review
- Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.Frontiers in cellular and infection microbiology · 2012Review
- Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships.Frontiers in microbiology · 2012Article
- How stands the Tree of Life a century and a half after The Origin?Biology direct · 2011Review
- LifePrint: a novel k-tuple distance method for construction of phylogenetic trees.Advances and applications in bioinformatics and chemistry : AABC · 2011Article
- Novel glycoside hydrolases identified by screening a Chinese Holstein dairy cow rumen-derived metagenome library.Applied and environmental microbiology · 2010Article
- MLTreeMap--accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.BMC genomics · 2010Article
- The ecological coherence of high bacterial taxonomic ranks.Nature reviews. Microbiology · 2010Review
- Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups.Photosynthesis research · 2010Review
- Signature proteins for the major clades of Cyanobacteria.BMC evolutionary biology · 2010Article
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4 authors.
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Abstract
Gene content has been shown to contain a strong phylogenetic signal, yet its usage for phylogenetic questions is hampered by horizontal gene transfer and parallel gene loss and until now required completely sequenced genomes. Here, we introduce an approach that allows the phylogenetic signal in gene content to be applied to any set of sequences, using signature genes for phylogenetic classification. The hundreds of publicly available genomes allow us to identify signature genes at various taxonomic depths, and we show how the presence of signature genes in an unspecified sample can be used to characterize its taxonomic composition. We identify 8,362 signature genes specific for 112 prokaryotic taxa. We show that these signature genes can be used to address phylogenetic questions on the basis of gene content in cases where classic gene content or sequence analyses provide an ambiguous answer, such as for Nanoarchaeum equitans, and even in cases where complete genomes are not available, such as for metagenomics data. Cross-validation experiments leaving out up to 30% of the species show that approximately 92% of the signature genes correctly place the species in a related clade. Analyses of metagenomics data sets with the signature gene approach are in good agreement with the previously reported species distributions based on phylogenetic analysis of marker genes. Summarizing, signature genes can complement traditional sequence-based methods in addressing taxonomic questions.
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