Researchers at the Doñana Biological Station – CSIC participate in the European Reference Genome Atlas (ERGA), an initiative to generate reference-quality genomes for all European Biodiversity, which includes at least 200,000 species. This effort should range from species that are threatened, endemic and keystone to species of importance for agriculture, fisheries, pests, ecosystem function, and stability. Yet, reference-quality genomes are available for only a small fraction of European species.
"To save, restore, and respect biodiversity we need to understand it, the European Reference Genome Atlas will establish key data to advance this much-needed knowledge", explains Robert Waterhouse, ERGA Vice-chair and researcher at the University of Lausanne. While the project is certainly ambitious, today's technological advances make it fundable, and a coordinated effort of pan-European and international research groups makes it feasible.
In a perspective paper, recently published in the journal Trends in Ecology and Evolution, the ERGA consortium highlights the need and importance of reference genomes in the context of conservation biology. "Reference genome is essentially a genome that is almost complete, with few unsequenced regions, few errors, and a high percentage of sequences assigned to chromosomes", explains María José Ruiz, a researcher at the Doñana Biological Station – CSIC, and an ERGA member. Genomes used to be obtained in many fragments, sometimes of relatively small sizes. This initiative aims to have as many contiguous sequences as chromosomes and to clearly define the different functional or structural regions.
Genomic, essential to conservation research
Genomic research – that uses genetic material to study individual organisms, populations and ecosystems- greatly benefits from reference-quality genomes by generating insight into the evolutionary make-up and adaptive potential of a species. The accuracy of these genomic resources significantly advances all fields of biological research and innovation. Especially for biodiversity conservation, the availability of high-quality reference genomes for a representative fraction of species will be fundamental. Analyzing a species' genomic diversity can serve as an early warning system to estimate resilience, predict declines and finally aid the strategic planning of conservation measures.
"We find an important example of the utility of these reference genomes in the Iberian lynx", says José A. Godoy, a researcher at the Doñana Biological Station – CSIC and also a member of ERGA. The genome of the Iberian lynx was one of the first ones to be obtained from an endangered species. Godoy's team published it in 2016 and, although it has not as good quality as the ones that can be done today, it has provided interesting information about this species' origin, its relationship with other lynxes, and its demographic history. "Having a reference genome has allowed us to verify that the Iberian lynx is one of the species with the least genetic diversity", explains the researcher. "Furthermore, thanks to having variation data available at the complete genome level, we have been able to generate very efficient tools that are now being used to monitor the species and to apply management that minimizes genetic problems". The team is currently generating an improved version that is close to the new standards for reference genomes.
European initiative coordinated with other similar ones at a global level
Biodiversity is under threat worldwide. According to the IUCN, in Europe this threat affects mammals (15%), reptiles (20%), amphibians (25%), freshwater fishes (37%) and marine (7.5%) fishes, birds (13%), bees (9%), butterflies (9%), grasshoppers (29%), beetles (18%), non-marine molluscs (22%), shrubs (48%), ferns (20%), and trees (42%). "This initiative allows us to connect with other institutions and infrastructures, making genomic tools available to sequence and analyze genomes that some groups and institutions could not afford otherwise", says the researcher María José Ruiz. "In addition, it allows the consolidation of an interdisciplinary and collaborative network between researchers from different areas throughout the whole continent".
ERGA consortium argues that specific measures for preserving species and ecosystems should consider a comprehensive description of genomes of European species. Reference genomes availability will provide a solid base to carry out biodiversity assessments, conservation management, and restoration measures. This initiative is coordinated with others at a global level, such as the Earth BioGenome Project, to obtain the reference genomes of the whole biosphere, a project that seems feasible in the medium-long term.
Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, laudio Ciofi, Angelica Crottini, José A. Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah A.Oomen , Sadye Paez, Per J. Palsbøll, Christophe Pampoulie, María J. Ruiz-López, Hannes Svardal, GabrielleZammit. The era of reference genomes in conservation genomics. Trends in Ecology and Evolution. https://doi.org/10.1016/j.tree.2021.11.008