Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data

The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Her...

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Автори: Alkan, Can, Ventura, Mario, Archidiacono, Nicoletta, Rocchi, Mariano, Sahinalp, S. Cenk, Eichler, Evan E
Формат: Стаття
Мова:English
Опубліковано: Public Library of Science 2007
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Research Article
Онлайн доступ:https://ncbi.nlm.nih.gov/pmc/articles/PMC1994983/
https://ncbi.nlm.nih.gov/pubmed/17907796
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1371/journal.pcbi.0030181
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spelling pubmed-19949832007-09-28 Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data Alkan, Can Ventura, Mario Archidiacono, Nicoletta Rocchi, Mariano Sahinalp, S. Cenk Eichler, Evan E PLoS Comput Biol Research Article The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution. Public Library of Science 2007-09 2007-09-28 /pmc/articles/PMC1994983/ /pubmed/17907796 http://dx.doi.org/10.1371/journal.pcbi.0030181 Text en © 2007 Alkan et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
institution US National Library of Medicine
collection PubMed Central
language English
format Article
topic Research Article
spellingShingle Research Article
Alkan, Can
Ventura, Mario
Archidiacono, Nicoletta
Rocchi, Mariano
Sahinalp, S. Cenk
Eichler, Evan E
Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
description The major DNA constituent of primate centromeres is alpha satellite DNA. As much as 2%–5% of sequence generated as part of primate genome sequencing projects consists of this material, which is fragmented or not assembled as part of published genome sequences due to its highly repetitive nature. Here, we develop computational methods to rapidly recover and categorize alpha-satellite sequences from previously uncharacterized whole-genome shotgun sequence data. We present an algorithm to computationally predict potential higher-order array structure based on paired-end sequence data and then experimentally validate its organization and distribution by experimental analyses. Using whole-genome shotgun data from the human, chimpanzee, and macaque genomes, we examine the phylogenetic relationship of these sequences and provide further support for a model for their evolution and mutation over the last 25 million years. Our results confirm fundamental differences in the dispersal and evolution of centromeric satellites in the Old World monkey and ape lineages of evolution.
author Alkan, Can
Ventura, Mario
Archidiacono, Nicoletta
Rocchi, Mariano
Sahinalp, S. Cenk
Eichler, Evan E
author_facet Alkan, Can
Ventura, Mario
Archidiacono, Nicoletta
Rocchi, Mariano
Sahinalp, S. Cenk
Eichler, Evan E
author_sort Alkan, Can
title Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
title_short Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
title_full Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
title_fullStr Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
title_full_unstemmed Organization and Evolution of Primate Centromeric DNA from Whole-Genome Shotgun Sequence Data
title_sort organization and evolution of primate centromeric dna from whole-genome shotgun sequence data
publisher Public Library of Science
publisher_facet Public Library of Science
publishDate 2007
url https://ncbi.nlm.nih.gov/pmc/articles/PMC1994983/
https://ncbi.nlm.nih.gov/pubmed/17907796
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1371/journal.pcbi.0030181
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