Rates and patterns of great ape retrotransposition

Rates and patterns of great ape retrotransposition

Hormozdiari, Fereydoun et al.-- Great Ape Genome Project

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Bibliographic Details
Main Authors: Hormozdiari, Fereydoun, Prado-Martinez, Javier, Hernando-Herraez, Irene, Marqués-Bonet, Tomàs, Eichler, Evan E.
Other Authors: National Institutes of Health (US)
Format: artículo biblioteca
Published: National Academy of Sciences (U.S.) 2013
Subjects:Retrotransposon, Structural variation, Genomics, Genetic diversity,
Online Access:http://hdl.handle.net/10261/115565
http://dx.doi.org/10.13039/100000002
http://dx.doi.org/10.13039/501100000781
http://dx.doi.org/10.13039/501100004837
http://dx.doi.org/10.13039/100000011
http://dx.doi.org/10.13039/501100002809
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spelling dig-ibe-es-10261-1155652021-11-22T13:10:36Z Rates and patterns of great ape retrotransposition Hormozdiari, Fereydoun Prado-Martinez, Javier Hernando-Herraez, Irene Marqués-Bonet, Tomàs Eichler, Evan E. National Institutes of Health (US) European Research Council Ministerio de Ciencia e Innovación (España) Howard Hughes Medical Institute Generalitat de Catalunya Retrotransposon Structural variation Genomics Genetic diversity Hormozdiari, Fereydoun et al.-- Great Ape Genome Project We analyzed 83 fully sequenced great ape genomes for mobile element insertions, predicting a total of 49,452 fixed and polymorphic Alu and long interspersed element 1 (L1) insertions not present in the human reference assembly and assigning each retrotransposition event to a different time point during great ape evolution. We used these homoplasy-free markers to construct a mobile element insertions-based phylogeny of humans and great apes and demonstrate their differential power to discern ape subspecies and populations. Within this context, we find a good correlation between L1 diversity and single-nucleotide polymorphism heterozygosity (r2 =0.65) in contrast to Alu repeats, which show little correlation (r2 =0.07). We estimate that the rate of Alu retrotransposition has differed by a factor of 15-fold in these lineages. Humans, chimpanzees, and bonobos show the highest rates of Alu accumulation-the latter two since divergence 1.5 Mya. The L1 insertion rate, in contrast, has remained relatively constant, with rates differing by less than a factor of three. We conclude that Alu retrotransposition has been the most variable form of genetic variation during recent human-great ape evolution, with increases and decreases occurring over very short periods of evolutionary time. This work was supported by National Institutes of Health (NIH) Grant HG002385 (to E.E.E.), NIH R01 Grant GM59290 (to M.A.B.), an European Research Council Starting Grant (260372) (to T.M.-B.), and Ministerio de Ciencia e Innovacion (MICINN - Spain) BFU2011-28549 (to T.M.-B.). P.H.S. is supported by a Howard Hughes International Student Fellowship; E.E.E. is an Investigator of the Howard Hughes Medical Institute; and T.M.-B. is a Research Investigator (Institut Catala d’Estudis i Recerca Avancats de la Generalitat de Catalunya). Peer Reviewed 2015-05-21T09:47:36Z 2015-05-21T09:47:36Z 2013 2015-05-21T09:47:36Z artículo http://purl.org/coar/resource_type/c_6501 doi: 10.1073/pnas.1310914110 issn: 0027-8424 Proceedings of the National Academy of Sciences 110(33): 13457-13462 (2013) http://hdl.handle.net/10261/115565 10.1073/pnas.1310914110 http://dx.doi.org/10.13039/100000002 http://dx.doi.org/10.13039/501100000781 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/100000011 http://dx.doi.org/10.13039/501100002809 23884656 http://dx.doi.org/10.1073/pnas.1310914110 Sí none National Academy of Sciences (U.S.)
institution IBE ES
collection DSpace
country España
countrycode ES
component Bibliográfico
access En linea
databasecode dig-ibe-es
tag biblioteca
region Europa del Sur
libraryname Biblioteca del IBE España
topic Retrotransposon
Structural variation
Genomics
Genetic diversity
Retrotransposon
Structural variation
Genomics
Genetic diversity
spellingShingle Retrotransposon
Structural variation
Genomics
Genetic diversity
Retrotransposon
Structural variation
Genomics
Genetic diversity
Hormozdiari, Fereydoun
Prado-Martinez, Javier
Hernando-Herraez, Irene
Marqués-Bonet, Tomàs
Eichler, Evan E.
Rates and patterns of great ape retrotransposition
description Hormozdiari, Fereydoun et al.-- Great Ape Genome Project
author2 National Institutes of Health (US)
author_facet National Institutes of Health (US)
Hormozdiari, Fereydoun
Prado-Martinez, Javier
Hernando-Herraez, Irene
Marqués-Bonet, Tomàs
Eichler, Evan E.
format artículo
topic_facet Retrotransposon
Structural variation
Genomics
Genetic diversity
author Hormozdiari, Fereydoun
Prado-Martinez, Javier
Hernando-Herraez, Irene
Marqués-Bonet, Tomàs
Eichler, Evan E.
author_sort Hormozdiari, Fereydoun
title Rates and patterns of great ape retrotransposition
title_short Rates and patterns of great ape retrotransposition
title_full Rates and patterns of great ape retrotransposition
title_fullStr Rates and patterns of great ape retrotransposition
title_full_unstemmed Rates and patterns of great ape retrotransposition
title_sort rates and patterns of great ape retrotransposition
publisher National Academy of Sciences (U.S.)
publishDate 2013
url http://hdl.handle.net/10261/115565
http://dx.doi.org/10.13039/100000002
http://dx.doi.org/10.13039/501100000781
http://dx.doi.org/10.13039/501100004837
http://dx.doi.org/10.13039/100000011
http://dx.doi.org/10.13039/501100002809
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