Biology subjects

Gibert, A.

Publications and source records attributed to Gibert, A..

11 recordsLinked to original sources

bioRxiv2026

Asymmetric inter-kingdom gene transfer and a horizontal transposon invasion in a powdery mildew fungus

Horizontal DNA transfer can introduce new genetic material into eukaryotic genomes, but how often recent transfers occur between multicellular lineages and what happens to transferred DNA after integration remain poorly understood. Plants and fungi provide a powerful system to address these questions because of their long-standing and intimate ecological associations. Here, we performed an annotation-independent, bidirectional whole-genome screen across 418 plant and 1,081 fungal genomes and identified 22 high-confidence recent horizontal transfer events. Twenty-one involved fungal DNA acquired by plants and were concentrated in bryophytes and Pooideae grasses, revealing pronounced directional and phylogenetic biases. The evolutionary fate of transferred DNA differed across recipient lineages. In Pooideae, fungal-derived genes underwent duplication, structural remodeling and expression divergence, and showed copy-number variation within species. In Marchantia polymorpha, transferred genes remained mostly single-copy but displayed presence-absence variation and ongoing loss among subspecies and natural accessions. In the opposite direction, we identified a plant-derived DNA transposon integrated into the genome of the tomato powdery mildew fungus Pseudoidium neolycopersici. Following transfer, this element remained active and generated a derived family of miniature inverted-repeat transposable elements that expanded to 172 copies. Recent detectable DNA transfer between plants and fungi is therefore uncommon and strongly asymmetric, but transferred sequences can remain highly dynamic after integration. Their subsequent loss, duplication, structural and regulatory diversification, or transposon-driven amplification links rare cross-kingdom acquisition events to ongoing genome variation and diversification.

evolutionary biology↗

bioRxiv2026

Life-history traits may buffer genetic erosion under isolation in mountain sky-island systems

Sky-island systems provide natural case studies for understanding how geography and Quaternary history shape genomes, phenotypes and life-history traits in mountain endemics. We investigated Xatartia scabra (Apiaceae), a monotypic scree specialist plant species restricted to sky-island summits in the eastern Pyrenees, by integrating population genomics with abiotic condition-informed distribution modeling. Using a ddRAD-seq-like protocol (nGBS), we genotyped 125 individuals (21,970 SNPs), and applied species distribution modeling to identify suitable environmental conditions from the Last Glacial Maximum to 2100. Genetic analyses revealed unexpected genetic "resilience", with moderate genome-wide diversity (HE = 0.17, Ho = 0.15) and low inbreeding (FIS = 0.07), despite small census sizes and strong isolation. Significant overall genetic differentiation (FST = 0.16), with pronounced summit-level structure and strong isolation-by-distance, supports deep valleys as barriers to gene flow. Abiotic niche reconstructions recovered extensive Heinrich Stadial 1 connectivity (+ 58,4% relative to present), followed by postglacial loss of suitable habitats at lower elevations and increasing fragmentation; projections under climate change forecast contraction (-61,2%, relative to present) of climatic suitability, expected to intensify drift in small, isolated populations. Demographic inferences align with this narrative, indicating postglacial decline in effective population sizes. Taken together, genetic, climatic, and demographic evidence supports a transition from historically connected lowland corridors to modern sky islands where distance-limited drift dominates. The maintenance of moderate genetic diversity and low inbreeding under strong isolation suggests that X. scabra may have evolved life-history strategies including outcrossing and monocarpy that allow limiting genetic erosion in such extreme and fragmented environments.

genomics↗

bioRxiv2026

A cryptic hybrid zone reveals the genomic basis of flower colour variation in a plant with a large and complex genome

