Biology subjects

Barbe, V.

Publications and source records attributed to Barbe, V..

13 recordsLinked to original sources

bioRxiv2026

Thermococcales pangenome uncovers new genera and modular evolution.

The order Thermococcales is unusual among Archaea in being known primarily from hundreds of lab-cultured isolates rather than metagenome-assembled genomes. Such cultivation is powerful for comparative genomics, allowing access to complete closed genomes rather than fragmented assemblies. We analysed 122 complete genomes, comprising all publicly available type species plus 67 new isolates, as a single pangenome. A combination of genome-scale metrics resolved 70 species across five genus-level clades, two proposed here as the new genera Oleococcus and Piezococcus, in addition to the canonical Pyrococcus, Palaeococcus, and Thermococcus. Only 6.1% of the 21,490 gene families are persistent, yet these contribute over half the genes in any genome. We observe that accessory functions, such as amino-acid biosynthesis, often behave modularly, being gained and lost as intact cassettes from genus-specific chromosomal loci. Combined with 114 mobile genetic elements, 72 of which are integrated in the chromosome at conserved tRNA genes, we find that Thermococcales genomes accommodate rapid horizontal turnover through a constrained chromosomal architecture.

genomics↗

bioRxiv2026

Coevolution and synchronized evolutionary rates in aphid dual endosymbiosis

Many insects rely on obligate bacterial endosymbionts for essential nutrients. However, long-term endosymbiosis drives genome erosion, frequently resulting in the acquisition of additional symbionts that complement or replace ancestral partners. In aphids, the primary nutritional symbiont Buchnera aphidicola can be supplemented by a co-obligate symbiont, most commonly Serratia symbiotica. The long-term evolutionary trajectory of this newly acquired symbiont and its impact on Buchnera remain unknown. Here, we assembled host mitochondrial and endosymbiont genomes from thirteen aphid species belonging to a clade in which Serratia has functioned as a co-obligate symbiont for approximately 25 million years. Phylogenomic analyses reveal that Serratia has undergone extensive genome reduction followed by strict codivergence with aphids and Buchnera. Bayesian molecular dating shows that substitution rates in Serratia and Buchnera are tightly correlated and fall within the range previously reported for Buchnera. Genome-wide analyses indicate pervasive purifying selection in both symbionts. Homologous host-provisioning genes retained in both symbionts did not exhibit elevated evolutionary rates. However, unlike other functional categories, their dN/dS values were not correlated between symbionts, suggesting that they no longer evolve under shared selective regimes, consistent with progressive metabolic specialization. Intraspecific patterns of polymorphism and phylogenies mirror macroevolutionary patterns across the clade. Fluorescence in situ hybridization shows that Serratia and Buchnera occupy distinct bacteriocytes, suggesting that similar demographic processes may contribute to their parallel evolution. Our findings demonstrate that, once integrated into an obligate partnership, newly acquired nutritional symbionts can converge on the long-term evolutionary dynamics of ancient obligate symbionts while undergoing functional specialization.

evolutionary biology↗

bioRxiv2025

Scratching on French PDO cheese surfaces sheds light on an unexplored microbial genomic and metabolic diversity

Cheeses are fermented dairy products consumed worldwide. Their global diversity results from various local variables, including technological practices, as well as the metabolic activity of diverse microorganisms. In Europe, this typicity is exemplified by Protected Designation of Origin (PDO) cheeses, for which genetic diversity remains largely unexplored. Combining culturomics (n = 373 bacterial genomes) and metagenomic (n = 146 metagenomes), we performed a national-scale survey of the microbial diversity encompassing 44 French PDO cheeses. Taxonomic (bacteria, fungi and viruses) and functional profiling reveal a high diversity in the cheese rind, mainly driven by the cheese technology. We also reconstructed 1,119 bacterial metagenome-assembled genomes (MAGs) encompassing seven phyla, including Actinomycetota, Bacillota, Pseudomonadota and Bacteroidota. Using GTDB as a reference, we identified 221 MAGs encompassing 46 genera, as well as 44 bacterial isolate genomes encompassing eight genera, which represent potentially 81 new species (based on <95% ANI). These species were particularly numerous among the genera Halomonas, Psychrobacter and Brachybacterium. Similar results were observed when compared with the cFMD database. We combined our genomic and metagenomic datasets into a catalog of 26.2 million protein clusters, with 50% of these clusters remaining unassigned to a known function and taxonomy. We illustrated the potential of this resource by searching for methionine gamma-lyase (MGL), an enzyme playing a significant role in cheese flavor. This protein was predominantly found in Pseudoalteromonas, a potentially new MGL-producing genus, Serratia, Pseudomonas, Proteus and Hafnia, and its prevalence varied with cheese technology. Our study provides a substantial genomic resource for food microbiologists and cheesemakers to further explore the biotechnological potential of PDO cheese biodiversity.

