Divide and conquer: enriching environmental sequencing data.
Divide and conquer: enriching environmental sequencing data.
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DOI：
10.1371/journal.pone.0000830
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发表时间：
2007-09-05
期刊：
影响因子：
3.7
通讯作者：
Poisson G
中科院分区：
文献类型：
--
作者：
Bergeron A;Belcaid M;Steward GF;Poisson G
在环境测序项目中，对来自整个微生物群落的DNA混合物进行片段化和测序，可能的目标之一是重建该群落成员的部分或完整基因组。在物种多样性较高的群落中，有相当比例的序列不与样品中的任何其他片段重叠。这个问题不仅会出现在许多物种分布相对均匀的情况下，而且也会出现在特定环境中的群落通常由相同的少数物种主导的情况下。在前一种情况下，可能根本没有基因组被组装，而在后一种情况下，环境中的少数优势物种总是以高覆盖度被测序，而损害了更多稀疏物种的覆盖。在这里，我们表明，在同样的全球测序努力下，在测序之前将物种分成两个或多个亚群落可以产生更高比例的可组装序列。我们首先利用Lander-Waterman模型表明，如果单例序列的预期百分比高于25%，那么在均匀分布假设下，分裂群落总是明智的选择。然后，我们构建模拟微生物群落，以表明结果适用于高度不均匀的分布。我们还表明，对于实验中考虑的分布，可以相当准确地估计两个亚群落的相对多样性。鉴于存在几种基于物理性质（如大小、密度、表面生物化学或光学性质）分裂微生物群落的方法，我们强烈建议参与环境测序并期望高多样性的群体考虑分裂其群落，以最大限度地提高其测序工作的信息含量。
In environmental sequencing projects, a mix of DNA from a whole microbial community is fragmented and sequenced, with one of the possible goals being to reconstruct partial or complete genomes of members of the community. In communities with high diversity of species, a significant proportion of the sequences do not overlap any other fragment in the sample. This problem will arise not only in situations with a relatively even distribution of many species, but also when the community in a particular environment is routinely dominated by the same few species. In the former case, no genomes may be assembled at all, while in the latter case a few dominant species in an environment will always be sequenced at high coverage to the detriment of coverage of the greater number of sparse species. Here we show that, with the same global sequencing effort, separating the species into two or more sub-communities prior to sequencing can yield a much higher proportion of sequences that can be assembled. We first use the Lander-Waterman model to show that, if the expected percentage of singleton sequences is higher than 25%, then, under the uniform distribution hypothesis, splitting the community is always a wise choice. We then construct simulated microbial communities to show that the results hold for highly non-uniform distributions. We also show that, for the distributions considered in the experiments, it is possible to estimate quite accurately the relative diversity of the two sub-communities. Given the fact that several methods exist to split microbial communities based on physical properties such as size, density, surface biochemistry, or optical properties, we strongly suggest that groups involved in environmental sequencing, and expecting high diversity, consider splitting their communities in order to maximize the information content of their sequencing effort.
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影响因子：
4.3
作者：
Chen K;Pachter L
通讯作者：
Pachter L
影响因子：
9.8
作者：
Rusch DB;Halpern AL;Sutton G;Heidelberg KB;Williamson S;Yooseph S;Wu D;Eisen JA;Hoffman JM;Remington K;Beeson K;Tran B;Smith H;Baden-Tillson H;Stewart C;Thorpe J;Freeman J;Andrews-Pfannkoch C;Venter JE;Li K;Kravitz S;Heidelberg JF;Utterback T;Rogers YH;Falcón LI;Souza V;Bonilla-Rosso G;Eguiarte LE;Karl DM;Sathyendranath S;Platt T;Bermingham E;Gallardo V;Tamayo-Castillo G;Ferrari MR;Strausberg RL;Nealson K;Friedman R;Frazier M;Venter JC
通讯作者：
Venter JC
影响因子：
3.1
作者：
SMITH, TJ
通讯作者：
SMITH, TJ
DOI：
10.1073/pnas.202488399
发表时间：
2002-10-29
影响因子：
11.1
作者：
Breitbart, M;Salamon, P;Rohwer, F
通讯作者：
Rohwer, F
DOI：
10.1073/pnas.0608549103
发表时间：
2006-11-28
影响因子：
11.1
作者：
Hallam, Steven J.;Konstantinidis, Konstantinos T.;DeLong, Edward F.
通讯作者：
DeLong, Edward F.