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PoPoolationTE2: comparative population genomics of transposable elements using Pool-Seq
- Source :
- Molecular Biology and Evolution
- Publication Year :
- 2016
- Publisher :
- Cold Spring Harbor Laboratory, 2016.
-
Abstract
- The evolutionary dynamics of transposable elements (TEs) are still poorly understood. One reason is that TE abundance needs to be studied at the population level, and despite recent advances in sequencing technologies, characterizing TE abundance in multiple populations by sequencing individuals separately is still too expensive. While sequencing pools of individuals (Pool-Seq) dramatically reduces sequencing costs, a comparison of TE abundance between pooled samples has been difficult, if not impossible, due to various biases. Here, we introduce a novel bioinformatic tool, PoPoolationTE2, which is specifically tailored for the comparison of TE abundance among pooled population samples or different tissues. Using computer simulations we demonstrate that PoPoolationTE2 not only faithfully recovers TE insertion frequencies and positions but, by homogenizing the power to identify TEs acrosss samples, it provides an unbiased comparison of TE abundance between pooled population samples. We anticipate that PoPoolationTE2 will greatly facilitate the analysis of TE insertion patterns in a broad range of applications.
- Subjects :
- Transposable element
0106 biological sciences
0301 basic medicine
Population level
Population
Genomics
comparative genomics
Computational biology
Biology
010603 evolutionary biology
01 natural sciences
DNA sequencing
Evolution, Molecular
Population genomics
03 medical and health sciences
Abundance (ecology)
Genetics
Animals
Selection, Genetic
education
Evolutionary dynamics
Molecular Biology
Ecology, Evolution, Behavior and Systematics
next generation sequencing
Comparative genomics
education.field_of_study
Models, Genetic
Pool-Seq
Computational Biology
comparative population genomics
Sequence Analysis, DNA
bioinformatics
Resources
Drosophila melanogaster
030104 developmental biology
Metagenomics
Evolutionary biology
DNA Transposable Elements
transposable elements
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Molecular Biology and Evolution
- Accession number :
- edsair.doi.dedup.....eae62a8093e1bfc3f6309625afdd9679
- Full Text :
- https://doi.org/10.1101/038745