De Novo Emerged Gene Search in Eukaryotes with DENSE.

ABSTRACT: The discovery of de novo emerged genes, originating from previously noncoding DNA regions, challenges traditional views of species evolution. Indeed, the hypothesis of neutrally evolving sequences giving rise to functional proteins is highly unlikely. This conundrum has sparked numerous studies to quantify and characterize these genes, aiming to understand their functional roles and contributions to genome evolution. Yet, no fully automated pipeline for their identification is available. Therefore, we introduce DENSE (DE Novo emerged gene SEarch), an automated Nextflow pipeline based on two distinct steps: detection of taxonomically restricted genes (TRGs) through phylostratigraphy, and filtering of TRGs for de novo emerged genes via genome comparisons and synteny search. DENSE is availabl

SUBMITTER: Roginski P 

PROVIDER: S-EPMC11363675 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature