Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454.
Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454.
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DOI：
10.1371/journal.pone.0181452
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Hidaka K
中科院分区：
文献类型：
--
作者：
Hirai J;Nagai S;Hidaka K
元遗传学是基于高通量测序仪产生的大量序列数据，在环境样本中揭示群落结构的一种快速和分类上全面的方法。由于浮游桡足动物的群落结构在海洋中具有高度的多样性和丰度，因此先前使用Roche 454对28S D2区域进行了元成因分析。然而，具有高序列输出的Illumina MiSeq平台在元成因中被更频繁地使用，而非鱿鱼类桡足类动物此前尚未得到充分评估。在此，我们利用模拟群落和先前使用Roche 454检测的野外采集样本，对基于Illumina miseq的群落结构进行了评价，并在形态学和元遗传学分析中比较了群落结构，包括非calanoid桡足类。在基于miseq的分析中，我们删除了一个单例读取，并应用适当的丰度阈值去除具有低丰度序列的错误分子操作分类单元（MOTUs）。结果表明，利用Illumina MiSeq成功地对桡足动物群落进行了表征。与Roche 454相比，MiSeq获得了更高质量的序列，这减少了对多样性的高估，特别是在MOTU聚类严格的99%相似阈值下。与基于Roche 454的分析相比，MiSeq-在生物量和物种存在/缺失方面的分类组成（包括非calanoid）更合适。我们的数据表明，由于成本更低，质量更高，使用Illumina MiSeq进行元遗传学分析比Roche 454更有助于揭示桡足动物群落。
Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated. Here, we evaluated an Illumina MiSeq-based metagenetic analysis using a mock community and field-collected samples that were examined in a previous study using Roche 454, and the community structure, including non-calanoid copepods, was compared among morphological and metagenetic analyses. We removed a singleton read and applied an appropriate abundance threshold to remove erroneous Molecular Operational Taxonomic Units (MOTUs) with low-abundance sequences in the MiSeq-based analysis. Results showed that the copepod community was successfully characterized using Illumina MiSeq. Higher-quality sequences were obtained using MiSeq than by Roche 454, which reduced the overestimation of diversity, especially at a strict 99% similarity threshold for MOTU clustering. Taxonomic compositions in terms of both biomass and presence/absence of species, including non-calanoids, were more appropriately represented in the MiSeq- than in Roche 454-based analysis. Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality.
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DOI：
10.1038/ismej.2012.8
发表时间：
2012-08
期刊：
The ISME journal
影响因子：
--
作者：
通讯作者：
--
影响因子：
46.9
作者：
Loman, Nicholas J.;Misra, Raju V.;Pallen, Mark J.
通讯作者：
Pallen, Mark J.
影响因子：
4.1
作者：
Blanco-Bercial, Leocadio;Bradford-Grieve, Janet;Bucklin, Ann
通讯作者：
Bucklin, Ann
影响因子：
64.8
作者：
Beaugrand, G;Brander, KM;Reid, PC
通讯作者：
Reid, PC
影响因子：
11
作者：
Degnan, Patrick H.;Ochman, Howard
通讯作者：
Ochman, Howard