Pleiotropy increases with gene age in six model multicellular eukaryotes

Abstract

Fundamental traits of genes, including function, length and GC content, all vary with gene age. Pleiotropy, where a single gene affects multiple traits, arises through selection for novel traits and is expected to be removed from the genome through subfunctionalization following duplication events. It is unclear, however, how these opposing forces shape the prevalence of pleiotropy through time. We hypothesized that the prevalence of pleiotropy would be lowest in young genes, peak in middle aged genes, and then either decrease to a middling level in ancient genes or stay near the middle-aged peak, depending on the balance between exaptation and subfunctionalization. To address this question, we have calculated gene age and pleiotropic status for several model multicellular eukaryotes, including Homo sapiens, Mus musculus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana. Gene age was determined by finding the most distantly related species that shared an ortholog using the Open Tree of Life and the Orthologous Matrix Database (OMAdb). Pleiotropic status was determined using both protein-protein interactions (STRINGdb) and associated biological processes (Gene Ontology). We found that middle-aged and ancient genes tend to be more pleiotropic than young genes, and that this relationship holds across all species evaluated and across both modalities of measuring pleiotropy. We also found absolute differences in the degree of pleiotropy based on gene functional class, but only when looking at biological process count. From these results we propose that there is a fundamental relationship between pleiotropy and gene age and further study of this relationship may shed light on the mechanism behind the functional changes genes undergo as they age. Impact statementPleiotropy, the phenomenon where a single gene acts on multiple traits, is fundamental to genomic organization and has profound consequences for fitness. This work identifies a previously unknown relationship between pleiotropy and gene age, highlighting the dynamism of pleiotropy across time. This relationship holds across six distantly related model organisms, suggesting that it could be a highly generalizable finding, at least among multicellular eukaryotes. Following from this work, future investigation into mechanisms dictating the prevalence of pleiotropy at the gene or cellular level could provide fundamental insight into the maintenance of pleiotropy despite the potential for constraining rapid adaptation.