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Identification of transposable elements using multiple alignments of related genomes

Caspi, Anat and Pachter, Lior (2006) Identification of transposable elements using multiple alignments of related genomes. Genome Research, 16 (2). pp. 260-270. ISSN 1088-9051. PMCID PMC1361722. doi:10.1101/gr.4361206.

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Accurate genome-wide cataloging of transposable elements (TEs) will facilitate our understanding of mobile DNA evolution, expose the genomic effects of TEs on the host genome, and improve the quality of assembled genomes. Using the availability of several nearly complete Drosophila genomes and developments in whole genome alignment methods, we introduce a large-scale comparative method for identifying repetitive mobile DNA regions. These regions are highly enriched for transposable elements. Our method has two main features distinguishing it from other repeat-finding methods. First, rather than relying on sequence similarity to determine the location of repeats, the genomic artifacts of the transposition mechanism itself are systematically tracked in the context of multiple alignments. Second, we can derive bounds on the age of each repeat instance based on the phylogenetic species tree. We report results obtained using both complete and draft sequences of four closely related Drosophila genomes and validate our results with manually curated TE annotations in the Drosophila melanogaster euchromatin. We show the utility of our findings in exploring both transposable elements and their host genomes: In the study of TEs, we offer predictions for novel families, annotate new insertions of known families, and show data that support the hypothesis that all known TE families in D. melanogaster were recently active; in the study of the host, we show how our findings can be used to determine shifts in the eu-heterochromatin junction in the pericentric chromosome regions.

Item Type:Article
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URLURL TypeDescription CentralArticle
Caspi, Anat0000-0001-8702-8273
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2006 Cold Spring Harbor Laboratory Press. The Authors acknowledge that six months after the full-issue publication date, the Article will be distributed under a Creative Commons CC-BY-NC License (Attribution-NonCommercial 4.0 International License, Accepted September 19, 2005. Received June 29, 2005. Published in Advance December 14, 2005. We thank Roger Hoskins for elucidating the problem of position-effect variegation for us. We also thank Colin Dewey for providing the MERCATOR alignments and access to his software library; and Sue Celniker, Michael Ashburner, and the anonymous reviewers for useful discussion and comments. Finally, we thank the Washington University in St. Louis Genome Sequencing Center and Agencourt for the draft assemblies of D. yakuba and D. virilis. Supplemental material is available at The site includes a table showing the coordinates, length, classification, and characterization of genomic environment of the new identified insertion regions of known TE families; a table showing the coordinates, length, and environmental characterization of the new TE families in D. melanogaster euchromatin resulting from our case study; and a table showing the genomic environmental characterization of the BDGP annotated TE instances. Our reported Wilcoxon rank test results are also available. Additionally, the alignments of all the new families and the known TE families with new insertions are available on that site.
Issue or Number:2
PubMed Central ID:PMC1361722
Record Number:CaltechAUTHORS:20170308-111109017
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Official Citation:Identification of transposable elements using multiple alignments of related genomes Anat Caspi and Lior Pachter Genome Res. February 2006 16: 260-270; Published in Advance December 14, 2005, doi:10.1101/gr.4361206
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74895
Deposited By: George Porter
Deposited On:08 Mar 2017 19:21
Last Modified:15 Nov 2021 16:28

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