Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.
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DOI：
10.1186/gb-2005-6-3-r23
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发表时间：
2005
期刊：
影响因子：
12.3
通讯作者：
Nelson WC
中科院分区：
文献类型：
--
作者：
Salzberg SL;Dunning Hotopp JC;Delcher AL;Pop M;Smith DR;Eisen MB;Nelson WC
通过搜索公开的DNA测序数据库，我们在三种不同的果蝇中发现了三种新的细菌内共生体Wolbachia pipientis：果蝇，D. simulans和D.莫哈韦西斯。Trace Archive是大规模基因组测序项目产生的原始未分析数据的存储库。这些数据的存在为科学家提供了发现原始测序之外的其他基因组序列的可能性。特别地，如果测序项目的源DNA来自被另一种生物定殖的物种，则该项目可以从共生或寄生生物产生大量的基因组DNA，包括接近完整的基因组。通过搜索公开的DNA测序数据库，我们在三种不同的果蝇中发现了三种新的细菌内共生体Wolbachia pipientis：果蝇，D. simulans和D.莫哈文斯。我们提取了与先前测序的沃尔巴克氏体菌株部分匹配的所有序列，并使用定制软件组装这些序列。对于三个新物种中的一个，恢复的数据足以产生覆盖超过95%的基因组的组装;对于第二个物种，数据产生相当于基因组的“轻猎枪”采样，覆盖估计75-80%的基因组;对于第三个物种，数据覆盖大约6-7%的基因组。这项研究的结果揭示了将原始数据存储在中央基因组序列库中的意想不到的好处：可以在这些数据中发现新物种。这三个新的沃尔巴克氏体基因组与先前测序的菌株之间的差异揭示了每个谱系中的许多重排和插入以及数百个新基因。这三个新的基因组及其注释已在GenBank中保藏。
By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.
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影响因子：
56.9
作者：
Salzberg, SL;White, O;Eisen, JA
通讯作者：
Eisen, JA
影响因子：
9.2
作者：
Heath, BD;Butcher, RDJ;Hubbard, SF
通讯作者：
Hubbard, SF
DOI：
10.1006/bbrc.2001.4906
发表时间：
2001-05-25
影响因子：
3.1
作者：
Masui, S;Kuroiwa, H;Ishikawa, H
通讯作者：
Ishikawa, H
影响因子：
7.4
作者：
Martin, W;Herrmann, RG
通讯作者：
Herrmann, RG
影响因子：
14.9
作者：
Chenna, R;Sugawara, H;Thompson, JD
通讯作者：
Thompson, JD