microbiology↗

bioRxiv2024

Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma

Oncogene amplification on extrachromosomal DNA (ecDNA) is strongly associated with treatment resistance and shorter survival for patients with cancer, including patients with glioblastoma. The non-chromosomal inheritance of ecDNA during cell division is a major contributor to intratumoral genetic heterogeneity. At present, the spatial dynamics of ecDNA, and the impact on tumor evolutionary trajectories, are not well understood. Here, we investigate the spatial-temporal evolution of ecDNA and its clinical impact by analyzing tumor samples from 94 treatment-naive human IDH-wildtype glioblastoma patients. We developed a spatial-temporal computational model of ecDNA positive tumors ( SPECIES) that integrates whole-genome sequencing, multi-region DNA FISH, and nascent RNAscope, to provide unique insight into the spatial dynamics of ecDNA evolution. Random segregation in combination with positive selection of ecDNAs induce large, predictable spatial patterns of cell-to-cell ecDNA copy number variation that are highly dependent on the oncogene encoded on the circular DNA. EGFR ecDNAs often reach high mean copy number (mean of 50 copies per tumor cell), are under strong positive selection (mean selection coefficient, s > 2) and do not co-amplify other oncogenes on the same ecDNA particles. In contrast, PDGFRA ecDNAs have lower mean copy number (mean of 15 copies per cell), are under weaker positive selection and frequently co-amplify other oncogenes on the same ecDNA. Evolutionary modeling suggests that EGFR ecDNAs often accumulate prior to clonal expansion. EGFR structural variants, including vIII and c-terminal deletions are under strong positive selection, are found exclusively on ecDNA, and are intermixed with wild-type EGFR ecDNAs. Simulations show EGFRvIII ecDNA likely arises after ecDNA formation in a cell with high wild-type EGFR copy number (> 10) before the onset of the most recent clonal expansion. This remains true even in cases of co-selection and co-amplification of multiple oncogenic ecDNA species in a subset of patients. Overall, our results suggest a potential time window in which early ecDNA detection may provide an opportunity for more effective intervention. HighlightsO_LIecDNA is the most common mechanism of focal oncogene amplification in IDHwt glioblastoma. C_LIO_LIEGFR and its variants on ecDNA are particularly potent, likely arising early in tumor development, providing a strong oncogenic stimulus to drive tumorigenesis. C_LIO_LIWild-type and variant EGFR ecDNA heteroplasmy (co-occurrence) is common with EGFRvIII or c-terminal deletions being derived from EGFR wild-type ecDNA prior to the most recent clonal expansion. C_LIO_LITumors with ecDNA amplified EGFR versus PDGFRA exhibit different evolutionary trajectories. C_LIO_LISPECIES model can infer spatial evolutionary dynamics of ecDNA in cancer. C_LIO_LIA delay between ecDNA accumulation and subsequent oncogenic mutation may give a therapeutic window for early intervention. C_LI

cancer biology↗

bioRxiv2024

Discordance between phylogenomic datasets in aphids: who is telling the truth?

Aphids (Hemiptera: Aphididae) are intensively studied due to their significance as pests and their captivating biological traits. Despite this considerable research interest, the evolutionary history of this insect family is poorly understood. Recent phylogenomic analyses have produced conflicting topologies, particularly at deep nodes, complicating our understanding of aphid trait evolution. In this work, we aimed to produce new data to unravel the backbone phylogeny of aphids. We sequenced partial and whole mitochondrial genomes from 87 species that were added to 31 published mitochondria. We additionally sequenced 42 nuclear loci across 95 aphid species and sourced 146 genes from 12 new and 61 published genomes from the primary aphid obligate endosymbiont, Buchnera aphidicola. We obtain data from these three sources for a subset of 51 aphid species, facilitating a comparative analysis of their phylogenetic signals. Our analyses confirm the monophyly of subfamilies, validating current taxonomic classifications, except for Eriosomatinae and Calaphidinae. However, relationships between subfamilies remain contentious in both mitochondrial and nuclear phylogenies. The topologies obtained with Buchnera appear fully resolved but exhibit some discordance with host phylogenies at deep evolutionary scales and conflict with views on the evolution of aphid morphology. We discuss alternative hypotheses for these discrepancies. Finally, the paucity of phylogenetic information at deep phylogenetic scales may stem from an initial rapid radiation. Though challenging to establish, this scenario may inherently hinder resolution in aphid phylogenetics.

