Phylogenomics pp 201-225 | Cite as

Retroposons: Genetic Footprints on the Evolutionary Paths of Life

  • Hidenori Nishihara
  • Norihiro Okada
Part of the Methods in Molecular Biology™ book series (MIMB, volume 422)


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.

Key Words

Short interspersed elements long-interspersed elements retroposons transposable elements mobile DNA genomic database bioinformatics 


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Copyright information

© Humana Press Inc., Totowa, NJ 2008

Authors and Affiliations

  • Hidenori Nishihara
    • 1
  • Norihiro Okada
    • 1
  1. 1.Graduate School of Bioscience and BiotechnologyTokyo Institute of TechnologyYokohamaJapan

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