Biology subjects

Flot, J.-F.

Publications and source records attributed to Flot, J.-F..

At least 19 recordsLinked to original sources

bioRxiv2026

High-resolution species delimitation in Acinetobacter baumannii using a novel Core-Gene Consensus Delimitation approach

Acinetobacter baumannii is a highly adaptable nosocomial pathogen with extensive antibiotic resistance, a disproportionately large accessory genome, and high genomic plasticity. Owing to these features, the World Health Organisation (WHO) classifies A.baumannii as a critical-priority pathogen. In this study, we analyzed 47 isolates from our VUB (Vrije Universiteit Brussel) collection and applied distance-based species-delimitation algorithms - Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP) - for the first time at the bacterial core-genome scale. By integrating conspecificity matrices, we extended these traditionally single-locus methods into a multi-locus framework, which we term Core-Gene Consensus Delimitation (CGCD). Across a range of gene-level co-occurrence thresholds, CGCD consistently recovered 11 stable groups using both ABGD and ASAP. Larger-scale validation using 856 A. baumannii genomes recovered the same 11 well-separated groups were recovered, demonstrating the robustness and reliability of our clustering approach. Mapping these groups onto a core-genome phylogeny revealed that each group forms a distinct clade, indicating that they represent evolutionarily independent lineages rather than arbitrary clusters. We further constructed a clustering tree based on accessory gene presence-absence patterns. In this tree, only one strain (AB231-VUB) clustered within group 11; otherwise, the groups remained tightly cohesive, sharing characteristic sets of accessory genes. Together, these results show that the groups defined by CGCD are genomically, evolutionarily, and functionally distinct, supporting their interpretation as separate species. Our findings highlight CGCD as a powerful, high-resolution framework for species delimitation. CGCD is threshold-free, gene-based, and universally applicable--the first species-delimitation approach that can be applied across all domains of life, from bacteria to animals and plants.

microbiology↗

bioRxiv2025

Proteomic insights into the photobiology of the Hawaiian rice coral Montipora capitata in response to decreased light intensity

Reef-building corals are sessile marine organisms that inhabit a wide range of light habitats along depth gradients. As coral biology is often studied in the context of global change and changing temperatures, knowledge gaps persist in our understanding of the molecular and cellular pathways involved in the responses to other factors than temperature, such as light intensity, which decreases exponentially in the water column and gradually changes the environment. To fill this gap, we tested the response of the Hawaiian rice coral Montipora capitata to decreased light intensity in a field experiment in K[a]neohe Bay, Oahu, Hawaii, using Data-Independent Acquisition (DIA) proteomics. There was a significant effect of light intensity on both the coral and zooxanthellae proteomes. In the M. capitata host, 69 proteins differed significantly in abundance between light levels after two years. The 50 proteins identified as significantly more abundant in the control condition were mostly involved in mRNA and RNA processing, pointing toward a positive correlation between metabolic activity, growth rates and increased light levels. The 19 proteins identified as significantly more abundant in the shade treatment were associated with calcium transport and with the structure of key cellular components, such as cell membrane and cytoskeleton. By contrast, zooxanthellae showed only minor changes in protein abundances, with photosynthesis proteins more abundant in the shade treatment and enzymes involved in fatty acid metabolism more abundant in the control treatment. Overall, these findings establish a baseline for our understanding of the cellular and metabolic processes driving Montipora capitatas acclimatization potential to different light intensities.

ecology↗

bioRxiv2025

SNooPy: a statistical framework for long-read metagenomic variant calling

Current long-read single-nucleotide variant callers were designed primarily for genomic data--particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inherent complexity of metagenomic samples. To date, no long-read variant caller has been purpose-built for metagenomic applications. To address this gap, we present SNooPy, a SNP-calling tool that implements a new statistical framework tailored to long-read metagenomic data. Unlike previous genomic methods, our approach makes no assumptions about the number of haplotypes present, their evolutionary relationships, or their sequence divergence. We demonstrate that SNooPy outperforms both traditional statistical and deep learning-based SNP callers. Our results suggest that future integration of this framework with deep learning approaches could further enhance variant calling performance. SNooPy is freely available on github.com/rolandfaure/snoopy.

bioinformatics↗

bioRxiv2025

Nature vs nurture? Light availability drives phenotypic plasticity within a reef coral species

Scleractinian corals exhibit wide intra-specific phenotypic variations. However, the extent to which these variations are explained by genotypic variation or phenotypic plasticity remains unclear. To elucidate this question, we devised a replicated experiment in which nine Montipora capitata coral colonies were cut into six pieces each, three of which were placed in shaded conditions (with a 73% reduction in light intensity) whereas the other three were kept in natural conditions as a control. After one year, we detected statistically significant morphological differences between corals of the same genotypes grown in different light environments, but no significant change in symbiont community structure. Colonies kept in control conditions exhibited high surface complexity and converged towards more digitate or corymbose morphs compared to shaded corals, which exhibited planar-like surfaces and converged toward laminar and foliose forms. Our data demonstrate the high level of light-driven phenotypic plasticity of Montipora capitata and suggest a trade-off between the amount of biomass per space area and the amount of absorption of incident light.

ecology↗

bioRxiv2025

Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching

BackgroundLong-read metagenomic assembly is becoming a critical bottleneck in microbiome analysis, as deep sequencing generates massive datasets that existing methods struggle to assemble while maintaining strain resolution. ResultsWe present Alice, a lightweight long-read assembler that achieves orders-of-magnitude speedups through a new sequence sketching technique, MSR sketching, compatible with classical assembly methods. Alice assembles a 235 Gbp soil metagenome in 5 hours using only 84 GB RAM--a task that causes most competing methods to exhaust our computational resources (500 GB RAM and 7 days runtime). Across diverse benchmarks, Alice delivered strain-resolved assemblies an order of magnitude faster than state-of-the-art approaches, while producing the most complete assemblies in some cases. ConclusionsMSR sketching overcomes computational barriers in metagenomic assembly, enabling fast, memory-efficient strain-resolved analysis of massive datasets. While Alices assemblies were more fragmented than with other assemblers, this approach establishes a promising paradigm for scalable metagenomic analysis.

bioinformatics↗

bioRxiv2025

Nanopore genome skimming with Illumina polishing yields highly accurate mitogenome sequences: a case study of Niphargus amphipods

With over 430 species currently described, the amphipod genus Niphargus Schiodte, 1849 is the most species-rich crustacean genus in subterranean waters. Previous phylogenetic studies of this genus have relied mainly on mitochondrial COI and nuclear 28S sequences, which do not resolve all the nodes in its phylogeny. As a first step towards a mitogenome-based phylogeny of niphargids, we present here the first complete mitogenome sequence of Niphargus. To obtain high-accuracy mitogenome sequences and annotations, genome skimming of three individuals of Niphargus dolenianensis Lorenzi, 1898 was performed using both short, accurate reads (Illumina) and long, noisier reads (nanopore). Whereas the direct assembly of Illumina sequences yielded structurally incorrect mitogenome sequences, the assembly of nanopore reads produced highly accurate sequences that were corroborated by the mapping of Illumina reads. Polishing the nanopore consensus using Illumina reads corrected a handful of errors at the homopolymer level. The resulting mitogenome sequences ranged from 14,956 to 15,199 bp and shared the same arrangement of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a putative control region. Phylogenetic analyses based on protein-coding genes confirmed that the Niphargidae family is sister to Pseudoniphargidae, resolving their relationships with other amphipod families. This highlights the utility of mtDNA genome sequences for studying the evolution of this groundwater genus, and the refinement of new methodological approaches, such as nanopore sequencing, is promising for the study of its origin and diversification.

genomics↗

bioRxiv2025

Refining Feulgen: low-cost and accurate genome size measurements for everyone

Feulgen image analysis densitometry (FIAD) has been extensively used for decades to measure genome sizes, but is usually considered less precise and less reproducible compared to other methods such as flow cytometry (FCM). However, FCM requires fresh tissue samples, which is a major impediment to using it on specimens collected in the field far from the lab. By contrast, FIAD works on ethanol-preserved samples kept at room temperature, which is a huge advantage for biodiversity genomics. In this study, we present refinements on the Feulgen protocol and downstream analyses that produce measurements at least as reliable and precise as those obtained using whole-genome sequencing. We illustrate it by measuring for the first time the genome size of the red bald uakari monkey Cacajao rubicundus using the American cockroach Periplaneta americana and the black garden ant Lasius niger as standards.

genomics↗

bioRxiv2025

New Swiss-knife activities of GroEL/Hsp60 proteins

GroEL/Hsp60 chaperonins are key proteins that control cell metabolism, stress adaptation and survival. They usually form a tetradecameric structure that assists, coupled to ATP hydrolysis, 10% of all cellular protein folding. Using recombinant E. coli, human mitochondrial and M. tuberculosis chaperonins, we found that these proteins have thioesterase, esterase and even, for some of them, auto-acyltransferase activities. The smaller oligomers of Hsp60 and M. tuberculosis GroEL1 were more prone to use the long acyl carbon chain substrate palmitoyl-CoA compared to tetradecameric E. coli GroEL and Hsp60. Enzymatic competition and replacement of M. tuberculosis GroEL1 residues allow identifying Asp86 and Thr89 in the ATP-binding pocket and an additional Ser393 influencing the thioesterase activity. Additionally, M. tuberculosis GroEL1 might enhance palmitoylation of the PpsE protein, which plays a role in the phthiocerol dimycocerosate (PDIM) biosynthesis. This could explain at least partly the involvement of GroEL1 in PDIM biosynthesis and antibiotic resistance.

biochemistry↗

bioRxiv2025

A rapid and inexpensive universal PCR protocol for DNA (meta)barcoding using a one-tube, 2-step PCR

DNA barcoding has become a widespread technique for species identification through the amplification of standardized gene regions. These include the cytochrome c oxy-dase subunit I (COI) for metazoans, ITS for fungi and plants or the 16S rRNA for bacteria and archaea. It has been shown to be more accurate than more traditional methods such as morphology, making it a now widespread method for species delimitation. The development of new sequencing methods such as Nanopore sequencing becoming more affordable and accurate has led to a growing use of those methods and a need for fast, standardized and cheap protocol. Although Sanger sequencing has become super-seded by next-generation sequencing for most genomic applications, using second or third-generation sequencing for amplicons remains an expensive and time-consuming approach, especially for laboratories that analyse many different markers. Amplicon sequencing typically occurs in the context of either DNA barcoding (sequencing one or a few markers of interest for each specimen in a collection) or DNA metabarcoding (investigating the composition of a community by using universal primers targeting a whole group of organisms). Pooling the resulting PCR products for e.g. Nanopore sequencing requires the use of barcodes that are generally added to amplicons once they are amplified (using either ligation or a second round of amplification), and these supplementary steps are time-consuming, expensive and prone to contamination. To alleviate these issues, we present here a quick, single-tube two-step PCR with four primers: two internal primers with tails, and two external barcode primers that anneal on the tails during the second phase of the PCR. we show an improved 4 primers PCR protocol by using a single tube "drop in the lid" method. 8 DNA extract from Asellus. sp were obtained and amplified using both, 2-step PCR and the 1-step PCR. Results shows a clear enhancement of PCR product using the 2-step PCR for both ITS and CO1 marker compare to the 1-Step protocol. Method SummaryTo maximize the cost and effectiveness of barcoding approaches, we developed barcodes based on the Native Barcoding Kit 96 V14 of Oxford Nanopore Technologies (ONT). This step allows to tag samples within the PCR rather than through the use of ligase enzymes. To avoid primer interaction between the inner primer and the barcodes, the latter were added within the PCR cycles through the implementation of a hold step between the inner primer cycles and the barcoding cycles. For this purpose, barcodes are dried on the lid, avoiding the opening PCR tubes and preventing potential contamination.

genomics↗

bioRxiv2025

Chromosome-level genome assembly and annotation of the chaetognath Flaccisagitta enflata

Chaetognaths, a phylum of enigmatic marine predators, present a significant challenge to phylogenetic reconstruction due to their uncertain evolutionary placement. While transcriptome analyses have suggested affinities with the Gnathifera clade, genomic data for this group remain scarce, hindering a comprehensive understanding of their evolution. Here, we present the first chromosome-level genome assembly of Flaccisagitta enflata, a species within the Aphragmophora order. The genome assembly includes 9 chromosome candidates with a total size of 794 Mb and a BUSCO score of 91.3% against the Metazoa lineage. This high-quality genome assembly provides a crucial resource for comparative genomic analyses within Chaetognatha and the broader Gnathifera clade, and it will facilitate investigations into chaetognath evolution and their phylogenetic relationships, addressing long-standing questions regarding their placement within the animal kingdom.

genomics↗

bioRxiv2024

Shading does not lower thermal tolerance in the coral Montipora capitata: implications for conservation intervention