evolutionary biology↗

bioRxiv2022

Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages

Aphids are a large family of phloem-sap feeders. They typically rely on a single bacterial endosymbiont, Buchnera aphidicola, to supply them with essential nutrients lacking in their diet. This association with Buchnera was described in model aphid species from the Aphidinae subfamily and has been assumed to be representative of most aphids. However, in two lineages, Buchnera has lost some essential symbiotic functions and is now complemented by additional symbionts. Though these cases break our view of aphids harbouring a single obligate endosymbiont, we know little about the extent, nature, and evolution of these associations across aphid subfamilies. Here, using metagenomics on 25 aphid species from nine subfamilies, re-assembly and re-annotation of 20 aphid symbionts previously sequenced, and 16S rRNA amplicon sequencing on 223 aphid samples (147 species from 12 subfamilies), we show that dual symbioses have evolved anew at least six times. We also show that these secondary co-obligate symbionts have typically evolved from facultative symbiotic taxa. Genome-based metabolic inference confirms interdependencies between Buchnera and its partners for the production of essential nutrients but shows contributions vary across pairs of co-obligate associates. Fluorescent in situ hybridisation microscopy shows a common bacteriocyte localisation of two newly acquired symbionts. Lastly, patterns of Buchnera genome evolution reveal that small losses affecting a few key genes can be the onset of these dual systems, while large gene losses can occur without any co-obligate symbiont acquisition. Hence, the Buchnera-aphid association, often thought of as exclusive, seems more flexible, with a few metabolic losses having recurrently promoted the establishment of a new co-obligate symbiotic partner.

genomics↗

bioRxiv2022

Pervasive gene duplications as a major evolutionary driver of coral biology

Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to these ecosystems, providing habitat and food to a great diversity of species. In the frame of the Tara Pacific expedition, we generated two coral genomes, Porites lobata and Pocillopora meandrina with vastly improved contiguity that allowed us to study the functional organisation of these genomes. We annotated their gene catalog and report a relatively higher gene number (43,000 and 32,000 genes respectively) than that found in other public coral genome sequences. This finding is explained by a high number of tandemly duplicated genes (almost a third of the predicted genes). We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to immune system and disease-resistance, which we suggest to be functionally linked to coral host resilience. At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

genomics↗

bioRxiv2021

Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection.

BackgroundStructural Variations (SVs) are very diverse genomic rearrangements. In the past, their detection was restricted to cytological approaches, then to NGS read size and partitionned assemblies. Due to the current capabilities of technologies such as long read sequencing and optical mapping, larger SVs detection are becoming more and more accessible. This study proposes a comparison in SVs detection and characterization from long-read sequencing obtained with the MinION device developed by Oxford Nanopore Technologies and from optical mapping produced by the Saphyr device commercialized by Bionano Genomics. The genomes of the two Arabidopsis thaliana ecotypes Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1) were chosen to guide the use of one or the other technology. ResultsWe described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 on the public reference Col-0 TAIR10.1. After filtering, 1 184 and 591 Ler-1 SVs were retained from ONT and BioNano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations in both technologies. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted. ConclusionsStructural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference, most of detected SVs were found in same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the later being more efficient to characterize large SVs. Even if both technologies are obvious complementary approaches, ONT data appears to be more adapted to large scale populations study, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference.

genomics↗

bioRxiv2020

Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes

Most endogenous viruses, an important proportion of eukaryote genomes, are doomed to slowly decay. Little is known, however, on how they evolve when they confer a benefit to their host. Bracoviruses are essential for the parasitism success of parasitoid wasps, whose genomes they integrated ~103 million years ago. Here we show, from the assembly of a parasitoid wasp genome, for the first time at a chromosomal scale, that symbiotic bracovirus genes spread to and colonized all the chromosomes. Moreover, large viral clusters are stably maintained suggesting strong evolutionary constraints. Genomic comparison with another wasps revealed that this organization was already established ~53 mya. Transcriptomic analyses highlight temporal synchronization of viral gene expression, leading to particle production. Immune genes are not induced, however, indicating the virus is not perceived as foreign by the wasp. This recognition suggests that no conflicts remain between symbiotic partners when benefits to them converge.

genomics↗

bioRxiv2019

Serial horizontal transfer of vitamin-biosynthetic genes enables the establishment of new nutritional symbionts in aphids' di-symbiotic systems

