Caroline Belser

The Eunicella cavolini reference genome provides an important resource to study the adaptation of this species to different environments and anthropic pressures. This species is impacted by human activities, including climate change, and this reference genome will be useful to study the genomic evolution of this species. The entirety of the genome sequence was assembled into 17 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.49 Gb, composed of 159 contigs and 46 scaffolds, with contig and scaffold N50 values of 7.7 Mb and 51.1 Mb, respectively.

Oceanian citrus species, including wild taxa native to Australia and Papua New Guinea, form a genetically distinct clade within the Citrus L. (1753) genus. These species remain largely underexplored, despite their adaptation to diverse environments and relevance for citrus improvement. To support their use in breeding and evolutionary studies, we generated a high-quality, chromosome-scale genome assembly of an Australian finger lime accession (SRA 1002), a natural interspecific hybrid. The genome was assembled using long-read sequencing, optical mapping, and a high-density genetic map, resulting in nine pseudomolecules covering over 97% of the genome. Using this reference, we analyzed whole-genome resequencing data from 132 accessions representing the diversity of Asian and Oceanian citrus. Variant calling across the dataset produced a high-resolution catalogue of single nucleotide polymorphisms (SNPs) and derived database of SNPs fully discriminant of 20 Citrus species (diagnostic SNPs, DSNPs), enabling detailed exploration of inter- and intraspecific diversity. The data reveal a strong population structure within the group with clear heterozygosity variation between ancestral species and admixed accessions, reflecting their complex evolutionary history and hybridization patterns. This study provides the first integrated genomic framework for Oceanian citrus diversity, offering essential tools for downstream applications in citrus breeding, conservation, and evolutionary genomics. The resources generated lay the groundwork for future association studies and the targeted introgression of beneficial traits into cultivated citrus.

Corals are complex holobionts, encompassing numerous prokaryotes, viruses, and protists. This associated microbial community strongly influences coral health and its resilience to global ocean warming. Corallicolid apicomplexans are widespread coral–infecting parasites, yet their impact on the coral host remains poorly understood. This knowledge gap largely stems from the low abundance of these parasites in coral tissues, which makes them difficult to isolate and access to their genetic material. Here we analyzed nearly 1,000 Pocillopora coral colonies collected from 32 islands during the Tara Pacific expedition to identify the drivers of corallicolid prevalence and abundance. Corallicolids were detected in almost all Pocillopora colonies with variable relative abundances between islands. The high abundance of specific corallicolid populations correlates with seawater temperature and levels of host protein carbonylation. We used a large collection of 297 metatranscriptomes to assemble a corallicolid transcriptome and we identified apicomplexan parasite signature genes, including the GRA9 and PV2 confirming the close phylogenetic relationship with the family of Eimeriidae. Gene expression patterns indicate that the high abundance of corallicolids correlates with a high transcription of genes encoding apical complex proteins and genes involved in the control of host immune defenses. Overall, this study provides new insights into corallicolid biology and its interaction with the coral host by combining a newly generated transcriptome with a large-scale sampling of Pocillopora corals across the Pacific Ocean.

Hanak’s bat ( Pipistrellus hanaki Hulva and Benda 2004) is one of the most range restricted mammals in Europe, since it occurs only in Cyrenaica, Libya, and Crete (Greece). It is currently classified as ‘Vulnerable’ on the IUCN Red List, with its foraging habitat threatened by a number of human activities. The reference genome of the Cretan subspecies ( Pipistrellus hanaki creticus) will provide a crucial resource for uncovering the species phylogenetic history and will help assess the degree of genetic isolation among the species populations. A total of 23 contiguous chromosomal pseudomolecules (sex chromosomes included) were assembled from the genome sequence. This chromosome-level assembly encompasses 1.9 Gb, composed of 447 contigs and 141 scaffolds, with contig and scaffold N50 values of 48.7 Mb and 89.1 Mb, respectively.

L'avènement des nouvelles technologies de séquençage puis du séquençage longues lectures a ouvert la voie vers la production de génomes de référence à un coût abordable. Les outils bioinformatiques, tout comme les techniques de laboratoire, ne cessent d'évoluer et il est important de tester et mettre en place toutes ces technologies de pointe.Ce mémoire de thèse présente, au travers de différentes publications, les développements méthodologiques mis en place dans le cadre d'assemblages de génomes de référence. Les longues lectures obtenues grâce au séquençage avec la technologie Oxford Nanopore nous ont permis d'améliorer la continuité de nos assemblages et de reconstituer plus fidèlement des régions souvent invisibles avec des méthodes traditionnelles, notamment les régions contenant des séquences répétées ou des clusters de gènes dupliqués. La technologie de carte optique proposée par Bionano Genomics, et le séquençage de banques Hi-C nous ont permis d'amener nos assemblages à l'échelle des chromosomes et d'accéder à la structure de régions dites complexes comme les centromères.J'ai pu mettre en évidence l'importance de ces nouveaux assemblages pour différents génomes de plantes, pour lesquels ils constituent une ressource très précieuse pour de futures recherches sur l'histoire évolutive des espèces, sur les adaptations à de nouvelles conditions de vie ou sur les gènes de résistance aux pathogènes.Ces développements vont être adaptés pour répondre aux besoins de nouveaux projets de production de génomes de référence à grande échelle et dont le but est de préserver l'information génétique de la biodiversité.

The main genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa whose radiation occurred in allopatry. In such context, GWAS analysis, genome diversity and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super‐pangenome for cultivated citrus, established with de novo assemblies of C. medica , C. reticulata and C. micrantha , released for the first time alongside a published chromosome‐scale assembly of C. maxima . Repetitive element annotation revealed that half of each genome consisted of transposable elements or DNA‐satellites. The new genome assemblies display strong synteny and collinearity, while discrepancies are observed with the C. maxima assembly. Resequencing information from 55 accessions helped to explore the intra‐ and interspecific diversity of the ancestral taxa and their relationships with horticultural groups. Diagnostic SNPs of the ancestral taxa revealed interspecific introgressions in several representative accessions of C. reticulata , C. maxima and C. medica as well as insights into the origin and phylogenomic structures of horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa. Diagnostic PAV analysis uncovered a large chloroplastic introgression in C. medica chromosome 4. The analysis of the functional enrichment and species‐specific adaptations in the citrus super‐pangenome revealed distinct functional specialisations. This highlights the evolutionary paths that have shaped species, contributing to the diversity in the citrus super‐pangenome while maintaining a shared foundation of essential biological processes. We established a Genome Hub, offering a platform for continuous genomic research.

The deep ocean hosts autochthonous pressure-adapted microorganisms that are unique to this environment, as well as allochthonous pressure-sensitive members transported from shallow depths by vertical advection and particle-sinking. However, conventional sampling instruments decompress and warm deep-sea samples during retrieval, potentially altering microbial properties when studied ex situ. Here, we assess this potential sampling bias by comparing seawater microbial communities collected with or without measures aimed at minimizing pressure and temperature effects. When compared to samples collected under pressurized conditions, conventional sampling (using Niskin bottles) was found to affect prokaryotic cells retrieved by reducing their total numbers, diminishing protein synthesis activity (>10%), and also causing overall shifts in the community composition. The most significant compositional change was a >20% decrease in metagenomic archaeal representation (TACK-group/Thaumarchaeota/Nitrososphaerota). Deep-sea bacterial groups had mixed responses to preserving pressure during retrieval, with some groups exhibiting higher representation when samples were maintained pressurized (e.g. members of the family Pelagibacteraceae, unclassified Thiotricales, Thioglobaceae, and Chitinophagaceae), whereas others increased their representation when decompressed (e.g. Burkholderiaceae, Comamonadaceae, and Oxalobacteraceae). This study reveals the existence of bias introduced by the complete decompression of samples retrieved with traditional instrumentation, as well as a decrease in overall bacterial activity when samples are completely decompressed during retrieval. Additionally, incubations lasting for >24 h were shown to transform the original prokaryotic community composition. Precautions addressing these effects are necessary to enhance the reliability of ex situ measurements and improve our understanding of deep-sea microbial ecology and biogeochemistry.

The deep-sea floor encompasses more than half of the surface of our planet, yet the extent and distribution of deep-sea biodiversity and its contribution to large biogeochemical cycles remain poorly understood. This knowledge gap stems from several factors, including sampling issues, the magnitude of the work required for morphological inventories, and the difficulty of integrating results from disparate local studies. The application of meta-omics to environmental DNA now makes it possible to assemble interoperable datasets at different spatial scales to move towards a global assessment of deep-sea biodiversity. We present a large-scale dataset on deep-sea biodiversity, with data and metadata openly accessible at ENA and Zenodo. The resource was generated using standardized protocols developed according to FAIR principles, covering fieldwork through bioinformatic analysis, within “ Pourquoi Pas les Abysses? ” and eDNAbyss projects. Together with information ensuring reproducibility, this dataset —combining metagenomics, metabarcoding across the Tree of Life and capture-by-hybridization— contributes to the international concerted effort to achieve a holistic view of the biodiversity in the largest biome on Earth.

Hanak's bat ( Pipistrellus hanaki Hulva and Benda 2004) is one of the most range restricted mammals in Europe, since it occurs only in Cyrenaica, Libya, and Crete (Greece). It is currently classified as 'Vulnerable' on the IUCN Red List, with its foraging habitat threatened by a number of human activities. The reference genome of Hanak's bat ( Pipistrellus hanaki) will provide a crucial resource for uncovering the species phylogenetic history and will help assess the degree of genetic isolation among its populations. A total of 23 contiguous chromosomal pseudomolecules (sex chromosomes included) were assembled from the genome sequence. This chromosome-level assembly encompasses 1.9 Gb, composed of 447 contigs and 141 scaffolds, with contig and scaffold N50 values of 48.7 Mb and 89.1 Mb, respectively.

The Eunicella cavolini reference genome provides an important resource to study the adaptation of this species to different environments and anthropic pressures. This species is impacted by human activities, including climate change, and this reference genome will be useful to study the genomic evolution of this species. The entirety of the genome sequence was assembled into 17 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.49 Gb, composed of 159 contigs and 46 scaffolds, with contig and scaffold N50 values of 7.7 Mb and 51.1 Mb, respectively.