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Published on: November 16, 2014
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AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.
Kerrin Mendler1, Han Chen1, Donovan H Parks2
1Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
Nucleic Acids Research
|May 14, 2019
Summary
AnnoTree visualizes functional traits across bacterial and archaeal genomes, revealing widespread gene gain and loss. This resource highlights patchy gene distributions, particularly for phage defense and antibiotic resistance genes in prokaryotes.
Area of Science:
- Microbial genomics
- Evolutionary biology
- Bioinformatics
Background:
- Bacterial genomics has advanced understanding of microbial life.
- Mapping functional traits across bacteria is challenging.
- Phylogenetic distribution of genes is key to understanding prokaryotic evolution.
Purpose of the Study:
- Introduce AnnoTree, an interactive, functionally annotated bacterial tree of life.
- Enable visualization of genome annotations and gene distributions.
- Facilitate exploration of gene gain/loss patterns in prokaryotes.
Main Methods:
- Integrated taxonomic, phylogenetic, and functional annotation data from >27,000 bacterial and 1,500 archaeal genomes.
- Developed AnnoTree for visualizing millions of precomputed genome annotations.
- Analyzed phylogenomic distributions of 28,311 gene/protein families.
Main Results:
- Revealed widespread phylogenetic "patchiness" in bacterial gene families.
- Identified genes involved in phage infection/defense, mobile elements, and antibiotic resistance as highly patchy.
- Observed frequent horizontal gene transfer for numerous metabolic enzymes.
Conclusions:
- AnnoTree is a valuable resource for exploring prokaryotic gene histories.
- The dynamic evolution of prokaryotic genomes is reflected in gene distributions.
- AnnoTree can catalyze biological and evolutionary hypothesis generation.
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