Shotgun sequence assembly and recent segmental duplications within the human genome

Xinwei She, Zhaoshi Jiang, Royden A. Clark, Ge Liu, Ze Cheng, Eray Tuzun, Deanna M. Church, Granger Sutton, Aaron L. Halpern and Evan E. Eichler ()
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Xinwei She: University of Washington School of Medicine
Zhaoshi Jiang: University of Washington School of Medicine
Royden A. Clark: Case Western Reserve University
Ge Liu: Case Western Reserve University
Ze Cheng: University of Washington School of Medicine
Eray Tuzun: University of Washington School of Medicine
Deanna M. Church: National Library of Medicine, National Institutes of Health
Granger Sutton: Applied Biosystems
Aaron L. Halpern: The Center for the Advancement of Genomics
Evan E. Eichler: University of Washington School of Medicine

Nature, 2004, vol. 431, issue 7011, 927-930

Abstract: Abstract Complex eukaryotic genomes are now being sequenced at an accelerated pace primarily using whole-genome shotgun (WGS) sequence assembly approaches. WGS assembly was initially criticized because of its perceived inability to resolve repeat structures within genomes. Here, we quantify the effect of WGS sequence assembly on large, highly similar repeats by comparison of the segmental duplication content of two different human genome assemblies. Our analysis shows that large (> 15 kilobases) and highly identical (> 97%) duplications are not adequately resolved by WGS assembly. This leads to significant reduction in genome length and the loss of genes embedded within duplications. Comparable analyses of mouse genome assemblies confirm that strict WGS sequence assembly will oversimplify our understanding of mammalian genome structure and evolution; a hybrid strategy using a targeted clone-by-clone approach to resolve duplications is proposed.

Date: 2004
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DOI: 10.1038/nature03062

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