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Smithsonian National Museum of Natural History
A rainbow-colored grid with letters A, T, C, and G spread across the picture. Unique combinations of three letters share a single color, representing the translation of DNA nucleotides to amino acids.

eDNA Reference Library

All living things contain DNA, and regions of DNA (genes) encode proteins that carry out cellular functions necessary for life. Some genes are shared across many different organisms but have a specific DNA sequence unique to an individual species. These genes, or “barcodes”, provide a means to identify species genetically rather than just by visual inspection.

A DNA reference library is a curated collection of high-quality DNA barcodes generated from specimens that are both identified by taxonomic experts and permanently housed in public collections. This means that scientists have high confidence in the species ID linked to each DNA sequence in the library, and if there are any doubts about the ID they can go back and re-check the source material. A well-curated DNA reference library allows scientists to identify species based on their DNA, rather than always having to have an expert on-hand.

A DNA reference library is also necessary to identify species from environmental DNA. Environmental DNA, or eDNA, is DNA sampled from the environment rather than from a single individual organism. Genetic material shed by micro- and macro-organisms in an environment (e.g., in water, soil, or gut contents) is collected, and the resulting sample contains DNA from a whole community of creatures. A single eDNA sample might contain the DNA from hundreds to thousands of different species! Analyzing eDNA involves comparing “unknown” DNA barcodes from the eDNA sample to the reference library to find out which species are in the community.

Since it is challenging to access and assess all organisms in mesophotic and deep benthic habitats in the Gulf of Mexico, eDNA analysis provides a quick, cheap and effective way to increase knowledge about these environments (see eDNA & Coral Biodiversity) For example, eDNA can help assess biodiversity, sort out dispersal patterns, document ecosystem structure, and detect invasive species. A comprehensive DNA reference library of Gulf of Mexico species is critical to successful eDNA analysis. As Gulf specimens are collected and curated (see Specimen Collection and Curation), NMNH-MDBC personnel are also extracting and sequencing DNA to build this DNA barcode reference library. This reference library is available via our (Protocols and Data) page. 

eDNA Processing

Technician Heather Shull sitting at a microscope and transferring specimen tissue to small tubes
MDBC collections technician Heather Shull samples specimen tissues into sterile tubes for DNA extraction. Photo credit: Savannah Bryant, Smithsonian NMNH.
A woman in a grey lab coat sits at a bench surrounded by scientific implements. She holds an 8-tipped scientific pipette and is transferring liquid to a translucent gridded plate.
MDBC collaborator Liz Whitson (Lehigh University) transfers coral tissues to specialized plates for automated DNA extraction in the Smithsonian NMNH Laboratories of Analytical Biology (L.A.B.) facility. Photo credit: Berit Kramer, Smithsonian NMNH.
A woman wearing a grey lab coat and purple latex gloves arranges rows of plates and trays containing liquid on a stainless steel platform below an open hatch with a handle
Plates containing tissue samples from Gulf of Mexico corals are loaded onto the Smithsonian NMNH automated extraction robot, which can isolate DNA for 384 samples at a time. Photo credit: Berit Kramer, Smithsonian NMNH.
A freezer shelf is full of stacks of rectangular boxes with clear plastic lids. The boxes are labeled with shorthand project codes in multi-colored tape, and circular capped tubes are just visible through each box’s clear lid.
Archival plates containing DNA extracted from Gulf of Mexico specimens sit in a freezer in the Smithsonian NMNH Laboratories of Analytical Biology (L.A.B.). Each plate stores the DNA from 96 individual specimens. Photo credit: Sarah Tweedt, Smithsonian NMNH.
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