Biology subjects

Fournier-Level, A.

Publications and source records attributed to Fournier-Level, A..

14 recordsLinked to original sources

bioRxiv2026

Historical genomes reveal scale-dependent predictability of climate adaptation

Predicting evolution remains a central challenge in biology. Contemporary spatial patterns are increasingly used as space-for-time proxies to forecast evolutionary responses to environmental change, yet the reliability of such predictions--and whether it varies among biological scales--remains unclear. Using historical and contemporary genomes of the invasive weed Ambrosia artemisiifolia--spanning the species' native range, invasions on two continents and nearly two centuries--we show that genomically predicted flowering-time clines remained stable in the native range while introduced populations re-evolved them. Haploblocks--likely structural variants--were likewise temporally stable in the native range, and two showed striking parallel evolution across all three ranges. Climate-associated SNPs with the strongest contemporary clines showed the greatest temporal change, with limited and variable parallelism among introduced ranges. Together, these results suggest adaptive evolution is partly predictable even when individual genomic trajectories remain flexible and contingent, with predictability emerging most clearly at the level of polygenic traits and large structural variants.

evolutionary biology↗

bioRxiv2026

Selection shapes the evolution of genome size in a globally invasive plant

O_LIBiological invasions provide powerful natural experiments for understanding how genome architecture responds to novel climatic environments. Transposable elements (TEs) can rapidly restructure genomes, yet their role in adaptive genome size evolution during invasion remains poorly understood. C_LIO_LIHere, we examined genome size and TE abundance in 439 individuals of globally invasive common ragweed (Ambrosia artemisiifolia L.) across native (North American) and invasive (European, Australian) ranges. By integrating whole-genome resequencing, flow cytometry, and trait versus genetic differentiation comparison (QST-FST), we tested whether genome size evolution is shaped by selection, climate, and life-history traits. C_LIO_LIGenome size was significantly larger in Australian genotypes, driven by increased TE and rRNA (ribosomal RNA) abundance. Crucially, trait versus genetic differentiation comparison provided evidence of divergent selection on genome size in North American and European populations, but not in Australia. Genome size was correlated with mean annual temperature (MAT) across all ranges, linking genomic traits to environmental variables. C_LIO_LIGenome size evolution during invasion can be rapid, adaptive, and range-specific, with TE-driven genome expansion emerging as a potential genomic response to the demographic and environmental pressures accompanying colonization of novel environments. C_LI

evolutionary biology↗

bioRxiv2025

A non-coding SNP in ELF3 alters expression of ELF3β and confers adaptation of Arabidopsis to a continental climate

Circadian clocks are biological timekeepers that influence most aspects of plant biology and allow organisms to predict and adapt to daily and seasonal environmental cycles. In particular, the important role of circadian clocks in phenology has led to numerous examples of both functional variation in circadian clock genes within natural and domesticated plant populations. To assess variation of circadian rhythms in natural Arabidopsis populations, we have phenotyped 287 accessions using a seedling transformation protocol with a circadian luciferase reporter. A genome wide association study of circadian period identified multiple single nucleotide polymorphisms (SNPs) in the core clock gene EARLY FLOWERING 3 (ELF3). We identified three ELF3 haplogroups that are associated with seasonal variability in temperature found in continental climates and found strong evidence of a selective sweep coinciding with the most recent de-glaciation period in Europe. One of the SNPs is located within intron 2 of ELF3 in the region upstream of an alternative transcription start site affecting expression of a shorter ELF3{beta} transcript. Our results indicate the important role of subtle variation in a core circadian clock gene in adaptation to changing climate.

plant biology↗

bioRxiv2025

Thermotolerance in Chia (Salvia hispanica L.) is Mediated by Rapid Heat-Induced Transcriptomic Reprogramming and Lipid Remodelling in Leaves

