The origin of taxonomically restricted genes in yeast
The evolutionary origins of taxonomically restricted "orphan" genes (TRGs), which lack known homologs outside of a specific taxon, have fueled a decades-long controversy. On the one hand, thousands of TRGs are proposed to have originated de novo from previously non-genic DNA. These include an expansive repertoire of newly discovered microproteins that were missed from genome annotations yet can…
The debate surrounding the origin of taxonomically restricted orphan genes (TRGs) in yeast has persisted for decades. Some researchers argue that these genes are created anew from non-genic DNA, while others claim they are merely the result of extreme sequence divergence. To settle this dispute, researchers systematically examined the origins of TRGs across the Saccharomyces taxon, employing a sensitive profile-profile alignment method to identify homologs that were previously missed.
The study reveals a shift in the mechanisms behind TRG formation. Most species-specific TRGs are indeed the result of genuine de novo gene births, while the majority of TRGs that are shared across the Saccharomyces genus originate from highly diverged ancestral genes. These ancestral genes are no longer detectable as homologs using conventional methods, indicating that homology detection has failed.
This research suggests that, in Saccharomyces, the rate of de novo gene creation is balanced by evolutionary attrition. Over a few million years, nearly all de novo genes are destined to disappear without contributing to the stable genetic repertoire. Despite this, these newly created genes play a crucial role in species-specific physiology and adaptation, providing important benefits in the present time.
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