We are pleased to announce the mini-symposium “Genomics of Biodiversity” which will take place on the afternoon of Thursday, July 10th, during JOBIM 2025 in Bordeaux.
The advent of large-scale sequencing initiatives, such as those coordinated by the Earth BioGenome Project (EBP), is transforming the field of comparative genomics. With thousands of high-quality reference genomes now being generated across entire taxonomic groups and geographic regions, the discipline stands at a pivotal inflection point. Major challenges include integrating this unprecedented volume of data, managing its inherent complexity, and leveraging its vast taxonomic breadth to deepen our understanding of genome evolution and biodiversity.
Several pioneering projects exemplify these efforts. The Vertebrate Genome Project (VGP) is nearing completion of its first phase, delivering one genome per vertebrate order, totalling almost 600 high-quality assemblies. The Darwin Tree of Life (DToL), which aims to sequence all eukaryotic species in the British Isles and Ireland, has produced almost 2,000 genome assemblies. The European Reference Genome Atlas (ERGA) brings together a diverse European research community to sequence continental Europe’s biodiversity.
In France, the ATLASea program is building capacity to sequence 4,500 marine species over the next seven years, with its first genomes already published. To address the scientific and technical challenges posed by these transformative initiatives, the BYTE-Sea project within ATLASea proposes a mini-symposium on biodiversity genomics, with a specific focus on eukaryotic comparative genomics.
The mini-symposium will explore:
- Bioinformatics developments needed to scale up methods to analyse thousands of genomes simultaneously.
- Applications that embrace the complexity of multi-genome datasets to uncover novel insights into genome evolution, organisation, and function.
The mini-symposium will feature four presentations, each lasting 30 minutes, followed by 10 to 15 minutes of discussion. The event will conclude with a roundtable session aimed at identifying key challenges and potential solutions in biodiversity genomics.
The organising committee comprises:
- Erwan Corre (BYTE-Sea Coordinator)
- Alexandra Louis (BYTE-Sea Comparative Genomics)
- Hugues Roest Crollius (ATLASea Director)
The invited speakers comprise an outstanding group of early- to mid-career scientists, recognized internationally for their contributions to biodiversity genomics:
Josefin Stiller, University of Copenhagen
Whole-genome perspectives on evolutionary history and biodiversity patterns
Large-scale genome sequencing across hundreds of species is transforming our understanding of how biodiversity originates and persists. Genomes preserve the signatures of evolutionary processes and comparative analysis allows us to uncover patterns of diversification, adaptation, and phylogenetic history. Here, I will highlight insights gained from two genome sequencing efforts. The Bird 10,000 Genome (B10K) project aims to sequence genomes for every living bird species and I will present on the contributions to resolving deep phylogenetic relationships of birds and in understanding the drivers of genomic change across lineages. I will also explore how my lab is using genomes for over 250 species of syngnathiform fishes (seahorses and their relatives) to identify the factors shaping diversification in marine systems. Together, these examples illustrate how biodiversity genomics can reveal both the broad evolutionary patterns and the genomic mechanisms that shape the diversity of life.
Matthieu Muffato, Wellcome Sanger Institute
Infrastructure for assembling and analysing thousands of genome assemblies
The Tree of Life department of the Wellcome Sanger Institute built a powerful “Genome Engine” that has generated about 3,000 reference eukaryote genomes so far. Our standard recipe uses PacBio Hii and Hi-C sequencing and the assembly tools recommended by the Earth Biogenome Project; all our genomes undergo extensive manual curation before being submitted to the public archives. I will give an overview of the systems we use to track and monitor the progress of a species, with a focus on the informatics pipelines and their orchestration. In particular, we also manage and run a suite of standard analysis pipelines, dubbed the Genome AfterParty, that takes public genome assemblies and produces analysis tracks and reports such as sequence composition or variant calls. Our aim is to extend the paradigm of sequence archives to analyses, in order to save compute and storage and reduce the footprint of biodiversity genomics.
Yannis Nevers, University of Strasbourg
Challenge and promises of biodiversity comparative genomics
Sequencing initiatives are producing an increasing number of genomes across the diversity of eukaryotes. Comparative genomics methods provide a way to characterize these genomes and gain insight about their functional elements, either by transfer or through the studies of evolutionary patterns. However, many of the existing methods for comparative genomics have been designed for a time where relatively few genomes were available and do not scale well with the current amount of data. In this talk, I will present my work in software development for large-scale comparative genomics and show examples of ways to address these challenges. First, I will discuss how to improve scalability in the content of orthology inference software. Second, I will highlight the importance of considering data quality with the OMArk software. Finally, I will exemplify the type of insight broad-scale comparative genomics analyses can yield.
Elise Parey, University College London
The brittle star genome reveals ancient gene expression programmes activated during arm regeneration
The ability to regenerate body parts is widespread across the animal kingdom. However, genomic resources for highly regenerating species still remain limited, hindering our ability to decipher the genetic bases of regeneration. To address this gap, we sequenced the genome of the brittle star Amphiura filiformis, a species with outstanding regeneration abilities: it can fully regenerate its arms, which include nerves, muscles, and endoskeleton, in just a few weeks. We profiled gene expression during brittle star arm regeneration and identified sequential waves of gene activation governing wound healing, cell proliferation, and differentiation. Through comparisons with two other species capable of appendage regeneration (the axolotl and a crustacean), we uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our study showcases how diversifying genomics models of regeneration is critical to detecting long-range conservation of gene expression programmes.