Comparing diversity levels in environmental samples: DNA sequence capture vs. metabarcoding approaches using 18S and COI genes. eDNA metabarcoding vs. DNA sequence-capture

Environmental DNA studies targeting multiple taxa using metabarcoding, provide remarkable insights into levels of species diversity in any habitat. The main drawbacks are the need for PCR amplification, primer bias and difficulty in identifying rare species. We tested a DNA sequence-capture method in parallel with the metabarcoding approach to reveal possible advantages of one method over the other. Both approaches were performed using the same eDNA samples and the same 18S and COI regions, followed by HTS. Metabarcoded eDNA libraries were PCR amplified with one primer pair from 18S and COI genes. DNA sequence-capture libraries were enriched with 3639 baits targeting the same gene regions.