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Capture and Conserve: The Role of Genomic Sequencing in Biodiversity

Trees in a rainforest.
Credit: Patty Jansen, Pixabay

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Our planet is reaching an ecological tipping point. Overall global biodiversity intactness has fallen to 75%, a level markedly under the agreed safe limit of 90% for warding off an “ecological recession”. Preserving biodiversity is critical in tackling many of the major global issues of today and the future. This includes minimizing the risk of food shortages for a growing global population; losses in biodiversity lead to significant environmental disruption, resulting in lower agricultural yields and reduced food security.

 

Innovations in biodiversity genomics have the potential to help scientists address threats to biodiversity and to track and conserve genetic variation. Highly accurate long-read genetic sequencing gives researchers a molecular-level insight into organisms to assess their health and population dynamics. This allows researchers to make DNA-driven decisions and to take early and targeted action, so strategies such as breeding programs and reforesting initiatives are successful. Below, we explore some of the ways genomics can deepen our understanding of the biosphere, and examples of how biodiversity genomics contributes to conservation.


Capture and catalog

 

The first stage in biodiversity research is capturing and cataloging species to expand our knowledge of ecosystems, how they operate and where dependencies are. Building reference genomes is critical to this work. The best method of creating quality reference genomes is highly accurate multiomic sequencing (i.e., including genome, proteome, transcriptome and epigenome data). The read length of sequences is also key, especially in species with complex genomes. For example, the desert locust (Schistocerca gregaria) has a genome nearly three times the length of the human genome – that’s almost nine billion base pairs. In the past, reference genomes have been developed by piecing together several short reads, a process likely to result in errors where there is such complexity. End-to-end multiomic long-read sequencing eliminates the risk of such errors.


A recent and promising advancement in the capturing and cataloging of species is the compilation of pangenomes (the entire set of genes within a species) from reference-quality genomes. Pangenomes help to uncover the genotypic wealth hidden within populations or species and can capture underlying variation that may be otherwise hidden, providing a molecular-level view to inform conservation action plans.


Identify mechanisms for adaptation

 

Once reference genomes are created, scientists can answer crucial questions about how species are evolving, including which genes are the most likely to lead to physical changes, and which genetic variations are most dominant. For example, scientists involved in the Darwin Tree of Life project – which aims to sequence the genomes of 70,000 species of eukaryotic organisms in Britain and Ireland – note that genomics will help us find the answer to important biological questions. These include why the badger is more susceptible to tuberculosis, or why hedgehogs have developed reproductive issues in recent years. Such insights can be used to design better breeding programmes by choosing plants and animals with more favorable adaptations – such as being resistant to disease or having higher yield.


Population management

 

Analyzing genetic variation over time can give an early indicator of when a species might go into decline in a certain location. Populations with high genetic diversity are more likely to survive new environmental pressures – which is increasingly important as the world’s climate continues to change and population increases. In contrast, species with low genetic diversity are less likely to adapt and might not survive. Therefore, it is crucial to monitor the dynamic between the number of individuals in a population and how much variation exists, to give researchers the opportunity to intervene with a view to preventing extinctions.


Targeted, successful species intervention and restoration projects

 

Biodiversity genomics is a growing field, with initiatives such as the Darwin Tree of Life, the African BioGenome Project, the European Reference Genome Atlas and the newly launched Biodiversity Genomics Europe Project, demonstrating the importance of international, collaborative and cross-sector partnerships. Restoration projects aim to restore or improve specific parts of an ecosystem, such as recovering a native species population, or increasing pollination. These projects have notoriously had elusive success, but the molecular-level data on adaptations and variation provided by genomics projects has the power to transform outcomes and design more successful conservation programs. 


For instance, a 2021 study published in Cell Genomics discussed the outcome from whole-genome sequencing of the critically endangered kakapo in New Zealand. Researchers were able to generate a high-quality reference genome as well as sequencing 49 kakapo genomes from smaller and large populations, in an effort to understand the extent of population size on deleterious mutations. The findings provided insights into kakapo breeding and recovery and aided the design of conservation strategies.


Realizing the promise of genomics

 

A collapsing ecosystem affects all species within it – including humans. Despite advances, we still have a long way to go in biodiversity research; fewer than 1% of the 13,505 species currently listed as threatened have a published genome. Uncatalogued species could hold huge opportunities for areas such as medicines. According to Reuters, more than two-thirds of all medicines with cancer-fighting properties come from rainforest plants, a region that still remains largely unexplored when it comes to genomics. To realize the promise of genomics in biodiversity research, there must be a greater uptake of complete and accurate sequencing projects, so researchers can get the full picture of genetic variation in nature.


About the author: 

Neil Ward is the Vice President and General Manager for the PacBio’s Europe, Middle East, and Africa (EMEA) region.


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