New Guide Seeks to Advance DNA Library of Marine Species

Story by:

• Brittany Hook- bhook@ucsd.edu

Topics covered:

• marine biology
• ocean science
• eDNA
• molecular biology

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A team of scientists has created a new guideto advance standards for collecting and cataloging DNA from marine species, enhancing a revolutionary method for monitoring ocean biodiversity.

The guide was developed by the West Coast Ocean Biomolecular Observing Network (WC-OBON)-a regional chapter of a global observatory sponsored by the United Nations Decade of Ocean Science for Sustainable Development-to improve accuracy and consistency in genetic reference libraries.

Integrating best practices from several fields, the guide offers recommendations for every stage of collecting and identifying marine specimens found across the ocean. It provides instructions on activities including field collection, specimen sorting and photography, tissue sampling, lab-based analysis, DNA extraction and amplification, barcode sequencing, data archiving, and submission to a publicly accessible DNA reference database.

The effort was led by WC-OBON leaders from UC San Diego's Scripps Institution of Oceanography, the NOAA Pacific Marine Environmental Laboratory (PMEL), and the California Cooperative Oceanic Fisheries Investigations (CalCOFI), with collaboration from a total of 15 scientists across 11 different research organizations, programs, and museums.

"This guide provides a valuable resource from the world's leading experts on biological specimen curation, taxonomic identification, and barcode sequencing to accelerate the production and publication of high-quality reference sequences," said Nastassia Patin, a molecular ecologist at Scripps Oceanography and the CalCOFI program, a leader at WC-OBON, and a co-author of the guide.

While research standards are already established across scientific fields, this guide offers diverse insights focusing on DNA barcode sequencing for marine species, compiling best practices into a single resource.

DNA barcodes sequences are short, unique identifiers for each species. By standardizing methods, the guide aims to ensure the accuracy and consistency of DNA submitted to global databases like GenBank or the Barcode of Life Data System.

"One fantastic part of this guide is that it brings together information on the entire end-to-end process of generating reference barcodes," said Zachary Gold, lead molecular ecologist at NOAA PMEL, a leader at WC-OBON, and a co-author of the guide. "There are lots of great resources out there that focus on field collection, sample preservation, DNA sequencing or biodiversity data standards, but this guide brings all that information into one place to make it easier for scientists and resource managers to have all the relevant information at their fingertips."

This guide will help advance the emerging field of environmental DNA (eDNA), a cost-effective, minimally invasive, and scalable tool for monitoring biodiversity. With eDNA, scientists can get an overview of a marine community by sampling seawater and extracting the DNA marine life leaves behind.

The new guide is publicly available on Zenodo.

"eDNA is increasingly being used to better track marine life, providing scientists with more and better eyes on the water to observe how marine ecosystems are changing," said Gold.

However, the effectiveness of eDNA depends on high-quality databases so that unknown sequences from the environment can be linked to their source organisms. This guide will serve as a how-to manual for researchers, including those specializing in field identification, museum curation, or DNA sequencing, to contribute to the holistic effort.

The idea for the guide emerged from meetings and conversations centered on a key question: How do we build these libraries from the ground up to meet gold standards? For example, if a researcher wanted to genetically identify a sea star, what steps would ensure that the specimen was expertly handled throughout the entire process-from collection to archival-while being properly linked to a barcode?

The guide recommends that voucher specimens-those preserved to the highest standards and accessible in a permanent scientific collection-should be prioritized. This ensures that entries in the database are identifiable and verifiable for potential further research.

Marine invertebrate voucher specimens in the Benthic Invertebrate Collection at Scripps Institution of Oceanography. Photo: Jordann Tomasek

Experts from the renowned Scripps Oceanographic Collections, along with specialists from the Smithsonian National Museum of Natural History and the Natural History Museum of Los Angeles, provided recommendations for this section of the guide.

"One of the things I appreciated about this collaborative project working with so many diverse experts was just how much knowledge and nuance there was to every facet of building DNA reference libraries," said Gold. "It gave me a profound appreciation for taxonomists and curators who do such important and often unsung work behind the scenes of museums to make specimens and data as valuable as possible."

Open science and fair practices are at the heart of the guide, which is designed to be a community resource to expand our understanding of marine biodiversity and ecosystems.

"Once we generate the sequence, we can make it available to everyone," said Patin. "This would allow a researcher who has collected eDNA, for example, to submit the data into the reference database and maybe get a match for something that they wouldn't have had a match for before."

In addition to eDNA applications, the team hopes the guide will help support emerging California-based projects focused on intertidal species.

"As biodiversity comes under increasing global threat, it is critical that we leverage new technologies to accelerate and improve ecosystem monitoring," said Patin. "This guide is a valuable resource to the scientific community that is eager to address this challenge."

The guide, "Introduction to Developing DNA Reference Barcode Sequences," is publicly available on Zenodo. The project was a voluntary effort led by members of the WC-OBON and collaborators, undertaken without dedicated funding.

Images of live benthic invertebrates from offshore California: 1) Hermissenda opalescens nudibranch, 2) Limaria hemphilli file clam, 3) Neanthes sp. polychaete worm, 4) Ophiuroidea brittle star, 5) Leptopecten latiauratus kelp scallop, 6) Munidopsis girguisi squat lobster, 7) Poraniopsis inflata sea star, 8) Fionoidea nudibranch, 9) Astrodia sp. brittle star on Swiftia sp. gorgonian. Photos: Charlotte Seid