Flower colour is known to be a classic magic trait, undergoing divergent selection pressures exerted by distinct pollinators and involved in reproductive isolation. However, variation at this trait may also results from other eco-evolutionary factors whose interpretation requires throughout context-specific analyses. Here, we investigated the eco-evolutionary causes of pink- and yellow-flowered morphs in Pedicularis comosa where their parapatric ranges form a contact zone in the East of the Pyrenees Mountains. First, we generated a near-chromosome-scale reference genome assembly for this species. We then used a Genotyping By Sequencing approach to infer patterns of genetic diversity and differentiation between populations and morphs at a total of 158 individuals from 11 localities. We found that neutral genetic structure is primarily consistent with geography rather than with colour. However, admixture analyses and clines suggest the existence of a cryptic hybrid zone between morphs. Outlier detection methods and examination of locus-by-locus cline features, then allowed to pinpoint candidate loci to explain colour variation. To gain insight into the functional aspects of these loci, we finally analysed floral transcriptomes and quantified pigments using Liquid Chromatography coupled with Mass Spectrometry (LC-MS) and confirmed the involvement of key genes in the anthocyanin metabolic pathway (e.g. DFR, FLS) and associated pigments (e.g. cyanidin and delphinidin). Our results show that implementing a highly integrative multi-omic approach can allow unraveling the genetic basis and the eco-evolutionary significance of adaptive traits with even very limited previous knowledge, on species with large and complex genomes.

evolutionary biology↗

bioRxiv2026

Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys)

Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last five million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as sexual swindling. However, the rapid and substantial diversification of this genus, combined with its capacity for hybridisation and large genome size, poses significant challenges in addressing its systematics. We used phylotranscriptomics as a genome complexity reduction technique to infer the phylogenetic relationships among Ophrys main lineages. More than seven thousand gene trees enabled us to determine the relative contributions of gene flow and incomplete lineage sorting (ILS) in Ophrys evolution. First, we propose a new phylogenetic hypothesis for the genus with an unprecedented resolution that largely confirms the relationships between the main Ophrys lineages, but also provides new insights within each sub-genera. By combining phylogenetic network inference with introgression analyses based on gene tree topologies and branch lengths, we then show that the numerous phylogenetic incongruences among gene tree topologies result from a pervasive background of ILS, over which stand out several well-supported, ancient and potentially adaptive gene flow events between lineages. These major gene flow events provide a new perspective on the evolution of the Ophrys genus and its pollination, questioning previous hypotheses inferred without considering its reticulate evolution, and providing a better understanding of discrepancies observed among previous phylogenetic studies of the genus.

evolutionary biology↗

bioRxiv2025

Role of methylation and siRNA on differential allelic expression in a hybrid of distantly related citrus species.

DNA methylation plays a central role in the regulation of gene expression. In plants, methylation occurs in the CG, CHG and CHH contexts, via distinct DNA methyltransferases including MET1, CMT3 and the RNA-directed DNA Methylation (RdDM) pathway via DRM2. In interspecific hybrids, these epigenetic mechanisms are confronted to a mixed small RNA population and two subgenomes harbouring specific methylation patterns, therefore generating unique expression profiles. The aim of this work was to understand these regulations by analysing gene expression, DNA methylation and small RNAs in a Citrus hybrid resulting from the cross between C. reticulata (mandarin) and C. australasica (finger lime). Haplotype-resolved subgenomes assembly identified hundreds of allele-specifically expressed genes. Asymmetric reprogramming of methylation was observed, in particular an increase in CHH in C. australasica haplotype. Surprisingly, CHH methylation, usually associated with gene silencing, was correlated here with increased expression, but also 24nt small RNA populations at their promoter regions. Similar analyses of the parental lines and other citrus species suggest the correlation between CHH methylation-enriched promoter and high expression level is not due to the hybridization, but seem to be generally true for all citrus. These observations suggest that, in citrus fruit, RdDM could activate transcription. This work also provides a full pipeline to analyse the expression profiles and DNA methylation in complex hybrids, which could be crucial for anticipating varieties resistant to diseases and the current threats affecting citriculture such as the Huanglongbing disease.

plant biology↗

bioRxiv2025

Non-invasive eDNA reveals the ecological and genetic status of the Western Capercaillie (Tetrao urogallus aquitanicus) in the Eastern Pyrenees

