Sequencing Life To Conserve Biodiversity

Biodiversity is crucial for the health of Earth and all the life that depends on it. Sadly, current rates of biodiversity loss are greater than ever before, with estimates suggesting around 1 million species are facing extinction. The Kunming-Montreal Global Biodiversity Framework, adopted in December 2022, is working to reverse these trends, with goals such as “by 2050, the extinction rate and risk of all species are reduced tenfold and the abundance of native wild species is increased to healthy and resilient levels.”

Several genomics-based projects are underpinning global efforts to improve our understanding of biodiversity and direct conservation efforts. Advances in technologies such as sequencing are giving researchers access to more and better data, helping to unravel the intricacies of biodiversity and how we can support it.

Technology Networks recently spoke to Neil Ward, vice president and general manager for Europe, Middle East and Africa at PacBio, to learn more about the role that genomics can play in conserving biodiversity and how innovative technologies such as HiFi sequencing are helping biodiversity projects.

Anna MacDonald (AM): What role can genomics play in conserving biodiversity?

Neil Ward (NW): Genomic sequencing arms researchers with molecular-level insights into organisms so they can understand genetic diversity, population dynamics and the evolutionary processes of species. By identifying how genetic variations underpin adaptive traits, genomics enables researchers to predict how species might respond to environmental changes and threats. Such granular data can be used to power early and targeted action for species at risk of decline before they reach endangered status, for example through breeding programs or reforesting initiatives.

AM: Why is it important to build reference genomes?

NW: Reference genomes are the starting point for genomics-based biodiversity research. They act as a standard template for the DNA of a particular species – like a blueprint. Scientists analyze these reference genomes to answer crucial questions about how species are evolving. This includes unfavorable traits species might have, such as exploring why the badger is more vulnerable to tuberculosis, or why red squirrels are susceptible to leprosy. These insights help inform breeding programs by pinpointing plants and animals with more favorable adaptations.

Reference genomes also give researchers an understanding of variation in local populations. This is important because populations with high genetic diversity are more likely to survive new environmental conditions, whereas species with low genetic diversity are less likely to adapt, increasing the risk of extinction. If genetic variation suddenly declines in a local population, scientists know to prioritize intervention in that area.

AM: Can you give us an overview of the Darwin Tree of Life project and the role PacBio is playing in it?

NW: The Darwin Tree of Life is a DNA-driven conservation project that aims to tackle the UK’s declining biodiversity. In the UK, the abundance of priority species has declined by 60% since 1970, making it the worst of the G7 countries. The project is in the process of sequencing all 70,000 species on the British Isles, to build detailed reference genomes that will be used to monitor the evolution of the UK’s ecosystems and aid conservation efforts.

The project, run out of the Wellcome Sanger Institute, chose to use PacBio’s HiFi sequencing to power much of this work. PacBio’s long-read systems afford the Darwin project’s researchers the deepest and most accurate insights into the UK’s wildlife, particularly into species with complex biology. Participating in such projects supports PacBio’s mission of accelerating scientific discoveries that better species’ health and the health of our planet.

The Darwin project has already sequenced many species to power new discoveries. The orca has been revealed to have a genome around 96% the size of the human genome, with British populations that can be small and highly inbred, making them prone to ill health. By understanding the orca genome, researchers can identify health problems earlier and help local populations to thrive. On the plant side, freshwater algae produce around one-third of all oxygen in the atmosphere, while simultaneously locking away enormous amounts of carbon dioxide. With a deeper understanding of the freshwater alga genome, researchers can harness its ability to confine carbon dioxide and produce more efficient biofuels.

AM: What advantages does HiFi sequencing bring to biodiversity projects such as this?

NW: PacBio’s long-read HiFi sequencing enables scientists to build higher quality, more accurate reference genomes. Traditional approaches to sequencing DNA – called short-reads – rely on breaking genomes down into small fragments and then piecing them back together to build a reference. However, this process is complex and can often lead to errors or an incomplete picture of an organism, especially for species with complex genomes. For example, the desert locust (Schistocerca gregaria) has a genome nearly three times the length of the human genome – which is a lot of genomic code to piece back together!

PacBio HiFi technology sequences DNA in much larger segments, which improves accuracy and completeness. A jigsaw with a few large pieces is much easier to assemble than one with many small pieces that all look similar. HiFi also gives researchers a multiomic view that enables them to go beyond the information encoded in DNA, which often doesn’t tell the whole biological story. Many changes linked to traits and disease appear in other parts of an organism’s biology, like the proteome, transcriptome and epigenome. HiFi offers access to these other “omes” to add another dimension of insight into species’ underlying biology.

AM: What factors are currently limiting the greater implementation of genomic techniques in conservation and biodiversity studies?

NW: Until recently, challenges included the cost of deploying long-read sequencing at scale, and the time and resources it required. The good news is that advances in sequencing technology have made long-read increasingly accessible and affordable. Our Revio machine, for instance, is capable of delivering 1,300 human whole genomes per year using far fewer consumables – this could potentially be even more for plants and animals with simpler genomes.

While projects like the Darwin Tree of Life are paving the way, an estimated 80% of the world’s species still await scientific discovery and description. Even for described species, many still lack the detailed reference genomes required to inform conservation initiatives. To further advance the field, greater investment in the latest sequencing technology is required to unlock the promise of genomics and conserve species before they are lost.

Neil Ward was speaking to Anna MacDonald, Senior Science Editor for Technology Networks.

About the interviewee:

Neil Ward is vice president and general manager for Europe, Middle East and Africa, PacBio. Neil is a genomics industry veteran with more than two decades of global experience. Neil has a passion for the role genomics can play in bettering human health, and he believes that this can be achieved by accelerating the utility of in-depth, highly accurate genomic applications. In his various commercial roles, Neil has served as a key contributor to many of the world’s largest genomics projects including Genomics England’s 100,000 Genome Project, the Estonian Genome Project and the whole-genome sequencing of the 500,000 UK Biobank samples.