Mots-Clés
familles multigéniques, orthologues, paralogues, amplifications, synténie, tandem repeats, génomique comparative
Description
Développement d’une approche de génomique comparative pour l’étude des expansions de familles de gènes et de l’évolution chromosomique et application aux nudibranches.
Dans la lignée des grands programmes internationaux de séquençage tels que Darwin Tree of Life (dToL), Vertebrate Genomes Project (VGP) et European Reference Genome Atlas (ERGA), le projet ATLASea, PEPR copiloté par le CNRS et le CEA, vise à générer des génomes de référence pour 4 500 espèces marines.
Le laboratoire de Bioinformatique pour la Génomique et la Biodiversité (LBGB) du Genoscope (CEA, Institut François Jacob) est en charge de l’assemblage et de l’annotation de ces génomes, ainsi que d’analyses de génomique comparative.
Dans ce cadre, nous proposons un stage de M2 visant à étudier l’évolution des familles multigéniques chez les mollusques et, plus particulièrement, la relation entre l’expansion de ces familles et leur organisation chromosomique. Le projet cherchera notamment à déterminer si les différents modes d’organisation des copies sont associés à l’ancienneté des expansions ou à l’histoire chromosomique des lignées.
L’objectif sera d’identifier les familles de gènes présentant des expansions à différents nœuds de l’arbre phylogénétique, puis de caractériser l’organisation chromosomique des copies dans les espèces concernées. Une attention particulière sera portée à la conservation ou à la dispersion des familles au cours de l’évolution, en mettant leur localisation en regard des groupes de liaison ancestraux (ancestral linkage groups, ALGs) et des réarrangements chromosomiques.
L’approche sera d’abord appliquée aux nudibranches, un groupe de mollusques encore peu exploré sur le plan génomique, afin de caractériser la diversité des trajectoires d’expansion des familles de gènes dans cette lignée, et pourra ensuite se poursuivre par une thèse.
Profil recherché: Master 2 en génomique/bioinformatique. Connaissance des méthodes d’analyse de génomes et de génomique comparative. Maîtrise des outils bioinformatiques et langages de programmation utilisés dans le domaine de la génomique (Python, R, …). Connaissance du système Unix et de l’utilisation d’infrastructures de calcul. Un goût pour les analyses exploratoires serait un plus.
Lieu du stage : Genoscope, Evry
Encadrante : France Denoeud
contact : stage_lbgb@genoscope.cns.fr
Date de début : A définir (janvier-mars 2027)
Durée : 6 mois
Descriptif détaillé en Anglais:
Developing a comparative genomics approach using chromosome-scale reference genomes to investigate gene family expansions and chromosome evolution: a case study in nudibranchs
Context and background
Gene duplications, whether resulting from whole-genome duplication, segmental duplication, or tandem duplication, are an important driver of evolution and the functional diversification of gene repertoires (Copley, 2020). These events generate new gene copies that may acquire modified or entirely new functions, thereby contributing to the evolutionary plasticity of species. They can lead to the formation of multigene families whose size and composition may vary greatly among lineages. Copies resulting from tandem duplications may remain clustered within the genome (Noel, 2024) or, conversely, become progressively dispersed through chromosomal rearrangements (Denoeud, 2014). The conservation or dispersion of these families may therefore depend both on the history of the duplications and on the lineage-specific dynamics of chromosome evolution.
Recent advances in sequencing and genome assembly technologies have led to a growing number of chromosome-scale reference genomes, including for non-model organisms. The ATLASea project, which aims to generate reference genomes for 4,500 marine species, thus provides an exceptional resource for studying the joint evolution of gene families and genome structure. In particular, ATLASea has generated the largest collection of nudibranch (sea slugs) genomes to date, providing an opportunity to investigate gene family evolution and chromosomal organization across this relatively poorly explored lineage.
Research questions and objectives
This internship will investigate the evolution of multigene families, with a particular focus on the relationship between gene family expansion and chromosomal organization. The central question is how the chromosomal organization of expanded gene families changes over evolutionary time in relation to the age of the expansion and the history of chromosome evolution. The approach will first be applied to nudibranchs to explore the diversity of gene family expansion trajectories within this lineage.
Methodology
Orthogroups will be constructed from a set of reference genomes using OrthoFinder v3 (Emms, 2026). The ability of this approach to incorporate newly annotated genomes into pre-existing orthogroups will be evaluated on a controlled dataset. An annotation quality-control and filtering step will be implemented to limit the impact of fragmented genes, redundant isoforms, and annotation models that could generate spurious gene family expansions. Gene families showing expansions at different nodes of the phylogenetic tree will then be identified from the orthogroups and gene trees.
For selected families, chromosomal locations of gene copies will be examined to distinguish tandemly duplicated copies from copies that have subsequently become dispersed to other loci or chromosomes. These locations will also be compared with ancestral chromosome organization, in particular using ancestral linkage groups (ALGs) (Istace, 2026). The chromosome-scale genomes generated by ATLASea will constitute the main dataset for this analysis, with an initial application to nudibranchs.
Expected results
The internship will provide a validated and reproducible approach for identifying gene family expansions from newly annotated genomes. It will be applied to nudibranchs as a case study, providing an initial characterization of the chromosomal organization of these expanded gene families.
In the longer term, this approach could be extended to other marine lineages to investigate how the history of gene duplications and chromosome evolution influences the conservation, dispersion, and diversification of gene families. It could in particular be used to determine whether certain types of gene families are preferentially amplified in particular lineages or evolutionary contexts, and to explore the potential role of these expansions in the adaptation and diversification of marine organisms.
References
Copley SD. Evolution of new enzymes by gene duplication and divergence. FEBS J. 2020 Apr;287(7):1262-1283. doi: 10.1111/febs.15299.
Denoeud F, Carretero-Paulet L, Dereeper A, et al. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science. 2014 Sep 5;345(6201):1181-4. doi: 10.1126/science.1255274.
Emms DM, Liu Y, Belcher L, Holmes J, Kelly S. OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability. Nat Methods. (2026). doi: 10.1038/s41592-026-03126-6. doi: 10.1038/s41592-026-03238-z.
Istace B, Denoeud F, Téodori E, Chorba N, Aury JM. Hobrac: a reference-guided workflow for genome comparison and synteny visualization. BioRxiv preprint. 2026 https://doi.org/10.64898/2026.07.17.739168
Noel B, Denoeud F, Rouan A, et al. Pervasive tandem duplications and convergent evolution shape coral genomes. Genome Biol. 2023 Jun 1;24(1):123. doi: 10.1186/s13059-023-02960-7.