{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T17:07:38Z","timestamp":1790788058340,"version":"4.1.0"},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"suppl_2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The endosymbiotic origin of mitochondria has resulted in a massive horizontal transfer of genetic material from an alpha-proteobacterium to the early eukaryotes. Using large-scale phylogenetic analysis we have previously identified 630 orthologous groups of proteins derived from this event. Here we show that this proto-mitochondrial protein set has undergone extensive lineage-specific gene loss in the eukaryotes, with an average of three losses per orthologous group in a phylogeny of nine species. This gene loss has resulted in a high variability of the alphaproteobacterial-derived gene content of present-day eukaryotic genomes that might reflect functional adaptation to different environments. Proteins functioning in the same biochemical pathway tend to have a similar history of gene loss events, and we use this property to predict functional interactions among proteins in our set.<\/jats:p>\n               <jats:p>Contact: \u00a0T.Gabaldon@cmbi.ru.nl<\/jats:p>\n               <jats:p>Supplementary information: Sequences and trees for the selected orthologous groups can be accessed at http:\/\/www.cmbi.kun.nl\/~jagabald\/table_groupsb.html<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti1124","type":"journal-article","created":{"date-parts":[[2005,10,3]],"date-time":"2005-10-03T21:33:25Z","timestamp":1128375205000},"page":"ii144-ii150","source":"Crossref","is-referenced-by-count":27,"title":["Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes"],"prefix":"10.1093","volume":"21","author":[{"given":"Toni","family":"Gabald\u00f3n","sequence":"first","affiliation":[{"name":"Center for Molecular and Biomolecular Informatics (CMBI) and Nijmegen Center for Molecular Life Sciences (NCMLS), Radboud University of Nijmegen Medical Center Toernooiveld 1, 6525 ED Nijmegen, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martijn A.","family":"Huynen","sequence":"additional","affiliation":[{"name":"Center for Molecular and Biomolecular Informatics (CMBI) and Nijmegen Center for Molecular Life Sciences (NCMLS), Radboud University of Nijmegen Medical Center Toernooiveld 1, 6525 ED Nijmegen, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2005,9,1]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/suppl_2\/ii144\/52089442\/bioinformatics_21_suppl2_ii144.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/suppl_2\/ii144\/52089442\/bioinformatics_21_suppl2_ii144.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,14]],"date-time":"2023-10-14T04:02:38Z","timestamp":1697256158000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/suppl_2\/ii144\/227428"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,9,1]]},"references-count":0,"journal-issue":{"issue":"suppl_2","published-print":{"date-parts":[[2005,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti1124","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,9]]},"published":{"date-parts":[[2005,9,1]]}}}