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Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME

  • Matthieu LerayEmail author
  • Nancy Knowlton
Part of the Methods in Molecular Biology book series (MIMB, volume 1452)

Abstract

PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of diversity for these massive datasets are essential. Efforts by microbiologists to understand the Earth and human microbiomes using high-throughput sequencing of the 16S rRNA gene has led to the development of several user-friendly, open-source software packages that can be similarly used to analyze eukaryotic datasets. Quantitative Insights Into Microbial Ecology (QIIME) offers some of the most helpful data visualization tools. Here, we describe functionalities to import OTU tables generated with any molecular marker (e.g., 18S, COI, ITS) and associated metadata into QIIME. We then present a range of analytical tools implemented within QIIME that can be used to obtain insights about patterns of alpha and beta diversity for marine eukaryotes.

Key words

Metabarcoding QIIME Alpha diversity Beta diversity Principal component analysis Rarefaction 

Notes

Acknowledgments

We thank Sarah Bourlat for inviting this submission. This work was supported by the Sant Chair and the Smithsonian Tennenbaum Marine Observatories Network, for which this is Contribution No. 3.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Department of Invertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonUSA

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