Heat stress poses a significant threat to crop productivity; however, the thermotolerance mechanisms in underutilised oilseed crops, such as chia (Salvia hispanica L.), remain poorly understood. Despite the growing interest in chia as a rich source of {omega}-3 fatty acids, its molecular response to heat stress, particularly in vegetative tissues, has not been explored. We conducted transcriptomic and lipidomic profiling to examine how chia leaves respond to short-term (3 h) and prolonged (27 h) heat stress, followed by recovery under ambient conditions. Heat stress induced differential expression in over 20% of transcripts in chia leaves, with distinct patterns involving Ca{superscript 2} signalling, heat shock factors, and other biological pathways contributing to cellular homeostasis. Gene expression and lipid profiles in chia leaves responded dynamically to both short-term (3 h) and prolonged (27 h) heat stress (38{degrees}C/20{degrees}C). An almost complete return to baseline was observed, with all but 0.3% of heat-responsive genes reverting to control expression levels after 24 h. Our analysis confirms the role of Ca{superscript 2}-mediated signalling pathways and molecular chaperones, including heat shock proteins and heat shock factors, which have been previously shown to contribute to maintaining cellular function during heat stress in other plant species. Among 287 annotated lipid species, TGs exhibited the most significant and reversible changes (>2-fold), suggesting their involvement in membrane remodelling. Our findings reveal adaptive mechanisms in chia that may open avenues for enhancing thermotolerance in other heat-sensitive oilseed crops. SIGNIFICANCE STATEMENTUnderstanding how crops respond to heat stress is crucial as global temperatures rise. This study indicates that in chia (Salvia hispanica), pathways responding to heat stress, like calcium signalling and heat shock proteins, are rapidly activated, and leaf triacylglycerol levels rise under heat stress before returning to baseline during recovery. By demonstrating near-complete recovery of gene expression following heat exposure, these findings highlight mechanisms of thermotolerance that may support improved stress tolerance in other crops.

plant biology↗

bioRxiv2024

Rapid parallel adaptation in distinct invasions of Ambrosia artemisiifolia is driven by large-effect structural variants

When introduced to multiple distinct ranges, invasive species provide a compelling natural experiment for understanding the repeatability of adaptation. Ambrosia artemisiifolia is an invasive, noxious weed and chief cause of hay fever. Leveraging over 400 whole-genome sequences spanning the native range in North America and two invasions in Europe and Australia, we inferred demographically distinct invasion histories on each continent. Despite substantial differences in genetic source and effective population size changes during introduction, scans of both local climate adaptation and divergence from the native range revealed genomic signatures of parallel adaptation between invasions. Disproportionately represented among these parallel signatures are 37 large haploblocks - indicators of structural variation - that cover almost 20% of the genome and exist as standing genetic variation in the native range. Many of these haploblocks are associated with traits important for adaptation to local climate, like size and the timing of flowering, and have rapidly reformed native range clines in invasive ranges. Others show extreme frequency divergence between ranges, consistent with a response to divergent selection on different continents. Our results demonstrate the key role of large-effect standing variants in rapid adaptation during range expansion, a pattern that is robust to diverse invasion histories.

genomics↗

bioRxiv2024

Trait genetic architecture and population structure determine model selection for genomic prediction in natural Arabidopsis Thaliana populations.

Genomic prediction applies to a wide range of agronomically relevant traits, with distinct ontologies and genetic architectures. Selecting the most appropriate model for the distribution of genetic effects and their associated allele frequencies in the training population is crucial. Linear regression models are often preferred for genomic prediction. However, linear models may not suit all genetic architectures and training populations. Machine Learning approaches have been proposed to improve genomic prediction owing to their capacity to capture complex biology including epistasis. However, the applicability of different genomic prediction models, including non-linear/non-parametric approaches, have not been rigorously assessed across a wide variety of plant traits in natural outbreeding populations. This study evaluates genomic prediction sensitivity to trait ontology and the impact of population structure on model selection and prediction accuracy. Examining 36 quantitative traits measured for 1000+ natural genotypes of the model plant Arabidopsis thaliana, we assessed the performance of penalised regression, random forest, and multilayer perceptron at producing genomic predictions. Regression models were generally the most accurate, except for biochemical traits where random forest performed best. We link this result to the genetic architecture of each trait - notably that biochemical traits have simpler genetic architecture than macroscopic traits. Moreover, complex macroscopic traits, particularly those related to flowering and yield, were strongly correlated to population structure, while molecular traits were better predicted by fewer, independent markers. This study highlights the relevance of machine learning approaches for simple molecular traits and underscores the need to consider ancestral population history when designing training samples. Article summaryMachine learning and linear models were tested for genomic prediction of multiple traits in the model plant Arabidopsis thaliana. We associate the performance of genomic prediction models to trait ontology, finding machine learning approaches applicable to biochemical traits, and linear models best for macroscopic traits. We link this result to the genetic architecture of each trait and patterns of selection in the association panels ancestral population, thus underscoring the relevance of these two sensitivities to genomic prediction in plant breeding.