The Anthropocene era is expected to bring about significant biodiversity and habitat loss for many species. These geographical changes, whether driven by climatic or anthropogenic factors, are likely to lead to considerable alterations in population size, structure, and genetic diversity. Monitoring natural populations is therefore essential to assess these impacts and enable informed conservation strategies for threatened species. The Western Capercaillie (Tetrao urogallus, L. 1758) has a widespread distribution in Boreal forests but fragmented in mountainous regions of the Palearctic, and is locally threatened by climate change, habitat destruction, and human disturbance. Our study focused on the eastern population of the subspecies T. u. aquitanicus, which is endemic to the Pyrenees mountains. The monitoring of this population has relied on direct methods and no genetic information had been generated so far. Here, we conducted a molecular study based on 229 non-invasive samples (faeces) to assess the ecological and genetic status of local population in the Catalan Nature Reserves of the Pyrenees-Orientales (Occitanie region, France). At the individual level, we assessed multi-locus genotypes, sexing, levels of inbreeding, stress level (Fecal Corticosterone Metabolites; FCMs) and diet. At the population level, we assessed sex ratio, genetic diversity and structure. We identified 62 individuals with a balanced sex ratio and estimated a census size of 79 individuals [95%CI = 68-92] in the study area. Genetic diversity was low and suggested significant inbreeding levels. FCM levels were lower in birds of areas considered as disturbed by humans and metabarcoding approach indicated a geographical structuring of diet composition at the reserve scale, with individuals exhibiting feeding behavior upon only one or few plant species. Our estimate of population census size was higher with figures assessed from lek counts, and the genetic approach provided additional insights on this population, establishing a baseline that will support conservation management plans.

ecology↗

bioRxiv2024

Epigenetic memory of temperature during somatic embryo maturation in 2-year-old maritime pine trees

Embryogenesis is a brief but potentially critical phase in the tree life cycle for adaptive phenotypic plasticity. Using somatic embryogenesis in maritime pine, we found that temperature during the maturation phase affects embryo development and post-embryonic tree growth for up to three years. We examined whether this somatic stress memory could stem from temperature- and/or development-induced changes in DNA methylation. To do this, we developed a 200 Mb custom sequence capture bisulfite analysis of genes and promoters to identify differentially methylated cytosines (DMCs) between temperature treatments (18, 23, and 28{degrees}C) and developmental stages (immature and cotyledonary embryos, shoot apical meristem of 2-year-old plants) and investigate if these differences can be mitotically transmitted from embryonic to post-embryonic development (epigenetic memory). We revealed a high prevalence of temperature-induced DMCs in genes (8-14%) compared to promoters (less than 1%) in all 3 cytosine contexts. Developmental DMCs showed a comparable pattern but only in the CG context, and with a high trend towards hypo-methylation, particularly in the promoters. A high percentage of DMCs induced by developmental transitions were found memorized in genes (up to 45-50%) and promoters (up to 90%). In contrast, temperature-induced memory was lower and confined to genes after both embryonic (up to 14%) and post-embryonic development (up to 8%). Using stringent criteria, we identified ten genes involved in defense responses and adaptation, embryo development and chromatin regulation that are candidates for the establishment of a persistent epigenetic memory of temperature sensed during embryo maturation in maritime pine. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=131 HEIGHT=200 SRC="FIGDIR/small/600784v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@17a70f1org.highwire.dtl.DTLVardef@18d186borg.highwire.dtl.DTLVardef@3e27f5org.highwire.dtl.DTLVardef@b15348_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2024

Contrasting patterns of differentiation among three taxa of the rapidly diversifying orchid genus Ophrys sect. Insectifera (Orchidaceae) where their range overlap

In rapidly diversifying groups, taxa defined on the basis of typological criteria can be difficult to support with genetic data. The diversity observed in the insect-mimicking orchid genus Ophrys perfectly illustrates this situation; among 400 described species only 9-10 lineages are detectable by genetic markers such as nrITS. The three taxa described in the Ophrys insectifera group: O. insectifera, O. subinsectifera and O. aymoninii, can be clearly distinguished by their flowers, which have evolved different phenotypes as a result of adaptation to specific pollinator insect species from three different families. However, genetic differentiation between these three taxa has never been really supported by population genetic data and their taxonomic status is still debated. Using population genomic approaches, we found a clustering consistent with the existence of three genetic entities where the geographic distributions of the three taxa overlap. Two of these clusters correspond to France populations of the widespread O. insectifera and the micro-endemic O. aymoninii. However, the last cluster grouped together all the Iberian individuals, suggesting that individuals phenotypically identified as either O. insectifera or O. subinsectifera are genetically weakly differentiated there. Populations of the two pairs of taxa thus may have experienced different patterns of inter-specific gene flow.

