ArticleNucleic acids research2019
AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 166 papers.
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166 citing papers in PubMed.
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- Identification of proteins influencing CRISPR-associated transposases for enhanced genome editing.Science advances · 2026Article
- Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance.Microbiology and molecular biology reviews : MMBR · 2025Review
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- Nitrogen-fixing microbes gain genes in diverse types of living environments.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.NAR genomics and bioinformatics · 2025Article
- DiazoTIME: a metabolically-resolved reference database of nitrogen-fixing microbial genomes.Microbiology resource announcements · 2025Article
- Evolutionary Flexibility of Ribosome Biogenesis in Bacteria.Molecular biology and evolution · 2025Article
- Host cyclophilin-mediated maturation of an obligate intracellular bacterial surface virulence factor.bioRxiv : the preprint server for biology · 2025Article
- MarK, a Novosphingobium aromaticivorans kinase required for catabolism of multiple aromatic monomers.The Journal of biological chemistry · 2025Article
- Structural and evolutionary determinants of Argonaute function.Nucleic acids research · 2025Article
- Root exudates protect rhizosphereApplied and environmental microbiology · 2025Article
- Anthropogenic climate change may reduce global diazotroph diversity.Nature communications · 2025Article
106 more citing papers are in PubMed but not listed here.
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6 authors.
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Abstract
Bacterial genomics has revolutionized our understanding of the microbial tree of life; however, mapping and visualizing the distribution of functional traits across bacteria remains a challenge. Here, we introduce AnnoTree-an interactive, functionally annotated bacterial tree of life that integrates taxonomic, phylogenetic and functional annotation data from over 27 000 bacterial and 1500 archaeal genomes. AnnoTree enables visualization of millions of precomputed genome annotations across the bacterial and archaeal phylogenies, thereby allowing users to explore gene distributions as well as patterns of gene gain and loss in prokaryotes. Using AnnoTree, we examined the phylogenomic distributions of 28 311 gene/protein families, and measured their phylogenetic conservation, patchiness, and lineage-specificity within bacteria. Our analyses revealed widespread phylogenetic patchiness among bacterial gene families, reflecting the dynamic evolution of prokaryotic genomes. Genes involved in phage infection/defense, mobile elements, and antibiotic resistance dominated the list of most patchy traits, as well as numerous intriguing metabolic enzymes that appear to have undergone frequent horizontal transfer. We anticipate that AnnoTree will be a valuable resource for exploring prokaryotic gene histories, and will act as a catalyst for biological and evolutionary hypothesis generation. AnnoTree is freely available at http://annotree.uwaterloo.ca.
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