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Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome\u2014the proportion of the genome harboring gene content difference for genome pairs\u2014varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%\u201333% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.<\/jats:p>","DOI":"10.1093\/femsle\/fnae068","type":"journal-article","created":{"date-parts":[[2024,9,14]],"date-time":"2024-09-14T01:42:13Z","timestamp":1726278133000},"source":"Crossref","is-referenced-by-count":5,"title":["A universal and constant rate of gene content change traces pangenome flux to LUCA"],"prefix":"10.1093","volume":"371","author":[{"given":"Katharina","family":"Trost","sequence":"first","affiliation":[{"name":"Faculty of Mathematics and Natural Sciences, Institute of Molecular Evolution, Heinrich Heine University D\u00fcsseldorf , 40225 D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R","family":"Knopp","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Natural Sciences, Institute of Molecular Evolution, Heinrich Heine University D\u00fcsseldorf , 40225 D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica L E","family":"Wimmer","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Natural Sciences, Institute of Molecular Evolution, Heinrich Heine University D\u00fcsseldorf , 40225 D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4291-2115","authenticated-orcid":false,"given":"Fernando D K","family":"Tria","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Natural Sciences, Institute of Molecular Evolution, Heinrich Heine University D\u00fcsseldorf , 40225 D\u00fcsseldorf ,","place":["Germany"]},{"name":"Los Alamos National Laboratory , Los Alamos, NM ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William F","family":"Martin","sequence":"additional","affiliation":[{"name":"Faculty of Mathematics and Natural Sciences, Institute of Molecular Evolution, Heinrich Heine University D\u00fcsseldorf , 40225 D\u00fcsseldorf ,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,8,20]]},"reference":[{"key":"2024102607410811000_bib1","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1038\/nrg.2016.39","article-title":"Evolution by gene loss","volume":"17","author":"Albalat","year":"2016","journal-title":"Nat Rev Genet"},{"key":"2024102607410811000_bib3","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1038\/ismej.2017.36","article-title":"Prokaryote genome fluidity is dependent on effective population size","volume":"11","author":"Andreani","year":"2017","journal-title":"ISME 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