title: TEMP: a computational method for analyzing transposable element polymorphism in populations.
abstract: Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to detect TE movements present with a wide range of frequencies in a population. By combining the information provided by pair-end reads and split reads, TEMP is able to identify both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples; accurately estimate the frequencies of transposition events in the population and pinpoint junctions of high frequency transposition events at nucleotide resolution. Simulation data indicate that TEMP outperforms other algorithms such as PoPoolationTE, RetroSeq, VariationHunter and GASVPro. TEMP also performs well on whole-genome human data derived from the 1000 Genomes Project. We applied TEMP to characterize the TE frequencies in a wild Drosophila melanogaster population and study the inheritance patterns of TEs during hybrid dysgenesis. We also identified sequence signatures of TE insertion and possible molecular effects of TE movements, such as altered gene expression and piRNA production. TEMP is freely available at github: https://github.com/JialiUMassWengLab/TEMP.git.
authors.affiliation: Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology.
authors.forename: Jiali
authors.initials: J
authors.lastname: Zhuang
authors.affiliation: Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology.
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.affiliation: Program in Cell and Developmental Dynamics Program in Molecular Medicine, and University of Massachusetts Medical School, Worcester, MA 01605, USA william.theurkauf@umassmed.edu.
authors.forename: William
authors.initials: W
authors.lastname: Theurkauf
authors.affiliation: Program in Bioinformatics and Integrative Biology, Department of Biochemistry and Molecular Pharmacology zhiping.weng@umassmed.edu.
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000465:Algorithms; D000818:Animals; D004331:Drosophila melanogaster / Q000235:genetics; D015870:Gene Expression; D023281:Genomics / Q000379:methods*; D006801:Humans; D020071:Interspersed Repetitive Sequences; D011110:Polymorphism, Genetic
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