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Taxonomy assignment approach determines the efficiency of identification of OTUs in marine nematodes

Journal article
Authors Oleksandr Holovachov
Quiterie Haenel
Sarah Bourlat
Ulf Jondelius
Published in Royal Society Open Science
Volume 4
Publication year 2017
Published at Department of marine sciences
Language en
Links dx.doi.org/10.1098/rsos.170315
rsos.royalsocietypublishing.org/con...
Keywords Barcode, Biodiversity, Identification, Meiobenthos, Metabarcoding, Nematodes
Subject categories Zoology, Genetics, Biological Systematics, Bioinformatics and Systems Biology

Abstract

© 2017 The Authors. Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of data. Identification of operational taxonomic units (OTUs) is one of the crucial steps in the process and can be accomplished using several different approaches, namely, alignment-based, probabilistic, tree-based and phylogenybased. The number of identified sequences in the reference databases affects the precision of identification. This paper compares the identification of marine nematode OTUs using alignment-based, tree-based and phylogeny-based approaches. Because the nematode reference dataset is limited in its taxonomic scope, OTUs can only be assigned to higher taxonomic categories, families. The phylogeny-based approach using the evolutionary placement algorithm provided the largest number of positively assigned OTUs and was least affected by erroneous sequences and limitations of reference data, compared to alignment-based and tree-based approaches.

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