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MBE Advance Access originally published online on September 15, 2004
Molecular Biology and Evolution 2005 22(1):135-141; doi:10.1093/molbev/msh262
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Molecular Biology and Evolution vol. 22 no. 1 © Society for Molecular Biology and Evolution 2005; all rights reserved.

Research Article

Patterns of Segmental Duplication in the Human Genome

Liqing Zhang*,{dagger}, Henry H. S. Lu{ddagger}, Wen-yu Chung§, Jing Yang* and Wen-Hsiung Li*

* Department of Ecology and Evolution, University of Chicago; {dagger} Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg; {ddagger} Institute of Statistics, National Chiao-Tung University, Hsinchu, Taiwan; and § Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park

E-mail: whli{at}uchicago.edu.

We analyzed the completed human genome for recent segmental duplications (size ≥ 1 kb and sequence similarity ≥ 90%). We found that approximately 4% of the genome is covered by duplications and that the extent of segmental duplication varies from 1% to 14% among the 24 chromosomes. Intrachromosomal duplication is more frequent than interchromosomal duplication in 15 chromosomes. The duplication frequencies in pericentromeric and subtelomeric regions are greater than the genome average by approximately threefold and fourfold. 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 intrachromosomal than in interchromosomal 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.

Key Words: gene density • recombination rate • repetitive elements • positive selection


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