evolutionary biology↗

bioRxiv2024

Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation processes

SummaryO_LIAdaptive radiation in Ophrys orchids leads to complex floral phenotypes that vary in scent, color and shape. C_LIO_LIUsing a novel pipeline to quantify these phenotypes, we investigated trait divergence at early stages of speciation in six populations of Ophrys aveyronensis experiencing recent allopatry. By integrating different genetic/genomic techniques, we investigated: (i) variation and integration of floral components (scent, color and shape), (ii) phenotypes and genomic regions under divergent selection, and (iii) the genomic bases of trait variation. C_LIO_LIWe identified a large genomic island of divergence, associated with phenotypic variation in particular in floral odor. We detected potential divergent selection on macular color, while convergent selection was suspected on floral morphology and for several volatile olfactive compounds. We also identify candidate genes involved in anthocyanin and in steroid biosynthesis pathways associated with standing genetic variation in color and odor. C_LIO_LIThis study sheds light on early differentiation in Ophrys, revealing patterns that often become invisible over time, i.e., the geographic mosaic of traits under selection and the early appearance of strong genomic divergence. It also supports a crucial genomic region for future investigation and highlights the value of a multifaceted approach in unraveling speciation within taxa with large genomes. C_LI

evolutionary biology↗

bioRxiv2023

Climate change promoted allopatric divergence and explains the current disjunct geographic distribution of the Ophrys aveyronensis species complex (Orchidaceae)

AimSpecies with disjunct geographic distributions provide natural opportunities to investigate incipient or recent allopatric divergence. The combination of both genetic and ecological data may be fruitful to decipher the causes of such pattern: i) actual vicariance, ii) successful colonization from one source range to a new range (dispersal, biological introduction) or iii) parallel convergent evolution. LocationSouthern France and Northern Spain. TaxonThe bee orchid Ophrys aveyronensis (and its two recognized subspecies O. a. subsp. aveyronensis and O. a. subsp. vitorica) displays a disjunct geographic distribution with two subranges separated by 600 km on both sides of the Pyrenees Mountains. MethodsThrough a combination of population genomics and Ecological Niche Modelling (ENM), we investigated the causes of this intriguing biogeographic pattern. ResultsThe population genomic data demonstrate that all the studied populations exhibit similar patterns of genetic diversity and dramatic decrease in effective size compared to the ancestral population. Significant genetic differentiation and reciprocal monophyly exist between populations of the two subranges of O. aveyronensis, despite a very recent divergence time as young as ca. 1500 generations ago. Moreover, (paleo-)ecological Niche Modelling analyses support that the disjunct geographic distribution of the O. aveyronensis is consistent with a range split of a broad ancestral range, contraction and distinct longitudinal and latitudinal shifts in response to climate warming during the Holocene. Main ConclusionThe congruence of the results obtained from both population genomics and ENM approaches documents how very recent continental allopatric divergence initiated speciation in this system. Ophrys aveyronensis provides a promising opportunity to study the onset of reproductive isolation and parallel evolution following an initial stage of geographic separation in a group with high diversification rate.

evolutionary biology↗

bioRxiv2020

Whole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae)

Some lineages of the Orchid genus Ophrys exhibit among the highest diversification rates reported so far. As a consequence of a such intense and rapid evolution, the systematics and the taxonomy of this genus remains unclear. A hybrid assembly approach based-on long- and short-read genomic data allowed us to outperform classical methods to successfully assemble whole plastid genomes for two new Ophrys species: O. aymoninii and O. lutea. Along with three other previously Ophrys plastid genome sequences, we then reconstructed the first whole plastome-based molecular phylogeny including representatives of the three mains recognized Ophrys lineages. Our results support the placement of the O. insectifera clade as sister group of non-basal Ophrys rather than a basal position. Our findings corroborate recent results obtained from genomic data (RAD-seq and transcriptomes) but contrast with previous ones. These results therefore confirm that molecular phylogenetic hypotheses based on a limited number of loci (e.g. nrITS, matK, rbcL) may have provided a biased picture of phylogenetic relationships within Ophrys and possibly other plant taxa.

evolutionary biology↗