Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution
Autor(a) principal: | |
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Data de Publicação: | 2013 |
Outros Autores: | , , , , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1186/gb-2013-14-1-r10 http://hdl.handle.net/11449/112398 |
Resumo: | Background: Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data.Results: Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution.Conclusions: While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes. |
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spelling |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolutionBackground: Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data.Results: Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution.Conclusions: While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.Joint USDA/DOE Office of Science Feedstock genomics grantNational Science FoundationNIH-NIGMSUniv Calif Davis, Dept Mol & Cell Biol, Davis, CA 95616 USAUniv Calif Davis, Genome Ctr, Davis, CA 95616 USAUniv Calif Davis, Dept Plant Biol, Davis, CA 95616 USAUSDA ARS, Western Reg Res Ctr, Albany, CA 94710 USAUniv Calif Davis, Dept Ecol & Evolut, Davis, CA 95616 USAUniv Calif San Francisco, Dept Biochem & Biophys, San Francisco, CA 94158 USAPacific Biosci, Menlo Pk, CA 94025 USAUniv Estadual Paulista, Dept Anim Prod & Hlth, IAEA Collaborating Ctr Anim Genom & Bioinformat, BR-16050680 Aracatuba, SP, BrazilHoward Hughes Med Inst, Chevy Chase, MD 20815 USAUSDA ARS, US Meat Anim Res Ctr, Clay Ctr, NE 68933 USAUniv Calif Davis, Dept Plant Sci, Ctr Populat Biol, Davis, CA 95616 USAUniv Estadual Paulista, Dept Anim Prod & Hlth, IAEA Collaborating Ctr Anim Genom & Bioinformat, BR-16050680 Aracatuba, SP, BrazilJoint USDA/DOE Office of Science Feedstock genomics grantDE-AI02-09ER64829National Science FoundationIOS-0922703National Science FoundationIOS-1026094NIH-NIGMST32-GM008799Biomed Central Ltd.Univ Calif DavisUSDA ARSUniv Calif San FranciscoPacific BiosciUniversidade Estadual Paulista (Unesp)Howard Hughes Med InstMelters, Daniel P.Bradnam, Keith R.Young, Hugh A.Telis, NatalieMay, Michael R.Ruby, J. GrahamSebra, RobertPeluso, PaulEid, JohnRank, DavidGarcia, José Fernando [UNESP]DeRisi, Joseph L.Smith, TimothyTobias, ChristianRoss-Ibarra, JeffreyKorf, IanChan, Simon W. L.2014-12-03T13:10:41Z2014-12-03T13:10:41Z2013-01-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article20application/pdfhttp://dx.doi.org/10.1186/gb-2013-14-1-r10Genome Biology. London: Biomed Central Ltd, v. 14, n. 1, 20 p., 2013.1465-6906http://hdl.handle.net/11449/11239810.1186/gb-2013-14-1-r10WOS:000320155200010WOS000320155200010.pdf9991374083045897Web of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengGenome Biologyinfo:eu-repo/semantics/openAccess2024-09-04T19:15:25Zoai:repositorio.unesp.br:11449/112398Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestrepositoriounesp@unesp.bropendoar:29462024-09-04T19:15:25Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution |
title |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution |
spellingShingle |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution Melters, Daniel P. |
title_short |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution |
title_full |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution |
title_fullStr |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution |
title_full_unstemmed |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution |
title_sort |
Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution |
author |
Melters, Daniel P. |
author_facet |
Melters, Daniel P. Bradnam, Keith R. Young, Hugh A. Telis, Natalie May, Michael R. Ruby, J. Graham Sebra, Robert Peluso, Paul Eid, John Rank, David Garcia, José Fernando [UNESP] DeRisi, Joseph L. Smith, Timothy Tobias, Christian Ross-Ibarra, Jeffrey Korf, Ian Chan, Simon W. L. |
author_role |
author |
author2 |
Bradnam, Keith R. Young, Hugh A. Telis, Natalie May, Michael R. Ruby, J. Graham Sebra, Robert Peluso, Paul Eid, John Rank, David Garcia, José Fernando [UNESP] DeRisi, Joseph L. Smith, Timothy Tobias, Christian Ross-Ibarra, Jeffrey Korf, Ian Chan, Simon W. L. |
author2_role |
author author author author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Univ Calif Davis USDA ARS Univ Calif San Francisco Pacific Biosci Universidade Estadual Paulista (Unesp) Howard Hughes Med Inst |
dc.contributor.author.fl_str_mv |
Melters, Daniel P. Bradnam, Keith R. Young, Hugh A. Telis, Natalie May, Michael R. Ruby, J. Graham Sebra, Robert Peluso, Paul Eid, John Rank, David Garcia, José Fernando [UNESP] DeRisi, Joseph L. Smith, Timothy Tobias, Christian Ross-Ibarra, Jeffrey Korf, Ian Chan, Simon W. L. |
description |
Background: Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data.Results: Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. We assumed that the most abundant tandem repeat is the centromere DNA, which was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond approximately 50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution.Conclusions: While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animal and plant genomes. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes. |
publishDate |
2013 |
dc.date.none.fl_str_mv |
2013-01-01 2014-12-03T13:10:41Z 2014-12-03T13:10:41Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1186/gb-2013-14-1-r10 Genome Biology. London: Biomed Central Ltd, v. 14, n. 1, 20 p., 2013. 1465-6906 http://hdl.handle.net/11449/112398 10.1186/gb-2013-14-1-r10 WOS:000320155200010 WOS000320155200010.pdf 9991374083045897 |
url |
http://dx.doi.org/10.1186/gb-2013-14-1-r10 http://hdl.handle.net/11449/112398 |
identifier_str_mv |
Genome Biology. London: Biomed Central Ltd, v. 14, n. 1, 20 p., 2013. 1465-6906 10.1186/gb-2013-14-1-r10 WOS:000320155200010 WOS000320155200010.pdf 9991374083045897 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Genome Biology |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
20 application/pdf |
dc.publisher.none.fl_str_mv |
Biomed Central Ltd. |
publisher.none.fl_str_mv |
Biomed Central Ltd. |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
repositoriounesp@unesp.br |
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1810021376333971456 |