Transposable Element‐driven Duplications during Hominoid Genome Evolution

Abstract

Hominoid genomes exhibit a significant number of large segmental duplications; these and other similar duplications in mammalian genomes are hypothesized to be mediated by transposable elements such as Alus or L1s in hominoids and rodents, respectively. The true evolutionary mechanisms that sculpted these duplications are emerging to be much more subtle and complex.

Keywords: segmental duplications (SD); low‐copy repeats (LCR); copy number variations (CNV); transposable elements; rearrangement hotspots

Figure 1.

Zhou–Mishra model. The model formulates the changes in the distribution of flanking region pairs over different states as a Markov process over evolution time. At a particular evolution time, t, the flanking region pairs are distributed over different states (circles) defined by the configuration of the repeats in the flanking region (−/−, +/− or +/+) and the age group of the duplicated segments (k). During evolution, in each time interval Δt, the flanking region pairs may change its state through many possible transitions (arrows). The change in the distribution of the flanking region pairs in a particular state at time tt from time t depends on how much has entered into this state from other states, as well as how much has exited out of this state into other states in interval Δt since time t. At the same time, the flanking region pairs in other states can change into state A2,k(dashed arrows). The difference between A2,k(t) and A2,k(tt) can be calculated by taking the difference between the sum of the outflows (grey arrows) and inflows (dashed arrows). Reproduced from Zhou and Mishra .

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Further Reading

Durand D and Hoberman R (2006) Diagnosing duplications – can it be done? Trends in Genetics 22(3): 156–164.

Web Links

Chimpanzee Segmental Duplication Database, Genome Sciences, University of Washington; URL Link: http://chimpparalogy.gs.washington.edu.

Ensembl Genome Browsers; URL Link: http://www.ensembl.org.

Human Genome Segmental Duplication Database, Hospital for Sick Children, University of Toronto; URL Link: http://projects.tcag.ca/humandup.

Human Segmental Duplication Database, Genome Sciences, University of Washington; URL Link: http://humanparalogy.gs.washington.edu.

UCSC Genome Bioinformatics; URL Link: http://genome.ucsc.edu.

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How to Cite close
Mishra, Bud(Apr 2008) Transposable Element‐driven Duplications during Hominoid Genome Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020756]