Shotgun sequence assembly and recent segmental duplications within the human genome

被引：184

作者：

She, XW

Jiang, ZX

Clark, RL

Liu, G

Cheng, Z

Tuzun, E

Church, DM

Sutton, G

Halpern, AL

Eichler, EE

机构：

[1] Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98195 USA

[2] Case Western Reserve Univ, Dept Genet, Cleveland, OH 44106 USA

[3] NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA

[4] Appl Biosyst Inc, Rockville, MD 20850 USA

[5] Ctr Advancement Genom, Rockville, MD 20850 USA

来源：

NATURE | 2004年 / 431卷 / 7011期

关键词：

D O I：

10.1038/nature03062

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

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：4

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