A global strategy published today aims to greatly accelerate the Earth BioGenome Project (EBP) – an ambitious global effort to better protect biodiversity by assembling ‘reference genomes’ for all known plants, animals, and other eukaryotic species. SIB contributed genomics data expertise to the strategy’s guidance on scaling production from 300 to 3,000 genomes per month. Our scientists also help deliver the project’s goals through coordination of European biodiversity sequencing initiatives, as well as development of resources able to handle the massive amounts of data being produced.
A moonshot project to sequence 1.67 million species
Full genome sequences are currently only available for 6,145, or 0.4%, of the world’s known eukaryotic species. The Earth BioGenome Project aims to generate the remaining 99.6% by 2035. This involves sequencing DNA from collected samples, assembling these sequences into full species ‘reference’ genomes, identifying the location and function of genes within each genome, and making all data and annotations openly available and discoverable. Further analyses of these data will help scientists understand biodiversity and support conservation – plus advance medical, agricultural, and biotech innovations.
SIB is a coordinating partner in the EBP, and helped develop state-of-the-art genome assembly and quality control workflows as part of the project’s set-up phase.
Generating biodiversity genomes at unprecedented scale
Researchers affiliated with the Earth Genome Project have sequenced the full DNA of over 3,000 animals, plants and other eukaryotic species since the project’s launch in 2021 – unlocking powerful insights for environmental protection, from designing breeding programs to understanding how well species may adapt to climate change. Phase II will greatly accelerate this work, targeting 150,000 high-quality genomes within four years. This represents a tenfold increase over the current output rate, from 300 to 3,000 genomes per month.
A moonshot project to sequence 1.67 million species
Full genome sequences are currently only available for 6,145, or 0.4%, of the world’s known eukaryotic species. The Earth BioGenome Project aims to generate the remaining 99.6% by 2035. This involves sequencing DNA from collected samples, assembling these sequences into full species ‘reference’ genomes, identifying the location and function of genes within each genome, and making all data and annotations openly available and discoverable. Further analyses of these data will help scientists understand biodiversity and support conservation – plus advance medical, agricultural, and biotech innovations.
SIB is a coordinating partner in the EBP, and helped develop state-of-the-art genome assembly and quality control workflows as part of the project’s set-up phase.
The EBP phase II strategy published today provides technical and other recommendations for generating and analysing genomes at this unprecedented scale. SIB contributed to guidance on ensuring meaningful insights can be derived from the massive increase in genomics data, through:
- quality standards for reference genome sequencing, processing, and characterization;
- bioinformatics innovations to efficiently and accurately process the data.
The strategy additionally addresses other critical factors for success, such as enhancing global coordination, creating an inclusive, global biodiversity genomics workforce, and developing effective access and benefit-sharing methodologies. It also focuses efforts on priority species, including those important to ecosystem health, food security, pandemic control, conservation, and Indigenous peoples and local communities.
SIB’s contribution to the strategy supports our objective to improve data and bioinformatics resources for environmental protection. Our scientists also contribute to implementing EBP guidelines and delivering the project’s goals in Switzerland and Europe through joint coordination of two biodiversity sequencing initiatives: the European Reference Genome Atlas (ERGA), which is the European EBP regional node, and the Biodiversity Genomics Europe (BGE) Horizon Europe project.
The EBP has already provided new insights into evolution, ecological interactions, and the genetic basis of species traits. Phase II will further transform our biological understanding of all life, with a wealth of applications from environmental protection to drug discovery.
SIB innovations for large-scale, high-quality genomics analyses
The strategy highlights the crucial role of gene annotation in unlocking value from genomes. This process involves identifying genes and their functions by comparing DNA sequences between different species, and adding this information to the full genome sequence.
A new tool developed by a SIB Group this year provides the computational capacity required for EBP phase II. FastOMA can accurately identify genes of common ancestry for thousands of eukaryotic genomes within a day – a task that existing methods cannot accomplish even in months. This marks a major step in scaling the SwissOrthology SIB Resource to the Tree of Life level, to meet the fast-evolving demands of biodiversity and other large genomics initiatives.
Reference(s)
Image credit: S N Pattenden / Unsplash
