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

TL;DR

This study compares different taxonomy assignment methods for marine nematode barcodes, finding that phylogeny-based approaches yield higher accuracy and are more robust to data limitations.

Contribution

It demonstrates that phylogeny-based taxonomy assignment outperforms other methods in identifying marine nematode metabarcodes under limited reference data.

Findings

Phylogeny-based approach assigns the most metabarcodes accurately.

Phylogeny-based method is less affected by erroneous sequences.

Limited reference data restricts taxonomic resolution to family level.

Abstract

Precision and reliability of barcode-based biodiversity assessment can be affected at several steps during acquisition and analysis of the data. Identification of barcodes 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. Number of identified sequences in the reference databases affects the precision of identification. This paper compares the identification of marine nematode barcodes using alignment-based, tree-based and phylogeny-based approaches. Because the nematode reference dataset is limited in its taxonomic scope, barcodes can only be assigned to higher taxonomic categories, families. Phylogeny-based approach using Evolutionary Placement Algorithm provided the largest number of positively assigned metabarcodes and was least affected by erroneous sequences and limitations of reference data, comparing to alignment-based and tree-based approaches.