Accessible sequencing for transforming conservation genomics

Conservation genomics to better understand biodiversity

Since the term ‘biodiversity’ was first coined in 1985 by Walter G. Rosen, public awareness has greatly increased, yet biodiversity is still in decline.

As Mrinalini Watsa highlighted in her talk at London Calling, we are losing species at a rate higher than we can record data for. Conservation genomics is a crucial tool for identifying at-risk populations, however, scientists globally are facing challenges, stemming from the high complexity of ecosystems, cost and resource limitations, ethical and legal issues, and inadequate reference databases. Read on to find out how the Nanopore Community are tackling these challenges.

Recognising data sovereignty whilst sequencing a complete dolphin genome

In July of this year, Nick McGrath and team generated one of the most complete and accurate marine mammal genomes of an hourglass dolphin, an understudied species due to the challenges of surveying Antarctic waters. This research could help clarify the dolphin’s evolutionary history and population changes, potentially aiding in conserving this species.

Local Māori tribes consider the species to be taonga (treasured). Because of this, the team prioritised Indigenous data sovereignty, completing the sequencing and genome assembly in New Zealand with just a single PromethION Flow Cell, a high-end gaming laptop and a low-resource genome assembler called Raven.

As they utilised only Oxford Nanopore Technology sequencing, this approach significantly reduced costs to less than a tenth of current estimated mammalian genome sequencing costs. New affordable technologies such as the PromethION 2 are enabling research outside resource-rich laboratories to support Indigenous data sovereignty, and can help ensure genomic research is more accessible to anyone, anywhere.

Portable sequencing, reducing research inequality to tackle lemur extinction

In Madagascar, lemurs face some of the highest risks of extinction, largely driven by human activities.

In other areas of the world, reference genomes have been used to improve conservation efforts by tracking genetic changes and adaptive traits in populations. However, because most sequencing facilities are concentrated in the Northern Hemisphere, this has left the biodiverse Southern Hemisphere underrepresented or having to outsource genome assembly at additional cost.

To address this, researchers from Rutgers University used the portable MinION device to generate the first reference genome for the endangered red-fronted brown lemur entirely within Madagascar. The team confirmed the presence of the vulnerable Danfoss’ mouse lemur and provided a public resource to aid in conservation efforts without the need to outsource this research.

In addition, the team used their mobile laboratory to conduct workshops for Malagasy students, providing access to sequencing equipment and hands-on learning that would otherwise be unavailable. The result... a valuable reference genome for conservation efforts and a new model to reduce research inequalities and expand global access to sequencing.

A cutting-edge method, resolving cost constraints to monitor a declining population

Malaysia’s freshwater fish populations have decreased by 83% since 1970. Labour-intensive monitoring methods like netting and electrofishing are slow, and when coupled with funding constraints, tackling this biodiversity crisis is a serious challenge.

Researchers have found that environmental DNA (eDNA) may help to streamline their conservation efforts. Munian and team demonstrated that the MinION device could be used to analyse eDNA from freshwater samples. The results showed they identified 13% more fish species than with conventional methods, including several rare and endangered species. This method could also reduce costs by 33.4%.

This study provides a cutting-edge method to enhance holistic diversity documentation for targeted habitats, and can facilitate effective conservation planning for not only Malaysia’s fish population, but also in resource limited settings.

Looking toward the future

Accessible technology is empowering scientists to complete research on their own terms, opening doors to new discoveries and methods to tackle global challenges. The data generated from these studies is a catalyst to improve conservation efforts as well as provide novel data to better understand population dynamics and potentially identify unknown species.

With lower costs and accessible devices, nanopore technology is enabling researchers to utilise genomic data in regions where this was not previously available, and these studies provide real-life examples of our mission to enable the analysis of anything by anyone, anywhere.