The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused...

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Authors: Marquès i Bonet, Tomàs, 1975-, Cheng, Ze, She, Xinwei, Eichler, Evan E., Navarro i Cuartiellas, Arcadi, 1969-
Format: article
Status:Published version
Publication Date:2008
Country:España
Institution:Universitat Pompeu Fabra
Repository:Repositorio Digital de la UPF
OAI Identifier:oai:repositori.upf.edu:10230/16388
Online Access:http://hdl.handle.net/10230/16388
http://dx.doi.org/10.1186/1471-2164-9-384
Access Level:Open access
Keyword:Genoma humà
Evolució humana
ADN
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oai_identifier_str oai:repositori.upf.edu:10230/16388
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repository_id_str
spelling The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangementsMarquès i Bonet, Tomàs, 1975-Cheng, ZeShe, XinweiEichler, Evan E.Navarro i Cuartiellas, Arcadi, 1969-Genoma humàEvolució humanaADNBackground: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements./nResults: Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion: We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.This research was supported by a grant to A.N. from the Ministerio de Ciencia y Tecnología (Spain, BFU2006 15413-C02-01) and by BE2005 and BP2006 fellowships to T.M.B from the "Departament d'Educació i Universitats de la Generalitat de Catalunya".BioMed Central201220122008info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/16388http://dx.doi.org/10.1186/1471-2164-9-384reponame:Repositorio Digital de la UPFinstname:Universitat Pompeu FabraInglésBMC Genomics. 2008;9:384info:eu-repo/grantAgreement/ES/2PN/BFU2006-15413-C02-01© 2008 Marquès-Bonet et al. Creative Commons Attribution Licensehttp://creativecommons.org/licenses/by/2.0/info:eu-repo/semantics/openAccessoai:repositori.upf.edu:10230/163882026-06-12T07:21:37Z
dc.title.none.fl_str_mv The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
title The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
spellingShingle The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
Marquès i Bonet, Tomàs, 1975-
Genoma humà
Evolució humana
ADN
title_short The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
title_full The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
title_fullStr The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
title_full_unstemmed The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
title_sort The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements
dc.creator.none.fl_str_mv Marquès i Bonet, Tomàs, 1975-
Cheng, Ze
She, Xinwei
Eichler, Evan E.
Navarro i Cuartiellas, Arcadi, 1969-
author Marquès i Bonet, Tomàs, 1975-
author_facet Marquès i Bonet, Tomàs, 1975-
Cheng, Ze
She, Xinwei
Eichler, Evan E.
Navarro i Cuartiellas, Arcadi, 1969-
author_role author
author2 Cheng, Ze
She, Xinwei
Eichler, Evan E.
Navarro i Cuartiellas, Arcadi, 1969-
author2_role author
author
author
author
dc.subject.none.fl_str_mv Genoma humà
Evolució humana
ADN
topic Genoma humà
Evolució humana
ADN
description Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements./nResults: Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion: We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.
publishDate 2008
dc.date.none.fl_str_mv 2008
2012
2012
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/16388
http://dx.doi.org/10.1186/1471-2164-9-384
url http://hdl.handle.net/10230/16388
http://dx.doi.org/10.1186/1471-2164-9-384
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv BMC Genomics. 2008;9:384
info:eu-repo/grantAgreement/ES/2PN/BFU2006-15413-C02-01
dc.rights.none.fl_str_mv © 2008 Marquès-Bonet et al. Creative Commons Attribution License
http://creativecommons.org/licenses/by/2.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv © 2008 Marquès-Bonet et al. Creative Commons Attribution License
http://creativecommons.org/licenses/by/2.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Repositorio Digital de la UPF
instname:Universitat Pompeu Fabra
instname_str Universitat Pompeu Fabra
reponame_str Repositorio Digital de la UPF
collection Repositorio Digital de la UPF
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,812429

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