Whole-genome shotgun assembly and comparison of human genome assemblies
Whole-genome shotgun assembly and comparison of human genome assemblies
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DOI：
10.1073/pnas.0307971100
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发表时间：
2004-02-17
影响因子：
11.1
通讯作者：
Venter, JC
中科院分区：
文献类型：
--
作者：
Istrail, S;Sutton, GG;Venter, JC
我们报道了2001年塞莱拉公司（Celera）所生成的人类基因组全基因组鸟枪法组装（称为WGSA）。塞莱拉公司产生的鸟枪法数据集包含2700万条测序读段，这些读段通过对来自鸟枪法克隆文库的2kbp、10kbp和50kbp插入片段进行末端测序而成对排列。经过质量修剪的读段覆盖基因组5.3倍，而获得成对读段的插入片段覆盖基因组39倍。随着近乎完整的人类DNA序列[美国国家生物技术信息中心（NCBI）Build 34]现已可用，有可能直接评估WGSA以及2001年2月在两篇具有里程碑意义的论文中所报道的人类基因组首次重建的质量、准确性和完整性[文特尔（Venter）, J. C., 亚当斯（Adams）, M. D., 迈尔斯（Myers）, E. W., 李（Li）, P. W., 穆拉尔（Mural）, R. J., 萨顿（Sutton）, G. G., 史密斯（Smith）, H. O., 扬德尔（Yandell）, M., 埃文斯（Evans）, C. A., 霍尔特（Holt）, R. A.等人（2001年）《科学》291卷，1304 - 1351页；国际人类基因组测序联盟（2001年）《自然》409卷，860 - 921页]。对WGSA的分析表明，与NCBI Build 34有97%的顺序和方向一致性，其中3%顺序不一致的序列大多是由于支架放置问题，而非支架自身内部的组装错误。此外，WGSA填补了NCBI Build 34中一些剩余的缺口。早期的基因组序列都覆盖了大致相同数量的基因组，但它们的覆盖方式不同。塞莱拉公司的结果提供了更多的顺序和方向，而联盟的序列则对精确和近乎精确的重复序列提供了更好的覆盖。
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries. The quality-trimmed reads covered the genome 5.3 times, and the inserts from which pairs of reads were obtained covered the genome 39 times. With the nearly complete human DNA sequence [National Center for Biotechnology information (NCBI) Build 34] now available, it is possible to directly assess the quality, accuracy, and completeness of WGSA and of the first reconstructions of the human genome reported in two landmark papers in February 2001 [Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J.,,Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) Science 291, 1304-1351; International Human Genome Sequencing Consortium (2001) Nature 409, 860-921]. The analysis of WGSA shows 97% order and orientation agreement with NCBI Build 34, where most of the 3% of sequence out of order is due to scaffold placement problems as opposed to assembly errors within the scaffolds themselves. In addition, WGSA fills some of the remaining gaps in NCBI Build 34. The early genome sequences all covered about the same amount of the genome, but they did so in different ways. The Celera results provide more order and orientation, and the consortium sequence provides better coverage of exact and nearly exact repeats.