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Originally published as Genetics Published Articles Ahead of Print on October 18, 2007.

Genetics, Vol. 178, 573-581, January 2008, Copyright © 2008
doi:10.1534/genetics.106.061861

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Biased Distributions and Decay of Long Interspersed Nuclear Elements in the Chicken Genome

György Abrusán*,{dagger},1, Hans-Jürgen Krambeck*, Thomas Junier{ddagger}, Joti Giordano{dagger} and Peter E. Warburton{dagger}

* Department of Ecophysiology, Max Planck Institute of Limnology, 24306 Plön, Germany, {ddagger} Computational Evolutionary Genetics Group 1211, University of Geneva, Geneva 4, Switzerland and {dagger} Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York 10029

1 Corresponding author: Laboratory of Aquatic Ecology and Evolutionary Biology, Department of Biology, Catholic University of Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium.
E-mail: gyorgy.abrusan{at}bio.kuleuven.be

The genomes of birds are much smaller than mammalian genomes, and transposable elements (TEs) make up only 10% of the chicken genome, compared with the 45% of the human genome. To study the mechanisms that constrain the copy numbers of TEs, and as a consequence the genome size of birds, we analyzed the distributions of LINEs (CR1's) and SINEs (MIRs) on the chicken autosomes and Z chromosome. We show that (1) CR1 repeats are longest on the Z chromosome and their length is negatively correlated with the local GC content; (2) the decay of CR1 elements is highly biased, and the 5'-ends of the insertions are lost much faster than their 3'-ends; (3) the GC distribution of CR1 repeats shows a bimodal pattern with repeats enriched in both AT-rich and GC-rich regions of the genome, but the CR1 families show large differences in their GC distribution; and (4) the few MIRs in the chicken are most abundant in regions with intermediate GC content. Our results indicate that the primary mechanism that removes repeats from the chicken genome is ectopic exchange and that the low abundance of repeats in avian genomes is likely to be the consequence of their high recombination rates.






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Copyright © 2008 by the Genetics Society of America.