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Identification and Analysis of Ingi-Related Retroposons in the Trypanosomatid Genomes

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Parasite Genomics Protocols

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1201))

Abstract

Transposable elements (TE), defined as discrete pieces of DNA that can move from one site to another site in genomes, represent significant components of eukaryotic genomes, including trypanosomatids. Up to 5 % of the trypanosomatid genome content is composed of retroposons of the ingi clade, further divided into subclades and subfamilies ranging from short extinct truncated elements (SIDER) to long active elements (ingi). Important differences in ingi-related retroposon content have been reported between trypanosomatid species. For instance, Leishmania spp. have expanded and recycled a whole SIDER family to fulfill an important biological pathway, i.e., regulation of gene expression, while trypanosome genomes are primarily composed of active elements. Here, we present an overview of the computational methods used to identify, annotate, and analyze ingi-related retroposons for providing a comprehensive picture of all these TE families in newly available trypanosomatid genome sequences.

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Acknowledgement

FB is supported by the Centre National de la Recherche Scientifique (CNRS), the Université Bordeaux Segalen, and the Laboratoire d’Excellence (LabEx) ParaFrap ANR-11-LABX-0024.

Ingihelper.pl is available at https://sites.google.com/a/nyu.edu/ghedin-lab/tools.

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Authors and Affiliations

  1. Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), UMR 5536 CNRS, Université de Bordeaux, 146, rue Léo Saignat, 33076, Bordeaux, France

    Frédéric Bringaud

  2. Centre for Vaccine Research, University of Pittsburgh, Biomedical Science Tower 3, Pittsburgh, PA, USA

    Matthew Rogers & Elodie Ghedin

  3. Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, USA

    Elodie Ghedin

Authors
  1. Frédéric Bringaud
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  2. Matthew Rogers
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  3. Elodie Ghedin
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Corresponding author

Correspondence to Frédéric Bringaud .

Editor information

Editors and Affiliations

  1. University of Western Australia, Nedlands, West Australia, Australia

    Christopher Peacock

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Bringaud, F., Rogers, M., Ghedin, E. (2015). Identification and Analysis of Ingi-Related Retroposons in the Trypanosomatid Genomes. In: Peacock, C. (eds) Parasite Genomics Protocols. Methods in Molecular Biology, vol 1201. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1438-8_6

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  • DOI: https://doi.org/10.1007/978-1-4939-1438-8_6

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1437-1

  • Online ISBN: 978-1-4939-1438-8

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