Faculty of Science and WCMR members A
ndrew Doxey and Laura Hug, with University of Waterloo students Kerrin Mendler, Han Chen, and Briallen Lobb have released AnnoTree, a tool that allows the visualization and exploration of a functionally annotated microbial tree of life. This tool was published in Nucleic Acids Research in April, 2019.
This interactive microbial (bacterial or archaeal) tree of life viewer lets researchers explore the presence/absence of genes and gene functions as they are mapped out onto the microbial tree of life. Enter a gene (such as FliC – KEGG number K02406) and you can see its distribution in bacteria. FliC is widespread amongst the bacteria because it is an important protein of bacterial mobility.
FliC protein is found on many of the branches of the bacterial tree of life (blue lines).
Using this method, researchers can identify lineage-specific gene families. For example, Endosymbiotic bacterial clade Endozoicomonas shows evidence of picking up some eukaryotic host proteins including genes involved in cytoskeletal organization (PFAM number PF01302). You can see from the picture created using AnnoTree that unlike the widespread mobility protein FliC this captured eukaryotic protein is limited to the clade Endozoicomonas.
The co-opted cytoskeletal protein is limited to only one branch of the bacterial tree of life (blue line).
The AnnoTree represents a valuable resource for exploring the evolution and distribution of genes and functional traits across the microbial tree of life.
- The AnnoTree application is available at: http://annotree.uwaterloo.ca
- Source code can be downloaded at: https://bitbucket.org/account/user/doxeylabcrew/projects/AN
- Documentation for AnnoTree is located at https://annotree-docs.readthedocs.io
See AnnoTree in action: