Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding.

Autor: Espinosa Prieto A; University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France., Hardion L; University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France., Debortoli N; Namur Molecular Tech, CHU UCL Namur, Yvoir, Belgium.; E-BIOM SA, Namur, Belgium., Beisel JN; University of Strasbourg, CNRS, Laboratoire Image Ville Environnement, UMR 7362, Strasbourg, France.; École Nationale du Génie de l'Eau et de l'Environnement de Strasbourg (ENGEES), Strasbourg, France.
Jazyk: angličtina
Zdroj: Molecular ecology resources [Mol Ecol Resour] 2024 May; Vol. 24 (4), pp. e13937. Date of Electronic Publication: 2024 Feb 16.
DOI: 10.1111/1755-0998.13937
Abstrakt: As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.
(© 2024 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)
Databáze: MEDLINE
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