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Updated: Aug 5, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra
Josué Barrera-Redondo1, Jaruwatana Sodai Lotharukpong2, Hajk-Georg Drost3
1Department of Algal Development and Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany. josue.barrera@tuebingen.mpg.de.
Abstract:
We present GenEra ( https://github.com/josuebarrera/GenEra ), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage-dependent, suggesting that plants are more prone to evolve novelty through the emergence of new genes compared to animals and fungi.
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