ArticlePloS one2013
Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed.
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- Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era.National science review · 2024Review
- Phylogenomic Testing of Root Hypotheses.Genome biology and evolution · 2023Article
- Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.Microbiome · 2022Article
- Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IFMicroorganisms · 2022Review
- Testing Phylogenetic Stability with Variable Taxon Sampling.Methods in molecular biology (Clifton, N.J.) · 2022Article
- New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia.International journal of microbiology · 2022Review
- Natural Selection Shapes Maintenance of Orthologous sRNAs in Divergent Host-Restricted Bacterial Genomes.Molecular biology and evolution · 2021Article
- The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum.Microbiome · 2021Article
- Reclassification ofInternational journal of systematic and evolutionary microbiology · 2021Article
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- Evolutionary and Comparative Analysis of Bacterial Nonhomologous End Joining Repair.Genome biology and evolution · 2020Article
- Intrinsic laws of k-mer spectra of genome sequences and evolution mechanism of genomes.BMC evolutionary biology · 2020Article
- Impact of C-terminal amino acid composition on protein expression in bacteria.Molecular systems biology · 2020Article
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5 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes. We identified 24, single-copy, ubiquitous genes suitable for this phylogenetic analysis. We used two approaches to combine the data for the 24 genes. First, we concatenated alignments of all genes into a single alignment from which a Maximum Likelihood (ML) tree was inferred using RAxML. Second, we used a relatively new approach to combining gene data, Bayesian Concordance Analysis (BCA), as implemented in the BUCKy software, in which the results of 24 single-gene phylogenetic analyses are used to generate a "primary concordance" tree. A comparison of the concatenated ML tree and the primary concordance (BUCKy) tree reveals that the two approaches give similar results, relative to a phylogenetic tree inferred from the 16S rRNA gene. After comparing the results and the methods used, we conclude that the current best approach for generating a single phylogenetic tree, suitable for use as a reference phylogeny for comparative analyses, is to perform a maximum likelihood analysis of a concatenated alignment of conserved, single-copy genes.
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