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      ReAS: Recovery of Ancestral Sequences for Transposable Elements from the Unassembled Reads of a Whole Genome Shotgun

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          Abstract

          We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs) from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

          Abstract

          Synopsis

          Transposable elements (TEs) are a major component of the genomes of multicellular organisms. They are parasitic creatures that invade the genome, insert multiple copies of themselves, and then die. All we see now are the decayed remnants of their ancestral sequences. Reconstruction of these ancestral sequences can bring dead TEs back to life. Algorithms for detecting TEs compare present-day sequences to a library of ancestral sequences. Unknown to many, pervasive use of whole genome shotgun (WGS) methods in large-scale sequencing have made TE reconstructions increasingly problematic. To minimize assembly errors, WGS methods must reject the highly repetitive sequences that characterize most TEs, especially the most recent TEs, which are the least diverged from their ancestral sequences (and most informative for reconstruction). This is acceptable to many, because the most important parts of the genes are not repetitive, but for the TE aficionados, it is a problem. ReAS is a novel algorithm that does TE reconstruction using only the unassembled reads of a WGS. Tested against the WGS for japonica rice, it is shown to produce a library that is superior to the manually curated Repbase database of known ancestral TEs.

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          Most cited references 27

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              Initial sequencing and comparative analysis of the mouse genome.

              The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Comput Biol
                pcbi
                PLoS Computational Biology
                1553-734X
                1553-7358
                September 2005
                23 September 2005
                : 1
                : 4
                Affiliations
                [1 ] James D. Watson Institute of Genome Sciences of Zhejiang University, Hangzhou, China
                [2 ] Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing, China
                [3 ] College of Life Sciences, Peking University, Beijing, China
                [4 ] UW Genome Center, Department of Medicine, University of Washington, Seattle, Washington, United States of America
                [5 ] The Institute of Human Genetics, University of Aarhus, Aarhus, Denmark
                [6 ] Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
                The National Center for Genome Resources, United States of America
                Author notes
                * To whom correspondence should be addressed. E-mail: gksw@ 123456genomics.org.cn (GKW), wangj@ 123456genomics.org.cn (JW)
                Article
                05-PLCB-RA-0052R1 plcb-01-04-04
                10.1371/journal.pcbi.0010043
                1232128
                16184192
                Copyright: © 2005 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                Categories
                Research Article
                Bioinformatics - Computational Biology
                Genetics/Genome Projects
                Genetics/Chromosome Biology
                Plant Science
                Plants
                Oryza
                Custom metadata
                Li R, Ye J, Li S, Wang J, Han Y, et al (2005) ReAS : Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput Biol 1(4): e43.

                Quantitative & Systems biology

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