Introducing ORG.one: a project to support rapid DNA sequencing of critically endangered species
Mon 19th April 2021
ORG.one is a pilot-stage project designed to support faster, more localised sequencing of critically endangered species, by enabling biologists to rapidly sequence those species close to the sample’s origin, using the latest ultra-long read approaches from Oxford Nanopore.
Loss of biodiversity is an urgent problem. Genomics can help with existing conservation work, as well as securing the DNA sequence of critically endangered species for future knowledge.
Current projects to sequence endangered species are making great progress, however they can be limited by complex workflows and capacity bottlenecks caused by the requirement to send samples to centralised, often overseas, locations for sequencing.
Through this pilot, data-rich, de novo whole genome assemblies will be enabled through the provision of consumable support that can be used with Oxford Nanopore sequencers, on the condition that the data generated will be openly shared with the scientific community.
Professor Tomas Marques-Bonet, Universitat Pompeu Fabra & Institute of Evolutionary Biology (CSIC-UPF), who plans to participate in the pilot phase, said:
"With this alarming rate of species extinctions due to human activity, our kids and future generations will always wonder why we did not preserve a legacy for them to enjoy. This project will help us to understand the impact of the changing environment on these species and it is one of the many steps needed to inform our decisions about their conservation."
How will the pilot work?
ORG.one is supported by Oxford Nanopore and the pilot phase of this project will support Oxford Nanopore’s current user Community to develop high quality de novo assemblies of genomes of a number of species in the IUCN Red List.
A number of users who currently have access to these samples will receive free-of-charge consumables, to enable them to sequence the samples with the latest nanopore tools and methods, with the aim of achieving the most comprehensive genome possible.
The free-of-charge consumables will be provided on the basis that the researchers are responsible for any local legal and ethical permits to generate the data and to share or export it, that no animals are harmed or killed for their DNA and that the data will be uploaded to a public database managed by EMBL’s European Bioinformatics Institute (EMBL-EBI) within 6 weeks.
As the program expands, more and more Oxford Nanopore users will be able to participate, leveraging the platforms distributed sequencing capacity and collaborating on a global scale to sequence hundreds and thousands of species per year collaboratively.
Dr Peter Harrison, Genome Analysis Team Leader, EMBL-EBI said:
“We are excited to contribute to the rapid and open distribution of data that will enable new scientific discoveries and conservation research on some of the globally most endangered species. The European Bioinformatics Institute will archive and freely disseminate all of the data produced by the ORG.one project through the European Nucleotide Archive. We will also contribute expertise in biodiversity genomics, metadata standards and data coordination to maximise the utility and benefit of these key biodiversity datasets.”
Craig Rhodes, EMEA Industry Lead AI for Health and Life Sciences, NVIDIA said:
“DNA sequencing is a huge computational challenge. To address this, NVIDIA will provide the ORG.one research teams access to the UK’s fastest supercomputer, Cambridge-1, which harnesses NVIDIA’s latest DGX A100 systems to run DNA analysis in hours instead of what had previously been days.”
Why is sequencing useful for conservation?
Sequencing is the process of identifying the order of bases — the molecules that make up DNA — to uncover a sequence that makes up that organism. This sequence data can be used to understand more about its biology and physiology, its development, and how its genome interacts with the environment, thereby allowing us to make more informed choices about its conservation.
Which organisms will be prioritised?
ORG.one supports the sequencing of critically endangered species from the IUCN Red List, specifically those on the critically endangered and extinct in the wild categories (more than 8000 species).
Established in 1964, the IUCN Red List of Threatened Species has evolved to become the world’s most comprehensive information source on the global conservation status of animal, fungi and plant species.