{"id":253,"date":"2015-05-22T15:28:58","date_gmt":"2015-05-22T19:28:58","guid":{"rendered":"https:\/\/people.clas.ufl.edu\/ebraun\/?page_id=253"},"modified":"2026-03-19T08:29:20","modified_gmt":"2026-03-19T12:29:20","slug":"ab03","status":"publish","type":"page","link":"https:\/\/people.clas.ufl.edu\/ebraun\/publications\/ab03\/","title":{"rendered":"Innovation from Reduction: Gene Loss, Domain Loss and Sequence Divergence in Genome Evolution"},"content":{"rendered":"\r\n<section class=\"fullwidth-text-block\">\r\n\t<div class=\"container px-0 pt-5\">\r\n\t\t<div class=\"row align-items-start\">\r\n\t\t\t<div class=\"col-12\">\r\n\t\t\t\t\n<h1 class=\"wp-block-heading\">Innovation from Reduction: Gene Loss, Domain Loss and Sequence Divergence in Genome Evolution<\/h1>\n\n\n\n<p><em>Applied Bioinformatics<\/em>, Vol. 2, pp. 13-34<\/p>\n\n\n\n\n\n<p>Download a\u00a0<a href=\"https:\/\/people.clas.ufl.edu\/ebraun\/content-removed\/\">reprint<\/a>\u00a0of this paper<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Innovation from Reduction: Gene Loss, Domain Loss and Sequence Divergence in Genome Evolution<\/h3>\n\n\n\n<p><strong>Edward L. Braun<sup>*<\/sup><wbr><\/wbr><\/strong><\/p>\n\n\n\n\n\n<p>Department of Zoology, University of Florida, Gainesville, Florida 32611<\/p>\n\n\n\n\n\n<p>Analyses of genome<sup>\u00a0<\/sup>sequences have revealed<sup>\u00a0<\/sup>a surprisingly variable<sup>\u00a0<\/sup>distribution of genes,<sup>\u00a0<\/sup>reflecting the<sup>\u00a0<\/sup>generation of novel<sup>\u00a0<\/sup>genes, lateral gene transfer<sup>\u00a0<\/sup>and gene loss.<sup>\u00a0<\/sup>The impact of gene<sup>\u00a0<\/sup>loss on organisms has<sup>\u00a0<\/sup>been difficult to examine,<sup>\u00a0<\/sup>but the loss of<sup>\u00a0<\/sup>protein coding genes,<sup>\u00a0<\/sup>the loss of domains<sup>\u00a0<\/sup>within proteins and<sup>\u00a0<\/sup>the divergence of<sup>\u00a0<\/sup>genes have made surprising<sup>\u00a0<\/sup>contributions to the<sup>\u00a0<\/sup>differences among<sup>\u00a0<\/sup>organisms. This paper<sup>\u00a0<\/sup>reviews surveys of<sup>\u00a0<\/sup>gene loss and divergence<sup>\u00a0<\/sup>in fungal and archaeal genomes<sup>\u00a0<\/sup>that indicate suites<sup>\u00a0<\/sup>of functionally related<sup>\u00a0<\/sup>genes tend to undergo<sup>\u00a0<\/sup>loss and divergence.<sup>\u00a0<\/sup>Instances of fungal gene<sup>\u00a0<\/sup>loss highlighted here suggest<sup>\u00a0<\/sup>that specific cellular<sup>\u00a0<\/sup>systems have changed,<sup>\u00a0<\/sup>such as Ca<sup>2+<\/sup>\u00a0biology in\u00a0<i>Saccharomyces<sup>\u00a0<\/sup>cerevisiae<\/i>\u00a0and peroxisome<sup>\u00a0<\/sup>function in\u00a0<i>Schizosaccharomyces<sup>\u00a0<\/sup>pombe<\/i>.<sup>\u00a0<\/sup>Analyses of loss and<sup>\u00a0<\/sup>divergence can provide<sup>\u00a0<\/sup>specific predictions<sup>\u00a0<\/sup>regarding protein-protein<sup>\u00a0<\/sup>interactions, and<sup>\u00a0<\/sup>the relationship<sup>\u00a0<\/sup>between networks of<sup>\u00a0<\/sup>protein interactions and<sup>\u00a0<\/sup>loss may form a part<sup>\u00a0<\/sup>of a parametric<sup>\u00a0<\/sup>model of genome<sup>\u00a0<\/sup>evolution.<\/p>\n\n\n\n<p><sup>*<\/sup>\u00a0Corresponding author<\/p>\n\n\n\n\n\n\n\r\n\t\t\t<\/div>\r\n\t\t<\/div>\r\n\t<\/div>\r\n<\/section>\r\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":544,"featured_media":0,"parent":19,"menu_order":19,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"featured_post":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-253","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/253","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/users\/544"}],"replies":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/comments?post=253"}],"version-history":[{"count":5,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/253\/revisions"}],"predecessor-version":[{"id":492,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/253\/revisions\/492"}],"up":[{"embeddable":true,"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/pages\/19"}],"wp:attachment":[{"href":"https:\/\/people.clas.ufl.edu\/ebraun\/wp-json\/wp\/v2\/media?parent=253"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}