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Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis)
- Source :
- Genome biology and evolution, Genome Biology and Evolution
- Publication Year :
- 2013
- Publisher :
- Oxford University Press. The Journal's web site is located at http://gbe.oxfordjournals.org, 2013.
-
Abstract
- Transposable 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.<br />published_or_final_version
- Subjects :
- 0106 biological sciences
Transposable element
Genome evolution
Xenopus
Retrotransposon
genome evolution
010603 evolutionary biology
01 natural sciences
Genome
Evolution, Molecular
03 medical and health sciences
Genome Components
Genetics
Animals
DNA transposon
Xenopus tropicalis
Repeated sequence
Western clawed frog
Ecology, Evolution, Behavior and Systematics
030304 developmental biology
Silurana
0303 health sciences
GC content
biology
Base Sequence
Terminal Repeat Sequences
Chromosome Mapping
natural selection
biology.organism_classification
Mutagenesis, Insertional
DNA Transposable Elements
gene expression
African clawed frogs
Research Article
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Genome biology and evolution, Genome Biology and Evolution
- Accession number :
- edsair.doi.dedup.....8f3f72647894838012677b429670781d