Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families

Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display compl...

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Veröffentlicht in:Genome biology and evolution Jg. 16; H. 6
Hauptverfasser: Rossier, Victor, Train, Clement, Nevers, Yannis, Robinson-Rechavi, Marc, Dessimoz, Christophe
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Oxford University Press 04.06.2024
Schlagworte:
Animals
Evolution, Molecular
Gene families
Multigene Family
Opsins
Phylogenetics
Phylogeny
Software
software tool
tree reconciliation
visualization
gene evolution
phylogenetic profile
ISSN:1759-6653, 1759-6653
Online-Zugang:Volltext
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Zusammenfassung:Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use “phylogenetic” profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence–absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex.
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ISSN:1759-6653
1759-6653
DOI:10.1093/gbe/evae100