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

Oleksandr Holovachov,Quiterie Haenel,Sarah J Bourlat,Ulf Jondelius

doi:10.1098/rsos.170315

Abstract

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 phylogeny-based. 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.

Highlights

Metabarcoding studies based on high-throughput sequencing of amplicons from marine samples have reshaped our understanding of the biodiversity of marine microscopic eukaryotes, revealing a much higher diversity than previously known [1]
We are evaluating to what extent sequences of unidentified putative species of marine nematodes can be assigned to family-level taxa using publicly available reference sequences, and which of three matching strategies, alignment-based, tree-based or phylogeny-based, provides the highest number of identified operational taxonomic units (OTUs)
As completeness of the reference databases for marine nematodes is insufficient to assign all OTUs to species level [6], one has to consider if they can be assigned to taxonomic categories above species level, and if this type of data can be used in research

Summary

Introduction

Metabarcoding studies based on high-throughput sequencing of amplicons from marine samples have reshaped our understanding of the biodiversity of marine microscopic eukaryotes, revealing a much higher diversity than previously known [1]. The most recent check of NCBI GenBank (February 2017) reveals that less than 180 genera and about 170 identified species of marine nematodes are included, compared to over 530 described genera and almost 4750 described species (based on [5] with updates). This summarized number of records in GenBank does not take into consideration which genes are represented (mostly near complete or partial 18S and partial 28S rDNA), but gives the total number of entries. As completeness of the reference databases for marine nematodes is insufficient to assign all OTUs to species level [6], one has to consider if they can be assigned to taxonomic categories above species level, and if this type of data can be used in research

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Conclusion