Shotgun sequence assembly and recent segmental duplications within the human genome

被引：0

作者：

Xinwei She

Zhaoshi Jiang

Royden A. Clark

Ge Liu

Ze Cheng

Eray Tuzun

Deanna M. Church

Granger Sutton

Aaron L. Halpern

Evan E. Eichler

机构：

[1] University of Washington School of Medicine,Department of Genome Sciences

[2] Case Western Reserve University,Department of Genetics

[3] National Library of Medicine,National Center for Biotechnology Information

[4] National Institutes of Health,undefined

[5] Applied Biosystems,undefined

[6] The Center for the Advancement of Genomics,undefined

来源：

Nature | 2004年 / 431卷

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摘要：

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.

引用

页码：927 / 930

页数：3

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