Many insects with a nutrient-restricted diet depend on obligate mutualistic bacteria for the provisioning of essential nutrients lacking from their food source, namely essential amino acids and B vitamins. Most aphids (Hemiptera: Aphididae), whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera for the supply of the aforementioned compounds. However, in some aphid lineages Buchnera have lost the capability of producing these nutrients and thus the symbiotic consortium has accommodated an extra bacterial partner to supplement Buchneras deficiencies. In this work, we explore the di-symbiotic nutritional endosymbiosis of a group of Cinara aphids which has been found to harbour both Buchnera and an Erwinia-related symbiont. Using fluorescence in situ hybridisation, we have located this symbiont to the bacteriome where it inhabits its own bacteriocytes. Through whole-genome sequencing of the endosymbionts of 9 species of Erwinia-associated Cinara aphids, we have found that Ewrinia genomes are highly syntenic and all show significant genome reduction. Additionally, Erwinia symbionts display phylogenetic congruency with Buchnera, suggesting long-term co-divergence. Most significantly, we found that not only is Erwinia capable of complementing Buchneras auxotrophies, but that the genes involved in the biosynthesis of two B vitamins have actually been horizontally acquired from a Sodalis-related bacterium. Finally, this B-vitamin biosynthetic genes have been further transferred to a new Hamiltonella co-obligate symbiont in a specific Cinara lineage, thus displaying a tri-symbiotic system. These results highlight the important role horizontal gene transfer plays in the establishment of new obligate nutritional symbionts.

genomics↗

bioRxiv2018

A Freeloader?: The Highly Eroded Yet Big-Genomed Serratia symbiotica symbiont of Cinara strobi

Genome reduction is pervasive among maternally-inherited bacterial endosymbionts. This genome reduction can eventually lead to serious deterioration of essential metabolic pathways, thus rendering an obligate endosymbiont unable to provide essential nutrients to its host. This loss of essential pathways can lead to either symbiont complementation (sharing of the nutrient production with a novel co-obligate symbiont) or symbiont replacement (complete takeover of nutrient production by the novel symbiont). However, the process by which these two evolutionary events happen remains somewhat enigmatic by the lack of examples of intermediate stages of this process. Cinara aphids (Hemiptera: Aphididae) typically harbour two obligate bacterial symbionts: Buchnera and Serratia symbiotica. However, the latter has been replaced by different bacterial taxa in specific lineages, and thus species within this aphid lineage could provide important clues into the process of symbiont replacement. In the present study, using 16S rRNA high-throughput amplicon sequencing, we determined that the aphid Cinara strobi harbours not two, but three fixed bacterial symbionts: Buchnera aphidicola, a Sodalis sp., and S. symbiotica. Through genome assembly and genome-based metabolic inference, we have found that only the first two symbionts (Buchnera and Sodalis) actually contribute to the hosts supply of essential nutrients while S. symbiotica has become unable to contribute towards this task. We found that S. symbiotica has a rather large and highly eroded genome which codes only for a few proteins and displays extensive pseudogenisation. Thus, we propose an ongoing symbiont replacement within C. strobi, in which a once competent\" S. symbiotica does no longer contribute towards the beneficial association. These results suggest that in dual symbiotic systems, when a substitute co-symbiont is available, genome deterioration can precede genome reduction and a symbiont can be maintained despite the apparent lack of benefit to its host.

genomics↗

bioRxiv2017

High-throughput optical mapping of replicating DNA

DNA replication is a crucial process for the universal ability of living organisms to reproduce. Existing methods to map replication genome-wide use large cell populations and therefore smooth out variability between chromosomal copies. Single-molecule methods may in principle reveal this variability. However, current methods remain refractory to automated molecule detection and measurements. Their low throughput has therefore precluded genome-wide analyses. Here, we have repurposed a commercial optical DNA mapping device, the Bionano Genomics Irys system, to map the replication signal of single DNA molecules onto genomic position at high throughput. Our methodology (HOMARD) combines fluorescent labelling of replication tracks and nicking endonuclease (NE) sites with DNA linearization in nanochannel arrays and dedicated image processing. We demonstrate the robustness of our approach by providing an ultra-high coverage (23,311 x) replication map of bacteriophage {lambda} DNA in Xenopus egg extracts. HOMARD opens the way to genome-wide analysis of DNA replication at the single-molecule level.

genomics↗

bioRxiv2016

Modeling trophic dependencies and exchanges among insects’ bacterial symbionts in a host-simulated environment

Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. Metabolic interactions with bacteria have been key drivers in the evolution of sap-feeding insects, enabling complementation of their deprived nutrition. The sap-feeding whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. We took advantage of the well-defined bacterial community in B. tabaci as a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented frequency of bacterial combinations. We first reconstructed the metabolic networks of five common B. tabaci symbionts (Portiera, Rickettsia, Hamiltonella, Cardinium and Wolbachia), and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species combinations, and (3) dependencies of each species on different media components.\n\nThe automatic-based predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggested several previously un-reported routes for complementary interactions. Highly abundant symbiont combinations were found to have the potential to produce a diverse set of complementary metabolites, in comparison to un-detected combinations. No clear association was detected between metabolic codependencies and co-occurrence patterns. The findings indicate a potential key role for metabolic exchanges as key determinants shaping community structure in this system.

systems biology↗