University of Waterloo researchers have developed a powerful new online tool that allows users to navigate through an interactive microbial tree of life, and to generate new scientific hypotheses and discoveries.
By integrating data across thousands of microbial genomes, “AnnoTree” provides a comprehensive framework for exploring the evolution of microbial genes and functions, and can be used to advance research across a wide range of industries including microbiology, biotechnology, industrial products, biofuels, and food science.
Increased understanding of gene function and diversity in microbes can lead to the identification of important biological phenomena, including the spread of antibiotic resistance, the evolution of bacterial pathogens, the origin of new gene families, and instances of gene transfer between specific bacterial genomes. AnnoTree is freely available at http://annotree.uwaterloo.ca.
AnnoTree interface overview. AnnoTree can be used to explore custom taxonomic trees and datasets.
Through AnnoTree’s web-based interface, users may query any gene of interest. The presence or absence of the gene will then be “painted” onto the microbial tree of life to highlight species that do or do not contain the gene. Users can then “zoom in” further and explore specific lineages of interest. Users may download publication-quality images, phylogenetic trees, gene sequences, and other information.
AnnoTree uses the recently developed Genome Taxonomy Database (GTDB), which provides a standardized, thorough description of the phylogeny and taxonomic nomenclature for over 27,000 bacteria and 1,500 archaea. All 28,941 microbial genomes in the GTDB were re-analyzed, and functional annotations were assigned to protein sequences during the development of AnnoTree. The resulting data is stored in an online database that is open and accessible to the research community. The AnnoTree database will be automatically updated to incorporate ongoing revisions to the GTDB taxonomy.
The AnnoTree application provides a reliable, automated tool for users to explore genes and functions of interest across microbes. The resulting genetic snapshots will enable researchers to quickly generate hypotheses, and identify genes and functions that are suitable for further study and application.
For more information about this research, please see Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC, AnnoTree: Visualization and exploration of a functionally annotated microbial tree of life. Nucleic Acids Research, 2019, 47(9): 4442–8.