The importance of molecular markers and primer design when characterizing biodiversity from environmental DNA

• Published in: Genome Vol. 60; no. 4; pp. 358 - 374
• Main Author: Freeland, Joanna R
• Format: Journal Article
• Language: English
• Published: Canada NRC Research Press 01.04.2017; Canadian Science Publishing NRC Research Press
• Subjects: ADN environnemental; barcoding; Biodiversity; biodiversité; codage à barres; conception d’amorces; Deoxyribonucleic acid; DNA; DNA barcoding; DNA Barcoding, Taxonomic - methods; DNA fragmentation; DNA Primers - genetics; DNA sequencing; ecosystems; Environment; Environmental DNA; genes; genetic markers; Genetic Markers - genetics; Genomics; high-throughput sequencing; metabarcoding; Methods; métacodage à barres; Observations; PCR; primer design; qPCR; researchers; soil; Species Specificity; séquençage à haut débit; codage à barres; metabarcoding; biodiversity; séquençage à haut débit; environmental DNA; métacodage à barres; ADN environnemental; biodiversité; conception d’amorces; barcoding; qPCR; primer design; PCR; high-throughput sequencing
• ISSN: 0831-2796; 1480-3321; 1480-3321
• DOI: 10.1139/gen-2016-0100

Environmental DNA (eDNA) comprises DNA fragments that have been shed into the environment by organisms, and which can be extracted from environmental samples such as water or soil. Characterization of eDNA can allow researchers to infer the presence or absence of species from a particular site without the need to locate and identify individuals, and therefore may provide an extremely valuable tool for quantifying biodiversity. However, as is often the case with relatively new protocols, methodological challenges remain. A number of earlier reviews have discussed these challenges, but none have provided extensive treatment of the critical decisions surrounding molecular markers and primer development for use in eDNA assays. This review discusses a number of options and approaches that can be used when determining which primers and gene regions are most appropriate for either targeted species detection or metabarcoding macro-organisms from eDNA. The latter represents a new field that is growing rapidly, and which has the potential to revolutionize future assessments of community and ecosystem diversity.