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, Gocayne J D, Amanatides P, Ballew R M, Huson D H, Wortman J R, Zhang Q, Kodira C D, Zheng X H, Chen L, Skupski M, Subramanian G, Thomas P D, Zhang J, Gabor Miklos G L, Nelson C, Broder S, Clark A G, Nadeau J, McKusick V A, Zinder N, Levine A J, Roberts R J, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian A E, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman T J, Higgins M E, Ji R R, Ke Z, Ketchum K A, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov G V, Milshina N, Moore H M, Naik A K, Narayan V A, Neelam B, Nusskern D, Rusch D B, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng M L, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers Y H, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint N N, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril J F, Guigó R, Campbell M J, Sjolander K V, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang Y H, Coyne M, Dahlke C, Deslattes Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X
Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.
Science. 2001 Feb 16;291(5507):1304-51. doi: 10.1126/science.1058040.
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
通过全基因组鸟枪法测序方法，生成了人类基因组常染色质部分29.1亿碱基对（bp）的一致序列。148亿碱基对的DNA序列是在9个月内，从5个人的DNA构建的质粒克隆两端的27271853个高质量序列读数（基因组覆盖度为5.11倍）中产生的。使用了两种组装策略——全基因组组装和区域染色体组装，每种策略都结合了赛雷拉公司和公共资助基因组计划的序列数据。公共数据被切割成550bp的片段，以对已测序的基因组区域产生2.9倍的覆盖度，且不包括公共资助团队所用克隆和组装过程中固有的偏差。这使得组装中的有效覆盖度达到8倍，减少了最终组装中缺口的数量和大小，相比5.11倍覆盖度所得到的结果有所改善。两种组装策略产生了非常相似的结果，在很大程度上与独立的图谱数据一致。这些组装有效地覆盖了人类染色体的常染色质区域。超过90%的基因组存在于100000bp或更长的支架组装中，25%的基因组存在于1000万bp或更大的支架中。对基因组序列的分析揭示了26588个有确凿证据支持的蛋白质编码转录本，以及另外约12000个通过计算推导且与小鼠匹配或有其他微弱支持证据的基因。尽管基因密集簇很明显，但几乎一半的基因分散在低G+C序列中，被大片明显非编码序列隔开。基因组中只有1.1%由外显子覆盖，而24%存在于内含子中，75%的基因组是基因间DNA。大小可达染色体长度的片段块重复在整个基因组中大量存在，揭示了复杂的进化历史。比较基因组分析表明，与神经元功能、组织特异性发育调控以及止血和免疫系统相关的基因在脊椎动物中有所扩张。一致序列与公共资助基因组数据之间的DNA序列比较确定了210万个单核苷酸多态性（SNP）的位置。一对随机的人类单倍体基因组平均每1250个碱基对中有1个碱基对存在差异，但全基因组多态性水平存在显著异质性。所有SNP中不到1%导致蛋白质变异，但确定哪些SNP具有功能后果的任务仍然是一个悬而未决的挑战。
