Biased distributions and decay of LINEs in the chicken genome
Gyorgy Abrusan 1*, Hans Juergen Krambeck 2, Thomas Junier 3, Joti Giordano 4 and Peter E. Warburton 4
1 K.U.Leuven
2 Max Planck Institute of Limnology
3 University of Geneva
4 Mount Sinai School of Medicine
* To whom correspondence should be addressed. E-mail: gyorgy.abrusan{at}bio.kuleuven.be.
Submitted on June 12, 2006
Revised on July 26, 2006
Accepted on 15 October 2007
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Abstract |
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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 in consequence the genome size of birds, we analysed the distributions of LINEs (CR1s) 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, 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, repeats are enriched in both AT rich and GC rich regions of the genome, but the CR1 families show large differences in their GC distribution and their change over time. 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 the low abundance of repeats in avian genomes is likely to be the consequence of their high recombination rates.
Key Words:
LINEs, ectopic recombination, sex chromosomes
