Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.
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DOI：
10.1186/gb-2002-3-12-research0079
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发表时间：
2002
期刊：
影响因子：
12.3
通讯作者：
Rubin GM
中科院分区：
文献类型：
--
作者：
Celniker SE;Wheeler DA;Kronmiller B;Carlson JW;Halpern A;Patel S;Adams M;Champe M;Dugan SP;Frise E;Hodgson A;George RA;Hoskins RA;Laverty T;Muzny DM;Nelson CR;Pacleb JM;Park S;Pfeiffer BD;Richards S;Sodergren EJ;Svirskas R;Tabor PE;Wan K;Stapleton M;Sutton GG;Venter C;Weinstock G;Scherer SE;Myers EW;Gibbs RA;Rubin GM
果蝇基因组是第一个用全基因组鸟枪测序的后生动物基因组。现在，测序已经在一个旨在缩小差距、提高测序质量和验证组装的过程中完成。果蝇基因组是第一个用全基因组鸟枪法测序的后生动物基因组。与这一成就相关的两个问题在基因组学界引起了广泛的争论：相对于碱基对(BP)的准确性和组装错误的频率，序列的准确性如何？而且，将WGS序列带到已完成序列的公认标准上有多难？我们现在能够回答这些问题。我们的精加工工艺旨在缩小差距、提高序列质量并验证组装。来自WGS的序列痕迹和单个细菌人工染色体(BAC)的测序草案被组装成BAC大小的片段。这些片段被提炼成高质量的片段，然后连接在一起构成每个染色体臂的序列。通过与有指纹的BAC克隆的物理图谱进行比较，验证了整个组装。在当前版本的116.9 Mb常染基因组中，称为Release 3，6个常染染色体臂由13个支架表示，总共有37个序列间隙。我们比较了版本3和版本2；在唯一序列的常染色体区域，版本2的错误率为1/20,000个碱基对。WGS策略可以高效地产生高质量的后生动物基因组序列，同时产生序列完成所需的试剂。然而，最初的重复组装方法是有缺陷的。我们在这里报告的序列，版本3，是分子遗传学实验和计算分析的可靠资源。
The Drosophila melanogaster genome was the first metazoan genome to be sequenced by whole-genome shotgun. Now, the sequence has been finished in a process designed to close gaps, improve sequence quality and validate the assembly. The Drosophila melanogaster genome was the first metazoan genome to have been sequenced by the whole-genome shotgun (WGS) method. Two issues relating to this achievement were widely debated in the genomics community: how correct is the sequence with respect to base-pair (bp) accuracy and frequency of assembly errors? And, how difficult is it to bring a WGS sequence to the accepted standard for finished sequence? We are now in a position to answer these questions. Our finishing process was designed to close gaps, improve sequence quality and validate the assembly. Sequence traces derived from the WGS and draft sequencing of individual bacterial artificial chromosomes (BACs) were assembled into BAC-sized segments. These segments were brought to high quality, and then joined to constitute the sequence of each chromosome arm. Overall assembly was verified by comparison to a physical map of fingerprinted BAC clones. In the current version of the 116.9 Mb euchromatic genome, called Release 3, the six euchromatic chromosome arms are represented by 13 scaffolds with a total of 37 sequence gaps. We compared Release 3 to Release 2; in autosomal regions of unique sequence, the error rate of Release 2 was one in 20,000 bp. The WGS strategy can efficiently produce a high-quality sequence of a metazoan genome while generating the reagents required for sequence finishing. However, the initial method of repeat assembly was flawed. The sequence we report here, Release 3, is a reliable resource for molecular genetic experimentation and computational analysis.