Genomes of 50 critically endangered species are sequenced in successful pilot of conservation project

Global conservation project with a goal to sequence all critically endangered species continues to publish all data to an open repository to ensure anyone, anywhere can use it to guide conservation efforts

The project today announced that the genome of a 50th critically endangered species, the Jararaca-de-Vitória snake (Bothrops otavioi) of Brazil, has been sequenced. This completes a pilot phase of this global, inclusive conservation project that launched in 2021. is a project supported by Oxford Nanopore Technologies that is designed to aid equitable, faster, and more localised sequencing of critically endangered species. It aims to enable biologists to study those species rapidly and in situ, or close to the sample’s origin, using the latest, information-rich sequencing approaches.

In order to understand any organism fully, it’s crucial to assemble a high-quality reference genome by sequencing its DNA. With a reference genome, conservationists can better understand the organism’s risk to certain diseases, the local population size, and demographics. Studying genetic diversity with high-resolution identification is important for programs such as genetic rescue and monitoring of breeding programs.

A key focus for is to deliver the significant benefits of genomics for the conservation of Critically Endangered Organisms. To maximise the project’s impact, is developing an open-access database of the most comprehensive high quality de novo draft assemblies of genomes to support the conservation of as many species classified as critically endangered on the IUCN Red list as possible and ensure anyone, anywhere can use that information to guide conservation efforts.

Diverse species

Across the 50 critically endangered organisms that have successfully been sequenced there is a range of species, for example:

Gabriela Pozo – brown-headed spider monkey, Ecuador

Gabriela Pozo, researcher at the USFQ Biotechnology Laboratory, and her collaborators have sequenced the genome of the brown-headed spider monkey (Ateles fusciceps fusciceps, 2.8 Gb), one of the 25 most endangered primates in the world, in situ in Ecuador. For Gabriela, the Oxford Nanopore MinION device has been “crucial” to their success by providing the USFQ Biotechnology Laboratory with access to an affordable sequencing technology that has enabled the team to generate high-quality draft reference genomes.

Gabriela has stressed the need for high-quality reference genomes of all species, especially those that are most endangered as this can help to develop molecular markers and to truly understand the genetic status of a species. This in turn can help to improve conservation efforts and breeding programmes.

Mrinalini Erkenswick Watsa – short-eared dog, Peru

Mrinalini and the In Situ Laboratory Initiative team are demonstrating the power of portable high throughput sequencing for conservation of the short-eared dog (Atelocynus microtis, 2.4 Gb) deploying the latest Oxford Nanopore sequencing device, the PromethION 2 (P2) Solo, in historically challenging environments. By delivering the most powerful PromethION Flow Cells close to the sample source in Peru, they are shortening the time to result as the data acquisition is performed locally, rather than shipping the sample to a remote sequencing centre. Mrinalini works for the ‘In situ Lab initiative’, which has at its core a commitment to do work as close to the site of sample collection as possible, led by a range of country scientists, which aligns with the core values.

Reindert Nijland – European sturgeon, Netherlands

Reindert Nijland and his team have been supported in the sequencing and assembly of the European sturgeon’s (Acipenser sturio, 1.6 Gb) genome. Their reference quality genome assembly is being used as a foundation for the development of an eDNA based, real-time monitoring method, using the portable MinION device, to track the reintroduction of the European sturgeon in the rivers and estuaries of the Netherlands, where their habitat has been under threat. Reindert's team also showed the potential for tracking in a controlled environment by detecting the organism in an aquarium, using eDNA without amplification, demonstrating the utility of a draft reference genome in conservation efforts.

Clive Brown, CTO, Oxford Nanopore Technologies, commented:

“We are excited that the genomes of 50 critically endangered species have been sequenced so far through the project and made available for anyone, anywhere to access. This is a huge step toward improving conservation efforts globally, and we’re just getting started. was designed with the belief that accessible, portable sequencing is key to supporting endangered species by allowing researchers to generate high quality data, rapidly and at source. We’re proud to support the expansion of this critical effort, and we appeal to anyone in the field working to support a particular endangered species to get in touch - we want to work with you.”

Nanopore sequencing for conservation

Oxford Nanopore’s technology enables reference-quality assembly of large, complex genomes which is essential for the delivery of the programme. Nanopore sequencing can process any length of DNA/RNA fragment, however longer nanopore reads can span SVs and repetitive sequences, enabling unprecedented resolution of the genomic diversity and genomic health of critically endangered populations. Oxford Nanopore technology can also provide accessible/portable, real-time analyses and is now being widely used to support conservation efforts through a variety of actions, such as non-invasive monitoring of eDNA, field deployable pathogen surveillance and support for successful breeding programs.

For more information on please visit the website and the database can be found here (please note the 50th genome will be available soon).