hide
Free keywords:
-
Abstract:
The emergence of new genes is an important driver of evolutionary novelty. Yet, we lack a conceptual and computational approach that accurately traces gene-family founder events and effectively associates them with trait innovation and major radiation events. 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 analyzed 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 the 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. We show that the transition to multicellularity in streptophytes, the terrestrialization of land plants and the origin of angiosperms are associated with gene-family founder bursts, as well as the evolution of bilateral symmetry in animals. Finally, we explore the emergence of novel genes in the brown algae, a fourth eukaryotic lineage that independently evolved complex multicellularity, and show how some of their youngest genes might have evolved de novo from intergenic DNA.
