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      Molecular dissection of a natural transposable element invasion

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          Abstract

          The first tracking of the dynamics of a natural invasion by a transposable element (TE) provides unprecedented details on the establishment of host defense mechanisms against TEs. We captured a D. simulans population at an early stage of a P- element invasion and studied the spread of the TE in replicated experimentally evolving populations kept under hot and cold conditions. We analyzed the factors controlling the invasion by NGS, RNA-FISH, and gonadal dysgenesis assays. Under hot conditions, the P- element spread rapidly for 20 generations, but no further spread was noted later on. This plateauing of the invasion was mediated by the rapid emergence of P- element-specific piRNAs. Under cold conditions, we observed a lower expression of the P- element and a slower emergence of the piRNA defense, resulting in a three times slower invasion that continued beyond 40 generations. We conclude that the environment is a major factor determining the evolution of TEs in their host.

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          Most cited references83

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          Fast and accurate long-read alignment with Burrows–Wheeler transform

          Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We designed and implemented a new algorithm, Burrows-Wheeler Aligner's Smith-Waterman Alignment (BWA-SW), to align long sequences up to 1 Mb against a large sequence database (e.g. the human genome) with a few gigabytes of memory. The algorithm is as accurate as SSAHA2, more accurate than BLAT, and is several to tens of times faster than both. Availability: http://bio-bwa.sourceforge.net Contact: rd@sanger.ac.uk
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            Evolution of genes and genomes on the Drosophila phylogeny.

            Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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              Non-homologous DNA end joining and alternative pathways to double-strand break repair

              In mammalian cells, DNA double-strand breaks (DSBs) are repaired predominantly by the non-homologous end joining (NHEJ) pathway, which includes subpathways that can repair different DNA-end configurations. Furthermore, the repair of some DNA-end configurations can be shunted to the auxiliary pathways of alternative end joining (a-EJ) or single-strand annealing (SSA).
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                Author and article information

                Journal
                Genome Res
                Genome Res
                genome
                genome
                GENOME
                Genome Research
                Cold Spring Harbor Laboratory Press
                1088-9051
                1549-5469
                June 2018
                : 28
                : 6
                : 824-835
                Affiliations
                Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria
                Author notes
                Article
                9509184
                10.1101/gr.228627.117
                5991514
                29712752
                3031b55e-7567-4f5c-9ad5-e80bde53c251
                © 2018 Kofler et al.; Published by Cold Spring Harbor Laboratory Press

                This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

                History
                : 3 August 2017
                : 10 April 2018
                Page count
                Pages: 12
                Funding
                Funded by: European Research Council , open-funder-registry 10.13039/100010663;
                Award ID: ArchAdapt
                Categories
                Research

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