The Dark Side of the Genome: Revealing the Native Transposable Element/Repeat Content of Eukaryotic Genomes
AffiliationArizona Genomics Institute, BIO5 Institute and School of Plant Sciences
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CitationThe Dark Side of the Genome: Revealing the Native Transposable Element/Repeat Content of Eukaryotic Genomes 2016 Molecular Plant
RightsCopyright © The Author 2016. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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AbstractThe majority of genome assemblies to date fail to represent the true structure of native genomes. This lack of completeness is largely due to the inability to assemble the variable (often significant) fraction of nuclear genomes that is composed primarily of repeated sequences (with either a structural function such as satellite DNA and simple sequence repeats or “selfish DNA” such as high-copy transposable elements [TEs]), herein defined as the “dark side of the genome.” To address this problem, we developed a method to detect and quantify the dark side of the genome and used it to infer the genomic composition and dynamic evolution of the majority of native repeats and TEs present within several test eukaryotic genomes.
NoteOpen access article.
VersionFinal published version
SponsorsThis work was supported by the US National Science Foundation under grants #0321678, #0638541, #0822284, and #1026200, the Bud Antle Endowed Chair of Excellence in Agriculture and Life Sciences, and the AXA Chair for Evolutionary Genomics and Genome Biology to R.A.W. Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the US National Science Foundation.
Except where otherwise noted, this item's license is described as Copyright © The Author 2016. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).