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Retroposons: Genetic Footprints on the Evolutionary Paths of Life

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Phylogenomics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 422))

Abstract

Retroposons such as short interspersed elements (SINEs) and long interspersed elements are abundant transposable elements in eukaryote genomes. Recent large-scale comparative genome analyses have revealed that retroposons are a major component of genomes, wherein they provide structural diversity between species and uniqueness to each species. SINEs have been used as powerful markers in phylogenetic analyses of various species. This approach, which has been termed the SINE insertion method, infers phylogenetic relationships based on the presence/absence of SINEs among lineages. However, the method is not yet used extensively among biologists, especially molecular phylogenetists, because it is based on an understanding of the molecular mechanisms of retroposition, which may be unfamiliar to many researchers. Moreover, the method may require a large amount of bench work to characterize a new SINE family and to screen genomic libraries of the species of interest. In this chapter, we present the basic theory and detailed technical steps involved in a SINE insertion analysis. Furthermore, we explain the isolation and characterization of a new SINE family from the genome of a species of interest using as an example a known SINE family in mammals.

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Authors and Affiliations

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

    Hidenori Nishihara & Norihiro Okada

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  1. Hidenori Nishihara
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  2. Norihiro Okada
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  1. Department of Veterinary Integrative Biosciences College of Veterinary Medicine and Biomedical Sciences Mail Stop 4458, Texas A&M University, Raymond Stotzer Parkway, Rm 107 VMA, College Station, TX, 77843-4458, USA

    William J. Murphy PhD

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© 2008 Humana Press Inc., Totowa, NJ

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Nishihara, H., Okada, N. (2008). Retroposons: Genetic Footprints on the Evolutionary Paths of Life. In: Murphy, W.J. (eds) Phylogenomics. Methods in Molecular Biology™, vol 422. Humana Press. https://doi.org/10.1007/978-1-59745-581-7_13

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  • DOI: https://doi.org/10.1007/978-1-59745-581-7_13

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-764-8

  • Online ISBN: 978-1-59745-581-7

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