Biology subjects

Duchene, C.

Publications and source records attributed to Duchene, C..

6 recordsLinked to original sources

bioRxiv2026

Cell position is more important than cell shape or age for the acquisition of cell identity in the brown alga Ectocarpus.

The brown alga Ectocarpus is a morphologically simple organism, with cells in the growing filament changing shape and position over time. In this study, we investigated the roles of cell shape, position, and age in establishing cell identity in Ectocarpus. Using laser capture microdissection, we isolated cells with different relative ages, shapes and positions from young sporophytes, and analysed their transcriptomes using differential RNA-seq to attribute a molecular signature to each cell. Five distinct cell transcriptomic signatures were found along the filament of WT Ectocarpus; the apical cell signature differed most from the others. To dissociate cell shape, age, and position, we analysed the transcriptomes of two mutants in which the relationships between these three parameters were disrupted. We found that the transcriptomic profile observed in the WT was significantly altered in these mutants. Overall, our data revealed that molecular cell signatures depend primarily on cell position along the filament and secondarily on cell shape.

developmental biology↗

bioRxiv2025

Latent endogenous viral elements drive active infection and inheritance in a multicellular host

Endogenous viral elements (EVEs) inserted in host genomes are often regarded as inert relics of past infections. Whether they can retain infective potential and contribute to active viral cycles has remained unresolved. Here, we demonstrate that EVEs in the brown alga Ectocarpus can reactivate and drive productive viral infections. Using long-read sequencing and transcriptomics, we identify full-length, transcriptionally active giant viruses integrated within the host genome. Reactivation of these elements is specific to reproductive cells, transforming gametangia into virus-producing structures, and viral symptoms strictly correlate to the presence of active EVEs. Genetic analyses show that these elements are stably inherited, while their activation is precisely regulated by developmental and environmental cues. By resolving the genomic integration sites, we propose a mechanism for Phaeovirus integration and replication. This work provides the first direct evidence that giant EVEs can reactivate, replicate, and transmit both horizontally and vertically in a multicellular eukaryote, establishing a new model to explore latency, inheritance and the evolutionary impact of large dsDNA viruses.

genetics↗

bioRxiv2024

Phytochromes Enable Social Behavior in Marine Diatoms

The phytochrome superfamily, a group of proteins that enable some organisms to detect changes in light intensity and quality, is widespread in terrestrial and marine microbes, fungi, algae, and plants. In terrestrial plants, these photosensory receptors monitor variations in the light environment by sensing red (R) and far-red (FR) regions of the spectrum and trigger important developmental, metabolic, and physiological responses. However, the role of these photosensors in marine microbes, living in environments where, due to absorption of water molecules R and FR radiation does not penetrate beyond the upper few meters, remains controversial. Here, we investigate the role of phytochromes in light perception of the marine diatom Phaeodactylum tricornutum and their involvement in light-driven collective behavior. We perform experiments comparing the social conduct of wild-type and phytochrome knock-out strains to different light wavelengths. Our results show that cell movements become synchronized in a coordinated wobbling dance upon activation of their phytochromes by blue or far-red light, therefore, demonstrating the key role of phytochrome in light-mediated diatom collective behaviour. Furthermore, our experiments suggest that the observed phytochrome-mediated concerted dance implies a form of intercell communication, proposedly mediated by variable R/FR autofluorescence emission in the frequency range of diatom wobbling movements. Our findings provide new insights into communication pathways in aquatic microorganisms and emphasize the importance of social conduct in the sea at all ecological levels.

ecology↗

bioRxiv2024

DiatOmicBase, a gene-centered platform to mine functional omics data across diatom genomes

Diatoms are prominent microalgae found in all aquatic environments. Over the last 20 years, thanks to the availability of genomic and genetic resources, diatom species such as Phaeodactylum tricornutum have emerged as valuable experimental model systems for exploring topics ranging from evolution to cell biology, (eco)physiology and biotechnology. Since the first genome sequencing in 2008, numerous genome-enabled datasets have been generated, based on RNA-Seq and proteomics, epigenomes, and ecotype variant analysis. Unfortunately, these resources, generated by various laboratories, are often in disparate formats and challenging to access and analyze. Here we present DiatOmicBase, a genome portal gathering comprehensive omics resources from P. tricornutum and two other diatoms to facilitate the exploration of dispersed public datasets and the design of new experiments based on the prior-art. DiatOmicBase provides gene annotations, transcriptomic profiles and a genome browser with ecotype variants, histone and methylation marks, transposable elements, non-coding RNAs, and read densities from RNA-Seq experiments. We developed a semi-automatically updated transcriptomic module to explore both publicly available RNA-Seq experiments and users private datasets. Using gene-level expression data, users can perform exploratory data analysis, differential expression, pathway analysis, biclustering, and co-expression network analysis. Users can create heatmaps to visualize precomputed comparisons for selected gene subsets. Automatic access to other bioinformatic resources and tools for diatom comparative and functional genomics is also provided. Focusing on the resources currently centralized for P. tricornutum, we showcase several examples of how DiatOmicBase strengthens molecular research on diatoms, making these organisms accessible to a broad research community. Significance statementIn recent years, diatoms have become the subject of increasing interest because of their ecological importance and their biotechnological potential for natural products such as pigments and polyunsaturated fatty acids. Here, we present an interactive web-based server that integrates public diatom omics data (genomics, transcriptomics, epigenomics, proteomics, sequence variants) to connect individual diatom genes to broader-scale functional processes.

genomics↗

bioRxiv2023

Diatom phytochromes integrate the entire visible light spectra for photosensing in marine environments

Aquatic life is strongly structured by light gradients, with gradual decrease in light intensity and differential attenuation of sunlight wavelengths with depth. How phytoplankton perceive these variations is unknown. By providing the first in vivo quantitative assessment of the action of marine diatom phytochrome photoreceptors (DPH), we show that they efficiently trigger photoreversible responses across the entire light spectrum, unlike current models of phytochrome photosensing. The distribution and activity of DPHs in the environment indicate that they are extremely sensitive detectors of spectral light variations related to depth and optical properties of the water column in temperate and polar oceans, revealing a completely novel view of how light is perceived in the marine environment.

plant biology↗

bioRxiv2021

Acquisition of cell identity in the brown alga Ectocarpus: which of time, cell shape or position matters most?

During development, cells undergo simultaneous changes of different types that together depict cell "identity". In the multicellular brown alga Ectocarpus sp., while ageing, cells change shape and relative position within the filament. Understanding how these factors act and interact to specify cell identity requires markers of cell identity and the ability to genetically separate age, shape and position. Here we used laser capture microdissection (LCM) to isolate specific cell types from young sporophytes of Ectocarpus, and performed differential RNA-seq analysis. Transcriptome profiles of cell types in the wild-type strain provided signatures of the five cell types that can be identified by shape and position. In two mutants, where the relationship between cell shape, position and age are altered, transcriptome signatures revealed that little differential expression could be identified when only shape was perturbed. More generally, although the two mutants are characterised by opposite morphological phenotypes, their transcriptomes were remarkably similar. We concluded that despite the robustness of cell differentiation during WT development, neither the shape nor the position of the cell could serve as a faithful gauge for tracking differentiation.

developmental biology↗