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MBE Advance Access published online on September 15, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh262
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted September 8, 2004

Research Article

Patterns of Segmental Duplication in the Human Genome

Liqing Zhang 1, Henry H.S. Lu 2, Wen-yu Chung 3, Jing Yang 4, and Wen-Hsiung Li 4*

1 Department of Ecology and Evolution, University of Chicago, 1101 East 57th St. Chicago, IL 60637; Department of Computer Science, Virginia Tech, 660 McBryde Hall, Blacksburg, VA 24061
2 Institute of Statistics, National Chiao-Tung University, 1001 Ta Hsueh Road, Hsinchu, Taiwan 30050
3 Department of Biochemistry and Molecular Biology, Penn State University, 108 Althouse Laboratory, University Park, PA 16802
4 Department of Ecology and Evolution, University of Chicago, 1101 East 57th St. Chicago, IL 60637

* To whom correspondence should be addressed. E-mail: whli{at}uchicago.edu.


  Abstract

We analyzed the completed human genome for recent segmental duplications (size ≥ 1 Kb and sequence similarity ≥ 90%). We found that ~ 4 % of the genome is covered by duplications and that the extent of segmental duplication varies from 1% to 14% among the 24 chromosomes. Intra-chromosomal duplication is more frequent than inter-chromosomal duplication in 15 chromosomes. The duplication frequencies in pericentromeric and subtelomeric regions are greater than the genome average by ~ 3 and ~ 4 fold. We examined factors that may affect the frequency of duplication in a region. Within individual chromosomes, the duplication frequency shows little correlation with local gene density, repeat density, recombination rate, and GC content except chromosomes 7 and Y. For the entire genome, the duplication frequency is correlated with each of the above factors. Based on known genes and Ensembl genes, the proportion of duplications containing complete genes is 3.4% and 10.7%, respectively. The proportion of duplications containing genes is higher in intra- than inter-chromosomal duplications, and duplications containing genes have a higher sequence similarity and tend to be longer than duplications containing no genes. Our simulation suggests that many duplications containing genes have been selectively maintained in the genome.

Keywords: gene density; recombination rate; repetitive elements; positive selection.
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