Identifying single copy orthologs in Metazoa.

The 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 ga...

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Autores principales:	Christopher J Creevey, Jean Muller, Tobias Doerks, Julie D Thompson, Detlev Arendt, Peer Bork
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/071b686e981e41969b2a48c248e6cecb
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spelling	oai:doaj.org-article:071b686e981e41969b2a48c248e6cecb2021-11-18T05:51:45ZIdentifying single copy orthologs in Metazoa.1553-734X1553-735810.1371/journal.pcbi.1002269https://doaj.org/article/071b686e981e41969b2a48c248e6cecb2011-12-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22144877/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The 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.Christopher J CreeveyJean MullerTobias DoerksJulie D ThompsonDetlev ArendtPeer BorkPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 7, Iss 12, p e1002269 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Christopher J Creevey Jean Muller Tobias Doerks Julie D Thompson Detlev Arendt Peer Bork Identifying single copy orthologs in Metazoa.
description	The 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.
format	article
author	Christopher J Creevey Jean Muller Tobias Doerks Julie D Thompson Detlev Arendt Peer Bork
author_facet	Christopher J Creevey Jean Muller Tobias Doerks Julie D Thompson Detlev Arendt Peer Bork
author_sort	Christopher J Creevey
title	Identifying single copy orthologs in Metazoa.
title_short	Identifying single copy orthologs in Metazoa.
title_full	Identifying single copy orthologs in Metazoa.
title_fullStr	Identifying single copy orthologs in Metazoa.
title_full_unstemmed	Identifying single copy orthologs in Metazoa.
title_sort	identifying single copy orthologs in metazoa.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/071b686e981e41969b2a48c248e6cecb
work_keys_str_mv	AT christopherjcreevey identifyingsinglecopyorthologsinmetazoa AT jeanmuller identifyingsinglecopyorthologsinmetazoa AT tobiasdoerks identifyingsinglecopyorthologsinmetazoa AT juliedthompson identifyingsinglecopyorthologsinmetazoa AT detlevarendt identifyingsinglecopyorthologsinmetazoa AT peerbork identifyingsinglecopyorthologsinmetazoa
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Identifying single copy orthologs in Metazoa.

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