How reliable is metabarcoding for pollen identification? An evaluation of different taxonomic assignment strategies by cross-validation.

ABSTRACT: Metabarcoding is a powerful tool, increasingly used in many disciplines of environmental sciences. However, to assign a taxon to a DNA sequence, bioinformaticians need to choose between different strategies or parameter values and these choices sometimes seem rather arbitrary. In this work, we present a case study on ITS2 and rbcL databases used to identify pollen collected by bees in Belgium. We blasted a random sample of sequences from the reference database against the remainder of the database using different strategies and compared the known taxonomy with the predicted one. This in silico cross-validation (CV) approach proved to be an easy yet powerful way to (1) assess the relative accuracy of taxonomic predictions, (2) define rules to discard dubious taxonomic assignme

SUBMITTER: San Martin G 

PROVIDER: S-EPMC10838070 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature