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      De Novo Assembly and Annotation of the Asian Tiger Mosquito ( Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito ( Aedes aegypti)

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          Abstract

          Repetitive DNA, including transposable elements (TEs), is found throughout eukaryotic genomes. Annotating and assembling the “repeatome” during genome-wide analysis often poses a challenge. To address this problem, we present dnaPipeTE—a new bioinformatics pipeline that uses a sample of raw genomic reads. It produces precise estimates of repeated DNA content and TE consensus sequences, as well as the relative ages of TE families. We shows that dnaPipeTE performs well using very low coverage sequencing in different genomes, losing accuracy only with old TE families. We applied this pipeline to the genome of the Asian tiger mosquito Aedes albopictus, an invasive species of human health interest, for which the genome size is estimated to be over 1 Gbp. Using dnaPipeTE, we showed that this species harbors a large (50% of the genome) and potentially active repeatome with an overall TE class and order composition similar to that of Aedes aegypti, the yellow fever mosquito. However, intraorder dynamics show clear distinctions between the two species, with differences at the TE family level. Our pipeline’s ability to manage the repeatome annotation problem will make it helpful for new or ongoing assembly projects, and our results will benefit future genomic studies of A. albopictus.

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          Most cited references38

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          The genome sequence of the malaria mosquito Anopheles gambiae.

          Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.
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            Retrotransposons revisited: the restraint and rehabilitation of parasites.

            Retrotransposons, mainly LINEs, SINEs, and endogenous retroviruses, make up roughly 40% of the mammalian genome and have played an important role in genome evolution. Their prevalence in genomes reflects a delicate balance between their further expansion and the restraint imposed by the host. In any human genome only a small number of LINE1s (L1s) are active, moving their own and SINE sequences into new genomic locations and occasionally causing disease. Recent insights and new technologies promise answers to fundamental questions about the biology of transposable elements.
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              LINE-1 elements in structural variation and disease.

              The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes.
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                Author and article information

                Journal
                Genome Biol Evol
                Genome Biol Evol
                gbe
                gbe
                Genome Biology and Evolution
                Oxford University Press
                1759-6653
                April 2015
                11 March 2015
                11 March 2015
                : 7
                : 4
                : 1192-1205
                Affiliations
                1Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France
                2Université de Lyon 1, Villeurbanne, France
                3Université de Lyon, Lyon, France
                4Ecologie Microbienne, UMR 5557, CNRS, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Villeurbanne, France
                5Université de La Réunion, UMR PIMIT, CNRS 9192, INSERM 1187, IRD 249
                Author notes
                *Corresponding author: E-mail: matthieu.boulesteix@ 123456univ-lyon1.f .

                Associate editor: Josefa Gonzalez

                Article
                evv050
                10.1093/gbe/evv050
                4419797
                25767248
                2d86ce9e-643d-46cd-bd6d-f8e7acb24ec9
                © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                : 6 March 2015
                Page count
                Pages: 14
                Categories
                Research Article

                Genetics
                transposable elements,repeated dna,te analysis,aedes albopictus,trinity,bioinformatic pipeline

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