Objective:
In this research theme, we conduct genome-enabled investigations to address fundamental questions concerning the evolution and functional diversification of phototrophic organisms. Specifically, we focus on the evolution of protein import machinery in endosymbiotic organelles, as well as the regulation of nuclear and chloroplast gene expression in photosynthetic eukaryotes (see also theme 1). To this end, we integrate evolutionary and functional genomics in a physiological perspective by laveraging the power of transcriptomics and proteomics data. In addition to exploiting large-scale omics data, we also generate new genomic and transcriptomic data from various diatom species and new metagenomic data to address specific questions related to the evolution and regulation of diatom plastids, photosensing, and circadian regulation. These datasets are integrated with ecophysiological data to shed light on the strategies that enable microalgae to play a fundamental role in the functioning of global ecosystems (in theme 3).
Key Research Areas:
1. Evolution of protein import into organelles
2. Genome structure, dynamics and function
3. Evolution of the regulation of gene expression
Recent Publications:
Villar E, Zweig N, Vincens P, Cruz de Carvalho H, Duchene C, Liu S, Monteil R, Dorrell RG, Fabris M, Vandepoele K, et al. 2025. DiatOmicBase: a versatile gene-centered platform for mining functional omics data in diatom research. The Plant Journal 121: e70061.
Cattelin C, Goulancourt R, Chatellet E, Astatourian A, Robert C, Wollman F-A, Lafontaine I. 2025. Searching α−solenoid proteins involved in organellar gene expression. Biorxiv 2025.09.09.674916.
Chaux F, Agier N, Eberhard S, Xu Z. 2024. Extraction and selection of high-molecular-weight DNA for long-read sequencing from Chlamydomonas reinhardtii. PLOS ONE 19: e0297014. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297014
Chaux F, Agier N, Garrido C, Fischer G, Eberhard S, Xu Z. 2023. Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii. Genome Res 33: 1582–1598.
Caspari OD, Garrido C, Law CO, Choquet Y, Wollman F-A, Lafontaine I. 2023. Converting antimicrobial into targeting peptides reveals key features governing protein import into mitochondria and chloroplasts. Plant Communications 100555.
Caspari OD. 2022. Transit Peptides Often Require Downstream Unstructured Sequence for Efficient Chloroplast Import in Chlamydomonas reinhardtii. Front Plant Sci 13: 825797.
Garrido C, Wollman F-A, Lafontaine I. 2022. The Evolutionary History of Peptidases Involved in the Processing of Organelle-Targeting Peptides. Genome Biology and Evolution 14:
Garrido C, Caspari OD, Choquet Y, Wollman F-A, Lafontaine I. 2020. Evidence Supporting an Antimicrobial Origin of Targeting Peptides to Endosymbiotic Organelles. Cells 9: 1795.
Chaux-Jukic F, O’Donnell S, Craig RJ, Eberhard S, Vallon O, Xu Z. 2021. Architecture and evolution of subtelomeres in the unicellular green alga Chlamydomonas reinhardtii. Nucleic Acids Res 49: 7571–7587.
Eberhard S, Valuchova S, Ravat J, Fulneček J, Jolivet P, Bujaldon S, Lemaire SD, Wollman F-A, Teixeira MT, Riha K, et al. 2019. Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants. Life Science Alliance 2.
Jolivet P, Serhal K, Graf M, Eberhard S, Xu Z, Luke B, Teixeira MT. 2019. A subtelomeric region affects telomerase-negative replicative senescence in Saccharomyces cerevisiae. Sci Rep 9: 1845.