loading page

Catching small fish in a big pond: targeted vs untargeted sequencing for marine eukaryotic eDNA
  • +2
  • Nastassia Patin,
  • Kathleen Pitz,
  • Jacoby Baker,
  • Francisco Chavez,
  • Kelly Goodwin
Nastassia Patin
University of California San Diego

Corresponding Author:[email protected]

Author Profile
Kathleen Pitz
Monterey Bay Aquarium Research Institute
Author Profile
Jacoby Baker
Monterey Bay Aquarium Research Institute
Author Profile
Francisco Chavez
Monterey Bay Aquarium Research Institute
Author Profile
Kelly Goodwin
Atlantic Oceanographic and Meteorological Laboratory
Author Profile

Abstract

Marker gene sequencing or “metabarcoding” is the primary sequencing approach currently used for molecular biodiversity surveys, but this approach is taxonomically limited and hampered by amplification biases. Shotgun metagenomes offer a PCR–free approach to environmental DNA (eDNA) sequencing, theoretically capturing the full taxonomic breadth of the eDNA pool. However, eukaryotic DNA is often a small component of metagenomes and it has seen limited use for metazoan biodiversity surveys. Here, we compare metabarcoding and shotgun metagenomes on a large (>200 sample size) set of marine water column eDNA samples and show that metagenomes can provide biodiversity information comparable to that of metabarcoding surveys. Moreover, as a result of biases in reference database composition, shotgun sequencing can outperform marker genes for certain taxa. Taxonomic database gaps remain an obstacle to accurate and comprehensive biodiversity surveys for both metabarcoding and shotgun metagenomes. We provide examples of taxa that may benefit from one approach over another and highlight cases of metagenomic utility.
04 Sep 2024Submitted to Molecular Ecology Resources
06 Sep 2024Submission Checks Completed
06 Sep 2024Assigned to Editor
06 Sep 2024Review(s) Completed, Editorial Evaluation Pending
19 Sep 2024Reviewer(s) Assigned