Marine heatwaves trigger severe coral bleaching events that result in dramatic losses of coral reefs worldwide. An increasingly common method used to mitigate coral bleaching is to shade portions of reefs. However, as shaded corals become less exposed to environmental stress, shading has also been hypothesized to lower their thermal tolerance, which would be detrimental for their survival. Here, we investigated how long-term shading modifies the response of Montipora capitata to both light and temperature stressors. After two years of growth, we used the Coral Bleaching Automated Stress System (CBASS) to compare responses of 73% shaded and unshaded corals during 1) temperature stress under ambient light, 2) temperature stress under low light, and 3) ambient temperature with light stress. Results show that shaded corals are less resistant than control ones to light stress and to heat stress under high light, but not to heat stress under low light, where no difference was detected. We further demonstrate that low light intensity during heat stress reduces the decline of photosynthetic efficiency when compared to heat stress at ambient light, regardless of the light history of the coral colonies. Our data support light-mediated stress, both independent of and synergistic with heat-induced stress, and suggest that light and heat stresses trigger different molecular and cellular pathways. We hereby confirm the benefits of coral shading under both short- and long-term temperature stress, and underline the importance of light acclimation in the conservation and restoration of coral reefs.

ecology↗

bioRxiv2024

Genetic and functional diversity of allorecognition receptors in the urochordate, Botryllus schlosseri

Allorecognition in Botryllus schlosseri is controlled by a highly polymorphic locus (the fuhc), and functionally similar to missing-self recognition utilized by Natural Killer cells-compatibility is determined by sharing a self-allele, and integration of activating and inhibitory signals determines outcome. We had found these signals were generated by two fuhc-encoded receptors, called fester and uncle fester. Here we show that fester genes are members of an extended family consisting of >37 loci, and co-expressed with an even more diverse gene family-the fester co-receptors (FcoR). The FcoRs are membrane proteins related to fester, but include conserved tyrosine motifs, including ITIMs and hemITAMs. Both genes are encoded in highly polymorphic haplotypes on multiple chromosomes, revealing an unparalleled level of diversity of innate receptors. Our results also suggest that ITAM/ITIM signal integration is a deeply conserved mechanism that has allowed convergent evolution of innate and adaptive cell-based recognition systems.

immunology↗

bioRxiv2024

First chromosome-level genome assembly of the colonial tunicate Botryllus schlosseri

Botryllus schlosseri (Tunicata) is a colonial chordate that has long been studied for its multiple developmental pathways and regenerative abilities and its genetically determined allorecognition system based on a polymorphic locus that controls chimerism and cell parasitism. We present the first chromosome-level genome assembly from an isogenic colony of B. schlosseri clade A1 using a mix of long and short reads scaf-folded using Hi-C. This haploid assembly spans 533 Mb, of which 96% are found in 16 chromosome-scale scaffolds. With a BUSCO completeness of 91.2%, this complete and contiguous B. schlosseri genome assembly provides a valuable genomic resource for the scientific community and lays the foundation for future investigations into the molecular mechanisms underlying coloniality, regeneration, histocompatibility, and the immune system in tunicates.

genomics↗

bioRxiv2024

A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids

The genomic basis of cladogenesis and adaptive evolutionary change has intrigued biologists for decades. Here, we show that the tectonics of genome evolution in clitellates, a clade composed of most freshwater and all terrestrial species of the phylum Annelida, is characterised by extensive genome-wide scrambling that resulted in a massive loss of macrosynteny between marine annelids and clitellates. These massive rearrangements included the formation of putative neocentromeres with newly acquired transposable elements and preceded a further period of genome-wide reshaping events, potentially triggered by the loss of genes involved in genome stability and homeostasis of cell division. Notably, while these rearrangements broke short-range interactions observed between Hox genes in marine annelids, they were reformed as long-range interactions in clitellates. Our findings reveal extensive genomic reshaping in clitellates at both the linear (2D) and three-dimensional (3D) levels, suggesting that, unlike in other animal lineages where synteny conservation constrains structural evolution, clitellates exhibit a remarkable tolerance for chromosomal rearrangements. Our study thus suggests that the genomic landscape of Clitellata resulted from a rare burst of genomic changes that ended a long period of stability that persists across large phylogenetic distances.

