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dc.contributor.authorCreevey, Christopher J.*
dc.contributor.authorMuller, Jean*
dc.contributor.authorDoerks, Tobias*
dc.contributor.authorThompson, Julie D.*
dc.contributor.authorArendt, Detlev*
dc.contributor.authorBork, Peer*
dc.date.accessioned2014-08-20T14:44:40Z
dc.date.available2014-08-20T14:44:40Z
dc.date.issued2011-12-01
dc.identifier.citationCreevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, et al. (2011) Identifying Single Copy Orthologs in Metazoa. PLoS Comput Biol 7(12): e1002269.en_GB
dc.identifier.urihttp://hdl.handle.net/11019/707
dc.descriptionpeer-revieweden_GB
dc.description.abstractThe identification of single copy (1-to-1) orthologs in any group of organisms is important for functional classification and phylogenetic studies. The Metazoa are no exception, but only recently has there been a wide-enough distribution of taxa with sufficiently high quality sequenced genomes to gain confidence in the wide-spread single copy status of a gene. Here, we present a phylogenetic approach for identifying overlooked single copy orthologs from multigene families and apply it to the Metazoa. Using 18 sequenced metazoan genomes of high quality we identified a robust set of 1,126 orthologous groups that have been retained in single copy since the last common ancestor of Metazoa. We found that the use of the phylogenetic procedure increased the number of single copy orthologs found by over a third more than standard taxon-count approaches. The orthologs represented a wide range of functional categories, expression profiles and levels of divergence. To demonstrate the value of our set of single copy orthologs, we used them to assess the completeness of 24 currently published metazoan genomes and 62 EST datasets. We found that the annotated genes in published genomes vary in coverage from 79% (Ciona intestinalis) to 99.8% (human) with an average of 92%, suggesting a value for the underlying error rate in genome annotation, and a strategy for identifying single copy orthologs in larger datasets. In contrast, the vast majority of EST datasets with no corresponding genome sequence available are largely under-sampled and probably do not accurately represent the actual genomic complement of the organisms from which they are derived.en_GB
dc.description.sponsorshipThis work was funded by the EURASNET grant (European Union FP6 Programme; Contract number LSH-2004-1.1.5-3)(http://www.eurasnet.info/). CJC wishes to acknowledge current support from the Science Foundation Ireland (SFI) Stokes Lectureship Programme (Reference number: 07/SK/B1236A)(http://www. sfi.ie).en_GB
dc.language.isoenen_GB
dc.publisherPLOSen_GB
dc.relation.ispartofseriesPloS Computational Biology;vol 7
dc.subjectsingle copy (1-to-1) orthologsen_GB
dc.subjectMetazoaen_GB
dc.subjectPhylogenetic analysisen_GB
dc.subjectExpressed sequenceen_GB
dc.subjectGenomicsen_GB
dc.titleIdentifying Single Copy Orthologs in Metazoaen_GB
dc.typeArticleen_GB
dc.identifier.rmisGEAB-0203-5959
dc.identifier.doihttp://dx.doi.org/10.1371/journal.pcbi.1002269
dc.contributor.sponsorEuropean Union
dc.contributor.sponsorScience Foundation Ireland
dc.contributor.sponsorGrantNumberLSH-2004-1.1.5-3
dc.contributor.sponsorGrantNumber07/SK/B1236A
refterms.dateFOA2018-01-12T08:10:38Z


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