PROJECT

Testing waters with DNA zoo technology to build genomic resources for critical marine habitat-forming species of seagrasses

Project Status: In progress

Investigators

Matthew Fraser
Research Fellow, Oceans Institute and School of biological Sciences, UWA

Belinda Martin
PhD Candidate, Oceans Institute and School of Biological Sciences, UWA

Parwinder Kaur
Director, DNA Zoo Australia, UWA School of Agriculture and Environment, UWA

Scope

The problem

Climate change is fundamentally altering our coastal and estuarine ecosystems in Western Australia, detrimentally impacting ecosystem services and placing the environmental, cultural and economic benefits they provide at risk. Where marine habitat-forming species (e.g. seagrasses, macroalgae, corals) are affected, negative impacts are magnified through bottom-up interactions. For example, climate-driven seagrass loss in the Shark Bay World Heritage Site has been cited as a dominant factor in the reduction of sightings of iconic megafauna (e.g. turtles and dugongs) and to the collapse of commercial scallop and crab fisheries, contributing to social and economic impacts.

The solution

Understanding the responses of key species to changing climate has therefore become a major conservation requirement in the Anthropocene. One major factor determining the response of organisms to stressors like increasing temperature is their genetic potential to acclimate and adapt. However, predictions of such “genetic resilience” is contingent on the availability of high-quality genome sequences. This has previously been cost-prohibitive, limiting the number of marine organisms with high quality genomes that have been published. Recent advances in sequencing technologies and bioinformatic analysis have reduced the cost of producing such genomes, opening up this exciting new resource for use in marine ecosystems. We propose to apply the novel approach of DNA Zoo to build high-quality, chromosome-length genomes for habitat-forming WA seagrasses. Genome sequences are currently available for four WA seagrasses (Publicly available –Halophila ovalis, Zostera muelleri,In-lab –Amphibolis antarctica, Posidonia australis). We propose to upgrade one of these sequences and scaffolds using the Hi-C approach working with DNA Zoo Australia team.

Outcomes

With DNA Zoo Australia being housed at UWA, this will position the Indian Ocean Marine Research Centre to build in-house capacity to develop world-class genomic resources for ocean organisms with a workflow that would be broadly applicable to a wide range of marine species. The availability of these sequences will provide a valuable resource for additional research in areas such as population genetics and genomics–both emerging components of marine ecosystem management. Given that these seagrasses provide critical fisheries habitat along the WA coastline, we also envisage this would be of broad interest to industry stakeholders. For example, the outcomes of this project will be of direct interest to Department of Biodiversity, Conservation and Attractions, complimenting their existing monitoring projects and would likely contribute to future, collaborative funding applications such as ARC Linkages. This research will also lead to a high-impact publication. This project would provide proof of concept of the ability of IOMRC to produce high quality, chromosome-length genomes for a relatively low cost (~$5000). The ability to produce such high-quality reference genomes would open up the potential to use genomic methods for monitoring potential industry impacts in marine ecosystems, where the lack of assembled genomes has previously proven an expensive entry barrier. For example, the availability of high-quality reference genomes for key habitat forming species would allow methods such as transcriptomics that would provide sub-lethal markers of stress that could be used to inform management decisions. Similarly, high-quality reference genomes also improve the accuracy of methods such as environmental DNA (eDNA) analysis aiming to detect the presence of key organisms from environmental samples (e.g. invasive species, species of conservation concern). The development of such techniques in a cost-effective manner would position IOMRC and the Oceans Institute as a key provider of novel genomics resources for the effective management of WA’s vast marine estate.Finally, this project involves two PhD students from the Oceans Institute, and will provide them with the opportunity to work alongside and learn key techniques from DNA Zoo team members, thus building further capacity for genomic research within the Oceans Institute.