evolutionary biology↗

bioRxiv2024

HairSplitter: haplotype assembly from long, noisy reads

MotivationLong-read assemblers face challenges in discerning closely related viral or bacterial strains, often collapsing similar strains into a single sequence. This limitation has been hampering metagenome analysis, as diverse strains may harbor crucial functional distinctions. ResultsWe introduce a novel software, HairSplitter, designed to retrieve strains from a partially or totally collapsed assembly and long reads. The method uses a custom variant-calling process to operate with erroneous long reads and introduces a new read binning algorithm to recover an a priori unknown number of strains. On noisy long reads, HairSplitter recovers more strains while being faster than state-of-the-art tools, both in the cases of viruses and bacteria. AvailabilityHairSplitter is freely available on GitHub at github.com/RolandFaure/HairSplitter. Contactroland.faure@irisa.fr

bioinformatics↗

bioRxiv2023

Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story

1Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript and Python. Although Haxe is becoming more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxes source code conversion functionality when it comes to implementing bioinformatic software.

bioinformatics↗

bioRxiv2023

Genomic comparison of the temperate coral Astrangia poculata with tropical corals yields insights into winter quiescence, innate immunity, and sexual reproduction

Facultatively symbiotic corals provide important experimental models to explore the establishment, maintenance, and breakdown of the mutualism between corals and members of the algal family Symbiodiniaceae. The temperate coral Astrangia poculata is one such model as it is not only facultatively symbiotic, but also occurs across a broad temperature and latitudinal gradient. Here, we report the de novo chromosome-scale assembly and annotation of the A. poculata genome. Though widespread segmental/tandem duplications of genomic regions were detected, we did not find strong evidence of a whole genome duplication (WGD) event. Comparison of the gene arrangement between A. poculata and the tropical coral Acropora millepora revealed 56.38% of the orthologous genes were conserved in syntenic blocks despite [~]415 million years of divergence. Gene families related to sperm hyperactivation and innate immunity, including lectins, were found to contain more genes in A. millepora relative to A. poculata. Sperm hyperactivation in A. millepora is expected given the extreme requirements of gamete competition during mass spawning events in tropical corals, while lectins are important in the establishment of coral-algal symbiosis. By contrast, gene families involved in sleep promotion, feeding suppression, and circadian sleep/wake cycle processes were expanded in A. poculata. These expanded gene families may play a role in A. poculatas ability to enter a dormancy-like state ("winter quiescence") to survive freezing temperatures at the northern edges of the species range.

genomics↗

bioRxiv2023

Evolutionary origin of morphologically cryptic species imprints co-occurrence and sympatry patterns

AimMorphologically cryptic species are an important part of global biodiversity, yet it remains unclear how these species contribute to and integrate into communities at different geographic scales. It is especially unclear at which scales they co-occur, and if and how their ranges overlap. To adequately protect biodiversity, an accurate understanding of the underlying processes and adequate level of protection is needed, in particularly for often overlooked cryptic species. QuestionWe analyzed patterns of syntopies (local co-occurrences) and sympatries (range overlap) to test how the evolutionary origin of cryptic species shapes biodiversity patterns at different geographic scales. We hypothesized i) that syntopies are more common among phylogenetically deeply divergent cryptic species than among close relatives, and ii) that sympatries are an outcome of phylogenetic relatedness and dispersal, with range size as a proxy of dispersal ability. LocationWestern Europe. TaxonSubterranean amphipod crustaceans of the polyphyletic Niphargus rhenorhodanensis species complex. MethodsUnilocus species delimitations (PTP, ASAP), calibrated multilocus phylogenetic analyses, co-occurrence analyses using a probabilistic model, generalized linear models (GLM). ResultsThe studied species complex comprises 37-48 molecular operational taxonomic units (MOTUs) from nine different clades. Syntopies are random or less frequent than expected, implying an insufficient between-MOTU differentiation allowing stable coexistence. GLM suggested that age of divergence does not predict species sympatries, although they emerge more frequently among MOTUs from different clades. By contrast, sympatries emerge when at least one MOTU disperses over a large geographic range. Biodiversity rich regions were found at the foothills of the Alps, the Jura and the Central Massif, regardless the inference method. Main conclusionsBiodiversity patterns of the herein studied species complex are driven mainly by dispersal and reflect geographic circumstances of speciation. While species richness on a local scale may be the outcome of competition and dispersal, regional biodiversity patterns emerged through biogeographic history on a clade-level.

ecology↗