File Download

There are no files associated with this item.

  Links for fulltext
     (May Require Subscription)
Supplementary

Article: Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis)

TitleGenomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis)
Authors
KeywordsAfrican clawed frogs
GC content
Xenopus tropicalis
gene expression
genome evolution
natural selection
Issue Date2013
PublisherOxford University Press. The Journal's web site is located at http://gbe.oxfordjournals.org
Citation
Genome Biology and Evolution, 2013, v. 5 n. 5, p. 998-1009 How to Cite?
AbstractTransposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variables and the presence of TEs and non-TE repeats in the complete genome sequence of the Western clawed frog (Silurana tropicalis). This analysis reveals patterns of TE insertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood model failed to attribute these differences in insertion frequencies to variation in selection pressure on different classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.
Persistent Identifierhttp://hdl.handle.net/10722/226669
ISSN
2015 Impact Factor: 4.098
2015 SCImago Journal Rankings: 3.220
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorShen, JJ-
dc.contributor.authorDushoff, J-
dc.contributor.authorBewick, AJ-
dc.contributor.authorChain, FJ-
dc.contributor.authorEvans, BJ-
dc.date.accessioned2016-06-23T02:05:35Z-
dc.date.available2016-06-23T02:05:35Z-
dc.date.issued2013-
dc.identifier.citationGenome Biology and Evolution, 2013, v. 5 n. 5, p. 998-1009-
dc.identifier.issn1759-6653-
dc.identifier.urihttp://hdl.handle.net/10722/226669-
dc.description.abstractTransposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variables and the presence of TEs and non-TE repeats in the complete genome sequence of the Western clawed frog (Silurana tropicalis). This analysis reveals patterns of TE insertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood model failed to attribute these differences in insertion frequencies to variation in selection pressure on different classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.-
dc.languageeng-
dc.publisherOxford University Press. The Journal's web site is located at http://gbe.oxfordjournals.org-
dc.relation.ispartofGenome Biology and Evolution-
dc.rightsPre-print: Journal Title] ©: [year] [owner as specified on the article] Published by Oxford University Press [on behalf of xxxxxx]. All rights reserved. Pre-print (Once an article is published, preprint notice should be amended to): This is an electronic version of an article published in [include the complete citation information for the final version of the Article as published in the print edition of the Journal.] Post-print: This is a pre-copy-editing, author-produced PDF of an article accepted for publication in [insert journal title] following peer review. The definitive publisher-authenticated version [insert complete citation information here] is available online at: xxxxxxx [insert URL that the author will receive upon publication here].-
dc.subjectAfrican clawed frogs-
dc.subjectGC content-
dc.subjectXenopus tropicalis-
dc.subjectgene expression-
dc.subjectgenome evolution-
dc.subjectnatural selection-
dc.titleGenomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis)-
dc.typeArticle-
dc.identifier.emailShen, JJ: janeshen91@gmail.com-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1093/gbe/evt065-
dc.identifier.pmid23645600-
dc.identifier.pmcidPMC3673623-
dc.identifier.volume5-
dc.identifier.issue5-
dc.identifier.spage998-
dc.identifier.epage1009-
dc.identifier.isiWOS:000324593500020-
dc.publisher.placeUnited Kingdom-

Export via OAI-PMH Interface in XML Formats


OR


Export to Other Non-XML Formats