Abstract
BackgroundTransposable elements (TEs) are major components of eukaryotic genomes and drivers of genome evolution, producing intraspecific polymorphism and interspecific differences through mobilization and non-homologous recombination. TE insertion sites are often highly variable within species, creating a need for targeted genome re-sequencing (TGS) methods to identify TE insertion sites.MethodsWe present a hemi-specific PCR approach for TGS of P-elements in Drosophila genomes on the Illumina platform. We also present a computational framework for identifying new insertions from TGS reads. Finally, we describe a new method for estimating the frequency of TE insertions from WGS data, which is based precise insertion sites provided by TGS annotations.ResultsBy comparing our results to TE annotations based on whole genome re-sequencing (WGS) data for the same Drosophilamelanogaster strain, we demonstrate that TGS is powerful for identifying true insertions, even in repeat-rich heterochromatic regions. We also demonstrate that TGS offers enhanced annotation of precise insertion sites, which facilitates estimation of TE insertion frequency.ConclusionsTGS by hemi-specific PCR is a powerful approach for identifying TE insertions of particular TE families in species with a high-quality reference genome, at greatly reduced cost as compared to WGS. It may therefore be ideal for population genomic studies of particular TE families. Additionally, TGS and WGS can be used as complementary approaches, with TGS annotations identifying more annotated insertions with greater precision for a target TE family, and WGS data allowing for estimates of TE insertion frequencies, and a broader picture of the location of non-target TEs across the genome.
Highlights
Transposable elements (TEs) are major components of eukaryotic genomes and drivers of genome evolution, producing intraspecific polymorphism and interspecific differences through mobilization and nonhomologous recombination
We further demonstrate that targeted genome re-sequencing (TGS) allows for identification of precise insertion sites for all annotated TEs, as compared to whole genome re-sequencing (WGS), where the absence of reads spanning the TE insertion breakpoint often limits the resolution of the annotations to a genomic window
We chose to pilot our approach by examining P-elements in the wild-derived strain RAL-492, which was collected from Raleigh NC in 2003 [35]
Summary
Transposable elements (TEs) are major components of eukaryotic genomes and drivers of genome evolution, producing intraspecific polymorphism and interspecific differences through mobilization and nonhomologous recombination. Transposable elements (TEs) are mobile genetic entities that are major contributors to the evolution of eukaryotic genomes. Transposition into novel genomic sites produces abundant intraspecific variation in the presence and absence of individual TE insertions [14,15,16]. Despite their contribution to genetic variation, population genomic studies of TEs remain challenging. TE insertions are often polymorphic within samples used for genome re-sequencing, meaning they are supported by few sequencing reads, and discerning between false positives and rare insertions can prove difficult [17,18,19,20]
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