Biology subjects

Confais, J.

Publications and source records attributed to Confais, J..

8 recordsLinked to original sources

bioRxiv2026

Genomic forecasting links climate-associated variation to spring phenology in the European wild apple, a crop wild relative of the cultivated apple

Climate-associated genomic variation is often used as a proxy for adaptive potential, yet whether it reflects adaptation with phenotypic consequences, rather than demography alone, is rarely tested in long-lived species. Genomic offsets forecast climate maladaptation from genotype-environment models but are seldom validated against phenotypes. We combined whole-genome resequencing, SNP and transposable element insertion polymorphism (TIP) variation, landscape genomics, genome-wide association, genomic offset, and common-garden phenotyping in the European wild apple (Malus sylvestris Mill.), a crop wild relative with a complex demographic history, to test this. Results: Of 148 resequenced accessions (135 wild, 13 cultivated), 89 wild individuals formed the core dataset. Population structure was associated with Last Glacial Maximum precipitation rather than contemporary climate, and genetic diversity increased from west to east. Genome-environment associations across 9.75 million SNPs identified climate-associated loci enriched in photoperiod-related flowering-time genes, with limited overlap with phenotype-associated loci. SNP-based genomic offset was associated with bud-break timing in the Saclay common garden (marginal R2 = 0.31), with higher offsets corresponding to earlier bud break, but not with growth or ecophysiological traits. This association depended on Austrian and Romanian populations and was clearest in non-admixed wild individuals. Offsets based on TIPs or glacial climate did not predict measured phenotypes. Conclusions: Climate association, phenotypic relevance, and predictive power of genomic variation are separable. In a long-lived tree, genomic offset predicted spring phenology, a key adaptive trait, but this signal varied across provenances and ancestries and was absent for transposable elements. Genomic offsets can therefore forecast potential phenological maladaptation, provided they are validated against phenotypes such as bud break.

ecology↗

bioRxiv2026

A reference genome assembly for Quercus canariensis Willd

The authors have withdrawn this manuscript because the sequenced individual was misidentified as Quercus canariensis following a label swap and was subsequently confirmed to be Quercus pyrenaica. A corrected manuscript focusing on Q. pyrenaica will be submitted shortly to avoid propagating the incorrect species attribution. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

genetics↗

bioRxiv2025

Genomic architecture of the self-incompatibility locus in apple provides insights into the evolution of collaborative non-self recognition

Self-incompatibility (SI) systems prevent self-fertilization, thereby maintaining genetic diversity in flowering plants. Among them, collaborative non-self recognition (CNSR) is the most widespread, yet the genomic organization and evolutionary maintenance of its multigenic recognition system remain poorly understood. Using 27 haplotype-resolved genomes from wild and domesticated apples (Malus spp.), we dissected the structure and evolution of the S-locus. We identified 17 S-RNase alleles and 500 pollen-expressed S-locus F-box brother (SFBB) genes across 18 families. The S-locus shows extensive structural divergence among alleles and transposable element accumulation, consistent with long-term restricted effective recombination. Despite this divergence, haplotypes carrying the same S-RNase allele retain remarkably conserved SFBB repertoires and gene organization, even across species boundaries, indicating that long-term balancing selection preserves highly conserved S-haplotype architectures associated with specific S-RNase lineages. Tandem duplication, positive selection, and signatures consistent with gene conversion contribute to the diversification of pollen-expressed SFBB genes while S-RNase-associated SFBB repertoires remain conserved across haplotypes carrying the same S-RNase allele. Our results reveal how a structurally dynamic yet evolutionarily constrained genomic region can sustain long-term S-allele diversity and preserve complex multigenic haplotype architectures in flowering plants.

genomics↗

bioRxiv2025

Building pangenomes for domesticated and wild tree species: genomic complexity and strategies

Long-read sequencing and pangenomics are revolutionizing crop research by providing more complete genome information and revealing crucial structural variations linked to important agricultural traits. Building on recent advances in intraspecific pangenome construction, this study addresses the challenge of creating broader, cross-taxon pangenomes, using the Armeniaca taxonomic section as a model. Leveraging a diverse panel of genome assemblies, we constructed a pangenome graph and cataloged associated single nucleotide polymorphisms (SNPs) and structural variants. We characterized the diversity of these variants and assessed the extent to which different taxa contribute to overall pangenome expansion. Additionally, we evaluated the performance of low-depth sample mapping to the graph-based reference, highlighting key technical limitations that may affect the quality of downstream analyses. We further identified specific subsets of SVs that exhibit associations with particular classes of transposable elements. As a case study illustrating the potential functional and phenotypic relevance of graph-derived SVs, we examined the genomic configuration of the DAM locus within the Armeniaca pangenome.

bioinformatics↗

bioRxiv2025

Comprehensive annotation of olfactory and gustatory receptor genes and transposable elements revealed their evolutionary dynamics in aphids

Understanding the molecular evolution of genes involved in parasite adaptation and the role of transposable elements (TEs) in driving their diversification is key to unraveling how populations adapt to their environments. In phytophagous insects like aphids, olfactory (OR) and gustatory receptor (GR) genes are crucial for host recognition, yet their post-duplication evolution remains insufficiently explored. Here, we analyzed 521 OR and 399 GR genes, alongside TEs, across 12 aphid genomes with varying host ranges. Aphid lineages with broader host ranges exhibited higher evolutionary rates, driven by gene family expansions linked to host interaction, including lipid metabolism, immune function, and transposase activity. The evolution of OR and GR genes post-duplication was shaped by diversifying selection, with bursts of positive selection followed by long periods of purifying selection, consistent with adaptation to new hosts. OR and GR genes originated from proximal and tandem duplications, with younger TE activity enriched near these genes compared to other genomic regions, suggesting a role for TEs in catalyzing tandem duplications and fueling diversification. The star-like topology of the OR phylogenetic tree, low synteny, and recent TE activity around OR genes support a faster evolutionary rate for ORs than GRs - a trend observed in other insect taxa. This study provides insights into molecular mechanisms underlying host adaptation in aphids and presents the first high-quality genome assembly of Dysaphis plantaginea, a major apple pest, with a comprehensive annotation of chemosensory genes and TEs. These resources offer a foundation for research on aphid genome evolution, insect-plant interactions.

molecular biology↗

bioRxiv2024

The Brachypodium distachyon pangenome highlights Transposable Element dynamics in the species

The role of transposable elements (TEs) in host adaptation has gained lots of interest in the recent past. Individuals of the same species undergo independent TE insertions, causing genetic variability upon which natural selection can fosters adaptation of individuals to their environment. While de novo assembled genomes are becoming increasingly affordable, overcoming bias introduced by a single reference genome, suitable pangenomic approaches are required to explore genomes of a species. We developed a new pipeline called panREPET that identifies TE insertions shared by groups of individuals. Unlike other pangenomic tools, panREPET operates independently of a reference genome and provides the precise sequence and genomic coordinates of each TE copy for each genome. We showcase here the potential of this tool on TE insertions shared among 42 Brachypodium distachyon genomes and compared our results against existing tools to demonstrate its better efficiency. With this tool, we were able to date two major TE bursts corresponding to major climate events: 22 kya during the Last Glacial Maximum and 10 kya during the Holocene, showing a potential link between environmental stress and TE activity.

genomics↗

bioRxiv2022

Preclinical efficacy, safety, and immunogenicity of PHH-1V, a second-generation COVID-19 vaccine, in non-human primates

SARS-CoV-2 emerged in December 2019 and quickly spread worldwide, continuously striking with an unpredictable evolution. Despite the success in vaccine production and mass vaccination programmes, the situation is not still completely controlled, and therefore accessible second-generation vaccines are required to mitigate the pandemic. We previously developed an adjuvanted vaccine candidate coded PHH-1V, based on a heterodimer fusion protein comprising the RBD domain of two SARS-CoV-2 variants. Here, we report data on the efficacy, safety, and immunogenicity of PHH-1V in cynomolgus macaques. PHH-1V prime-boost vaccination induces high levels of RBD-specific IgG binding and neutralising antibodies against several SARS-CoV-2 variants, as well as a balanced Th1/Th2 cellular immune response. Remarkably, PHH-1V vaccination prevents SARS-CoV-2 replication in the lower respiratory tract and significantly reduces viral load in the upper respiratory tract after an experimental infection. These results highlight the potential use of the PHH-1V vaccine in humans, currently undergoing Phase III clinical trials.

immunology↗

bioRxiv2019

On the relationship between LFP beta oscillation amplitude and firing rate of individual neurons in monkey motor cortex

It is a long-standing controversial issue whether an intrinsic relationship between the local field potential (LFP) beta oscillation amplitude and the spike rate of individual neurons in the motor cortex exists. Beta oscillations are prominent in motor cortical LFPs, and their relationship to the local neuronal spiking activity has been extensively studied. Many studies demonstrated that the spikes of individual neurons lock to the phase of LFP beta oscillations. However, the results concerning whether there is also an intrinsic relationship between the amplitude of LFP beta oscillations and the firing rate of individual neurons are contradictory. Some studies suggest a systematic mapping of spike rates onto LFP beta amplitude, and others find no systematic relationship. To resolve this controversy, we correlated the amplitude of LFP beta oscillations recorded in motor cortex of two male macaque monkeys with spike counts of individual neurons during visuomotor behavior, in two different manners. First, in an analysis termed task-related correlation, data obtained across all behavioral task epochs was included. These task-related correlations were frequently significant, and in majority of negative sign. Second, in an analysis termed trial-by-trial correlation, only data from a fixed pre-cue task epoch was included, and correlations were calculated across trials. Such trial-by-trial correlations were weak and rarely significant. We conclude that there is no intrinsic relationship between the firing rate of individual neurons and LFP beta oscillation amplitude in macaque motor cortex, beyond each of these signals being modulated by external factors such as the behavioral task.\n\nSIGNIFICANCE STATEMENTWe addressed the long-standing controversial issue of whether there is an intrinsic relationship between the local field potential (LFP) beta oscillation amplitude and the spike rate of individual neurons in the motor cortex. In two complementary analyses of data from macaque monkeys, we first demonstrate that the unfolding behavioral task strongly affects both the LFP beta amplitude and the neuronal spike rate, creating task-related correlations between the two signals. However, when limiting the influence of the task, by restricting our analysis to a fixed task epoch, correlations between the two signals were largely eliminated. We conclude that there is no intrinsic relationship between the firing rate of individual neurons and LFP beta oscillation amplitude in motor cortex.

neuroscience↗