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The future of biodiversity conservation: why reference genomes matter

In a new paper recently published in the Journal Trends in Genetics, members of the European Reference Genome Atlas (ERGA) advocate for reference genomes as fundamental resources in biodiversity conservation, showcasing genomics as an emerging powerful tool for species conservation. The review illustrates that reference genomes have the combined power of speeding up genomic analysis and making results more reliable: exactly what is needed in conservation science.


Some of the species presented in the review as case studies that illustrate the power of genomics in conservation. The authors thank Antonio Rivas, Nelson Lauzon, Marco Thines and Sally Leys, for the pictures of the Iberian lynx, the European beech, and the freshwater sponge, respectively.

Genomes for biodiversity conservation - the connection between these might not be evident at first, but genetics provides critical evidence for scientifically informed management decisions. In a paper recently published in the Journal Trends in Genetics, a group of researchers affiliated to the European Reference Genome Atlas reviews the potential of genomic data in safeguarding global biodiversity, emphasising the advantages of reference genomes for increased speed and reliability of results.


Biodiversity is the variety and variability of life on Earth, a prerequisite for ecosystem functioning and health. Human actions have resulted in the ongoing extinction wave which poses a significant threat not only to other living creatures, but to humanity itself. To effectively protect biodiversity, we must first understand it. Scientists have known for a long time that the origin for all the astonishing variation we see in living species - from shape, size, colour, behaviour and many other characteristics - is encoded in their genomes. The genome of an organism is the complete set of its genetic material (usually DNA) stored inside its cells. The genetic material serves as a “blueprint” for the construction and organisation of the organism's body, containing the instructions for it to function and allowing it to pass its characteristics onto the next generations.


In spite of being the basis for all other levels of biodiversity, this underlying genetic diversity has often been neglected in biodiversity assessments and conservation efforts. “Many factors can explain this neglect, including lack of awareness, technical limitations, costs and the complexity of studying genetic diversity”, explains Kathrin Theissinger, Researcher at LOEWE centre for Translational Biodiversity Genomics in Germany and one of the first co-authors of a recently published paper that reviews the application of genomic tools to conservation efforts. “Despite these challenges, the importance of genetic diversity is now widely recognized, and even mentioned as a central goal in the recent COP15 conference. Conservation efforts are increasingly incorporating genetic information into their assessments and planning. Advances in technology and methods for studying genetic diversity have made it easier and more affordable to assess genetic variation, and there is a growing awareness of the importance of maintaining genetic diversity for the long-term survival of biodiversity.” complements Theissinger.


In recent years the accelerated technological advances in the field of genomics have indeed made the goal of obtaining the complete genome of each species on the planet seem more feasible than ever. While it took humanity over ten years and around $300 million dollars to sequence the first human draft genome, a high-quality reference genome of comparable size can now be obtained in a matter of weeks for around 5,000 dollars. Of course, sequencing all life is still a very ambitious goal, and scientists across the world are connecting through the Earth BioGenome Project (EBP) - an extensive multinational network - to tackle this collective challenge. At a regional level, researchers have formed the European Reference Genome Atlas (ERGA), the European node of EBP. “ERGA is a scientific consortium that aims to promote the generation of high-quality reference genomes for European eukaryotic biodiversity while building a distributed genomic structure across Europe and facilitating the exchange of genomics expertise across the whole continent”, says Camila Mazzoni, group leader at the Leibniz Institute for Zoo and Wildlife Research and chair of ERGA.


ERGA has a strong conservation genomics component and was recently funded through a Horizon Europe call on Biodiversity and Ecosystem Services. In the coming years the consortium will be generating hundreds of genomes ranging from endangered species, species of importance for ecosystem function and stability, to key species for agriculture, forestry, and fisheries, but also non-model organisms from underrepresented groups that make up a huge yet overlooked proportion of biodiversity.


Sequencing complete high-quality genomes for multiple individuals is still not feasible for most endangered species, but as highlighted in the review, one or a few excellent quality genomes can take species conservation a long way. This is because a single high-quality reference genome can be used to support and enhance an array of different analyses, based on data that can be obtained at lower cost. “Genomics allows geneticists and managers to arrive at more precise study of parameters which have been in focus for decades such as the genetic consequences of fragmentation on diversity, divergence and inbreeding.” explains Jacob Höglund, Professor of Animal Conservation Biology at the Uppsala University and corresponding author of the paper. “It also opens up for new conceptual advances and new questions concerning the study of these issues. For example the interaction between population size and isolation, genetic load, inbreeding depression, evolvability and extinction.”


Conclusions drawn from analysing a species' genomic diversity can then be applied to the real world in multiple ways. “Genomic data provides a powerful tool for understanding the genetic basis of biodiversity, giving a high-resolution insight into the genetic composition and therefore the adaptive potential of a species, a population or a community, and can be used to inform and guide conservation efforts in the Anthropocene.” says Theissinger. This knowledge can for example help practitioners decide which areas should be prioritised as conservation units or which individuals to include in a breeding program in order to optimise the genetic outcomes for the species.


“Genomic knowledge in threatened species opens up numerous future possibilities for research and application, including the characterization and management of functional variation and genetic load, and the design of improved genetic rescue programs.” says Carlos Fernandes, a wildlife genetics scientist at the University of Lisbon and one of the first co-authors of the paper.


Overall, this review provides a valuable resource for those who wish to obtain a first grasp of the interface between genomics and conservation. As Giulio Formenti, one of the paper’s first authors and a founding member of ERGA, puts it: “This collective work provides an excellent review on how reference genomes and genomics in general can aid conservation efforts. As such, it will constitute an essential resource to train the next generation of conservation genomicists.” Fernandes complements: “We hope that our work can contribute to bridging the gap and increase dialogue and synergies between conservation genomicists and practitioners for the sake of biodiversity conservation."


Publication

Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido R. Gallo, José A. Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich D. Jarvis, Miklós Bálint, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni, Jacob Höglund, How genomics can help biodiversity conservation,

Trends in Genetics, 2023, ISSN 0168-9525, https://doi.org/10.1016/j.tig.2023.01.005.

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