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Mobile Genetic Elements pp 189–226Cite as

Retroposon Mapping in Molecular Systematics

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 260))

Abstract

Advances in genome sciences are demonstrating the dynamic nature of noncoding DNA regions, which are comprised largely of repetitive elements with no apparent function. Retroposons are one class of mobile genetic elements that amplify and move about the genome via a copy-and-paste mechanism that employs an RNA intermediate. Short and long interspersed elements (SINEs and LINEs, respectively) are types of retroposons of particular interest because of their active role in shaping the architecture of genomes and their diagnostic value as evolutionary markers for studies of phylogeny and population biology. Although the use of SINEs and LINEs for molecular systematic studies is proliferating, a comprehensive laboratory protocol that explicitly outlines how to isolate and characterize retroposons for systematic studies in a detailed, step-by-step fashion has been lacking. The present chapter addresses this gap in the literature by focusing on the strategy for isolating new SINEs from a genomic library, the screening process, the sequencing and characterization of clones into subfamilies, quantification of copy number in host taxa, and the critical diagnosis of phylogenetically informative SINE and LINE insertion patterns. Practical limits to the method are discussed in relation to sampling design, systematic character theory, and the empirical distribution of elements observed in eukaryotic lineages. Major steps in the experimental process are illustrated with case examples from a diversity of taxonomic groups and by published results in the molecular biology and systematics literature.

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Authors and Affiliations

  1. Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan

    Norihiro Okada & Masato Nikaido

  2. Department of Zoology, University of Washington, Seattle, WA

    Andrew M. Shedlock

Authors
  1. Norihiro Okada
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  2. Andrew M. Shedlock
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  3. Masato Nikaido
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Editors and Affiliations

  1. AG General Genetics, Institute of Medical Biology, University of Vienna, Vienna, Austria

    Wolfgang J. Miller

  2. Laboratoire Populations, Génétique et Evolution, CNRS, Gif-sur-Yvette, France

    Pierre Capy

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Okada, N., Shedlock, A.M., Nikaido, M. (2004). Retroposon Mapping in Molecular Systematics. In: Miller, W.J., Capy, P. (eds) Mobile Genetic Elements. Methods in Molecular Biology, vol 260. Humana Press. https://doi.org/10.1385/1-59259-755-6:189

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  • DOI: https://doi.org/10.1385/1-59259-755-6:189

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-007-6

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