Gene-boosted assembly of a novel bacterial genome from very short reads.
Gene-boosted assembly of a novel bacterial genome from very short reads.
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来自非常短的读物的新型细菌基因组的基因促进组装。
DOI：
10.1371/journal.pcbi.1000186
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发表时间：
2008-09-26
影响因子：
4.3
通讯作者：
Lee, Vincent T.
中科院分区：
文献类型：
--
作者：
Salzberg, Steven L.;Sommer, Daniel D.;Puiu, Daniela;Lee, Vincent T.
最近的技术进步使DNA测序比以往任何时候都更快，更有效。新技术产生高度精确的序列，但一个缺点是最有效的技术产生最短的读取长度。短读测序已成功应用于人类基因组和其他物种的基因组重测序，但尚未应用于新生物的全基因组测序。在这里，我们描述了一种新的临床分离的铜绿假单胞菌，菌株PAb1，使用非常短的读取技术的测序和组装。从8，627，900个读段（每个读段长度为33个核苷酸）中，我们将基因组组装成含有6，290，005个核苷酸的76个有序连续序列的一个支架，包括一个跨越512，638个核苷酸的重叠群，加上另外436个含有416，897个核苷酸的无序重叠群。我们的方法包括一种新的基因增强算法，该算法使用来自预测蛋白质的氨基酸序列来构建更好的组装。这项研究证明了非常短的读取测序的细菌基因组测序的可行性，特别是那些相关物种已经测序之前，并扩大了这种新技术的潜在应用，以最已知的原核物种。在本文中，我们证明了细菌基因组，铜绿假单胞菌，可以使用非常短的DNA序列，即，那些产生的最新一代的DNA测序仪，如Solexa测序仪从Illumina解码。我们的方法包括一种新的算法，该算法使用来自其他物种的蛋白质序列来帮助组装新的基因组。这种算法将基因组分解成基因大小的块，这些块可以相对容易地重新组合在一起，即使是短至30个碱基的DNA序列片段。我们还利用了相关物种的基因组，将它们用作参考菌株来协助组装。通过结合这些技术和其他技术，我们能够将铜绿假单胞菌670万个碱基中的94%组装成76个大片段。剩下的6%包含在436个较小的碎片中。我们已经在开源许可证下免费提供了我们所有的软件，我们已经将新组装的基因组保存在公共基因库数据库中。
Recent improvements in technology have made DNA sequencing dramatically faster and more efficient than ever before. The new technologies produce highly accurate sequences, but one drawback is that the most efficient technology produces the shortest read lengths. Short-read sequencing has been applied successfully to resequence the human genome and those of other species but not to whole-genome sequencing of novel organisms. Here we describe the sequencing and assembly of a novel clinical isolate of Pseudomonas aeruginosa, strain PAb1, using very short read technology. From 8,627,900 reads, each 33 nucleotides in length, we assembled the genome into one scaffold of 76 ordered contiguous sequences containing 6,290,005 nucleotides, including one contig spanning 512,638 nucleotides, plus an additional 436 unordered contigs containing 416,897 nucleotides. Our method includes a novel gene-boosting algorithm that uses amino acid sequences from predicted proteins to build a better assembly. This study demonstrates the feasibility of very short read sequencing for the sequencing of bacterial genomes, particularly those for which a related species has been sequenced previously, and expands the potential application of this new technology to most known prokaryotic species. In this paper we demonstrate that a bacterial genome, Pseudomonas aeruginosa, can be decoded using very short DNA sequences, namely, those produced by the newest generation of DNA sequencers such as the Solexa sequencer from Illumina. Our method includes a novel algorithm that uses the protein sequences from other species to assist the assembly of the new genome. This algorithm breaks up the genome into gene-sized chunks that can be put back together relatively easily, even from sequence fragments as short as 30 bases of DNA. We also take advantage of the genomes of related species, using them as reference strains to assist the assembly. By combining these and other techniques, we were able to assemble 94% of the 6.7 million bases of P. aeruginosa into just 76 large pieces. The remaining 6% is contained in 436 smaller fragments. We have made all of our software available for free under open-source licenses, and we have deposited the newly assembled genome in the public GenBank database.
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细菌外多糖产生所需的环状-DI-GMP受体。
影响因子：
3.6
作者：
Lee, Vincent T;Matewish, Jody M;Kessler, Jennifer L;Hyodo, Mamoru;Hayakawa, Yoshihiro;Lory, Stephen
通讯作者：
Lory, Stephen
影响因子：
7
作者：
Chaisson, Mark J.;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
基因组分析表明，铜绿假单胞菌的毒力是组合。
影响因子：
12.3
作者：
Lee DG;Urbach JM;Wu G;Liberati NT;Feinbaum RL;Miyata S;Diggins LT;He J;Saucier M;Déziel E;Friedman L;Li L;Grills G;Montgomery K;Kucherlapati R;Rahme LG;Ausubel FM
通讯作者：
Ausubel FM
影响因子：
7
作者：
Jaffe, DB;Butler, J;Lander, ES
通讯作者：
Lander, ES
DOI：
10.1073/pnas.0511090103
发表时间：
2006-02-21
影响因子：
11.1
作者：
Kulesekara, H;Lee, V;Lory, S
通讯作者：
Lory, S