R&D is transforming the underwater genomics landscape.

Accessing intracellular DNA is the first step in processing biodiversity genomes. When the species involved are as different from one another as corals are from grizzly bears, it’s no surprise that extraction protocols must be adapted and refined to suit each sample type. Marine species add an extra layer of complexity, as thick mucus, tough shells, and associated compounds can all interfere with the release of high-quality DNA. Every successful extraction begins with careful optimization, matching method to material. The Tree of Life Laboratory at the Wellcome Sanger Institute recently published new insights and protocols developed from the first 2,000 Tree of Life genome assemblies. Here, we explore a few marine examples that showcase these advances.

Case Study 1 – Getting Access to Coral DNA
Corals (R&D by Ben Jackson & Elizabeth Sinclair)
Extracting DNA from corals has proven extremely challenging, especially in hard, stony species. Standard disruption approaches such as PowerMasher and CryoPrep (see protocols link) were unsuitable, leading to inefficient cell breakage and low DNA yields.

At the Tree of Life lab in the Wellcome Sanger Institute, coral R&D experts have been refining these methods and sharing key protocols that are improving extraction success for these complex organisms. After confirming that standard methods produced suboptimal results, researchers Ben Jackson and Elizabeth Sinclair tested an alternative disruption strategy using cryogenic bead beating to physically break apart coral cells and release their DNA. Following months of experimentation with different bead sizes, the team discovered that large zirconium beads were needed to sufficiently disrupt the samples for downstream laboratory processes.

Case Study 2 – Sharing Methods and Squeezing the Sponges
Sponges (R&D by Elizabeth Sinclair & Graeme Oatley)

Working within the EBP network of cutting-edge biodiversity genomics projects naturally fosters collaboration and the exchange of innovative laboratory techniques. Graeme Oatley’s research on sponge DNA extraction illustrates just how demanding R&D can be. After months of trials and repeated setbacks using standard extraction methods, the Wellcome Sanger team shared their frustrations with colleagues in the EBP-affiliated Aquatic Symbiosis Genomics Project.

What began as a friendly debrief over laboratory challenges led to a breakthrough: members of the sponge community introduced the concept of sponge “squeezing.” This gentle approach allowed Graeme Oatley and Elizabeth Sinclair to carefully isolate sponge cells from their supporting skeleton. Using these purified cells in downstream processes significantly improved DNA quality across many sponge species in the ASG project.

Case Study 3 – Cracking the Code for Jellyfish DNA
Jellyfish (R&D by Amy Denton)

Jellyfish present a unique challenge for DNA extraction. Their bodies are small, composed mostly of water and a gelatinous matrix, which makes isolating DNA particularly complex. As a first step, researchers increased the amount of tissue used in each extraction to boost DNA yield. When this approach still produced low quantities, they began incorporating ideas from a range of commercial kits to refine their methods.

After several rounds of R&D, the team identified a breakthrough: using the lysis buffer from the Omega BioTek E.N.Z.A. kit, combined with the introduction of magnetic beads during the DNA isolation step, significantly improved both yield and quality. The resulting DNA was finally suitable for PacBio HiFi sequencing.

This optimized method is now being adapted for other challenging marine taxa, including molluscs and echinoderms, expanding the toolkit for high-quality genome assemblies across diverse ocean species.