title: Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME.
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.
authors.affiliation: Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave., NW, Washington, DC, 20560, USA. leray.upmc@gmail.com.
authors.forename: Matthieu
authors.initials: M
authors.lastname: Leray
authors.affiliation: Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave., NW, Washington, DC, 20560, USA.
authors.forename: Nancy
authors.initials: N
authors.lastname: Knowlton
mesh_terms: D044822:Biodiversity; D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D064307:Microbiota / Q000235:genetics; D025341:Principal Component Analysis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Alpha diversity; Beta diversity; Metabarcoding; Principal component analysis; QIIME; Rarefaction