Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities.
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities.
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DOI：
10.1371/journal.pone.0130035
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Blomster J
中科院分区：
文献类型：
--
作者：
Majaneva M;Hyytiäinen K;Varvio SL;Nagai S;Blomster J
扩增子读码测序已经彻底改变了微生物多样性研究领域。该技术已开发用于细菌组合，并已通过模拟社区进行了严格的测试。然而，由于真核生物的巨大复杂性和不同rDNA拷贝的数量，分析真核生物的多样性比分析细菌或模拟社区更苛刻，因此需要研究测试分类上不同的自然社区的分析方法。在这项研究中，我们使用了20个样本收集波罗的海的冰，雪泥和冰下水调查三个程序包（UPARSE，Mothur和QIIME）和18个不同的生物信息学策略，在他们实施。我们的目的是评估生物信息学策略的初始步骤对分析天然真核生物群落结果的影响。我们发现，在所得到的读长，OTU的数量和多样性的估计，以及明显的差异，在社区的分类组成的策略之间的显着差异。差异的产生主要是因为通过预处理步骤的嵌合读段的数量可变。单例去除和去噪大大降低了错误的数量。我们的研究表明，生物信息学扩增子读段处理策略的初始步骤在应用于真核生物群落之前需要仔细考虑。
Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities. In this study, we used 20 samples collected from the Baltic Sea ice, slush and under-ice water to investigate three program packages (UPARSE, mothur and QIIME) and 18 different bioinformatic strategies implemented in them. Our aim was to assess the impact of the initial steps of bioinformatic strategies on the results when analyzing natural eukaryotic communities. We found significant differences among the strategies in resulting read length, number of OTUs and estimates of diversity as well as clear differences in the taxonomic composition of communities. The differences arose mainly because of the variable number of chimeric reads that passed the pre-processing steps. Singleton removal and denoising substantially lowered the number of errors. Our study showed that the initial steps of the bioinformatic amplicon read processing strategies require careful consideration before applying them to eukaryotic communities.
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影响因子：
3.7
作者：
Egge E;Bittner L;Andersen T;Audic S;de Vargas C;Edvardsen B
通讯作者：
Edvardsen B
影响因子：
3.4
作者：
Epstein, Slava;Lopez-Garcia, Purificacion
通讯作者：
Lopez-Garcia, Purificacion
影响因子：
5.8
作者：
Huber, T;Faulkner, G;Hugenholtz, P
通讯作者：
Hugenholtz, P
影响因子：
4.4
作者：
Ashelford, KE;Chuzhanova, NA;Weightman, AJ
通讯作者：
Weightman, AJ
影响因子：
4.4
作者：
Ashelford, Kevin E.;Chuzhanova, Nadia A.;Weightman, Andrew J.
通讯作者：
Weightman, Andrew J.