genetics↗

bioRxiv2024

Controlling the frequency dynamics of homing gene drives for intermediate outcomes

Gene drives have enormous potential for solving biological issues by forcing the spread of desired alleles through populations. However, to safeguard from the potentially irreversible consequences on natural populations, gene drives with intermediate outcomes that neither fixate nor get removed from the population are of outstanding interest. To elucidate the conditions leading to intermediate gene drive frequency, a stochastic, individual allele-focused gene drive model accessible was developed to simulate the diffusion of a homing gene drive in a population. The frequencies of multiple alleles at a locus targeted by a gene drive were tracked under various scenarios. These explored the effect of gene drive conversion efficiency, strength and frequency of resistance alleles, presence and strength of a fitness cost for the gene drive, its dominance and the level of inbreeding. Four outcomes were consistently observed: Fixation, Loss, Temporary and Equilibrium. The latter two are defined by the frequency of the gene drive peaking then crashing or plateauing, respectively. No single variable determined the outcome of a drive, instead requiring a combination of variables. The difference between the conversion efficiency and resistance level differentiated the Temporary and Equilibrium outcomes. The frequency dynamics of the gene drive within outcomes varied extensively, with different variables driving this dynamics between outcomes. These simulation results highlight the possibility of fine-tuning gene drive outcomes and compensating through biotechnological design constraint imposed by population features. To that end, we provide a web application implementing our model which will guide the safer design of gene drives able to achieve a range of controllable outcome tailored to population management needs.

synthetic biology↗

bioRxiv2024

A basic framework governing splice-site choice in eukaryotes

Changes in splicing are observed between cells, tissues, organs, individuals, and species. These changes can mediate phenotypic variation ranging from flowering time differences in plants to genetic diseases in humans. However, the genomic determinants of splicing variation are largely unknown. Here, we quantified the usage of individual splice-sites and uncover extensive variation between individuals (genotypes) in Arabidopsis, Drosophila and Humans. We used this robust quantitative measure as a phenotype and mapped variation in splice-site usage using Genome-Wide Association Studies (GWAS). By carrying out more than 130,000 GWAS with splice-site usage phenotypes, we reveal genetic variants associated with differential usage of specific splice-sites. Our analysis conclusively shows that most of the common, genetically controlled variation in splicing is cis and there are no major trans hotspots in any of the three analyzed species. High-resolution mapping allowed us to determine genome-wide patterns that govern splice-site choice. We reveal that the variability in the intronic hexamer sequence (GT[N]4 or [N]4AG) differentiates intrinsic splice-site strength and is among the primary determinants of splice-site choice. Experimental analysis validates the primary role for intronic hexamer sequences in conferring splice-site decisions. Transcriptome analyses in diverse species across the tree of life reveals that hexamer rankings explains splice-site choices from yeast to plants to humans, forming the basic framework of the splicing code in eukaryotes.

genetics↗

bioRxiv2024

A circadian transcriptional sub-network and EARLY FLOWERING 3 control timing of senescence and grain nutrition in bread wheat

Circadian clocks control daily and seasonal timing of physiology and development. Because of their influence on photoperiodic flowering, variants in circadian clock genes have been selected for phenology during domestication of cereal crops. To explore the potential impact of this genetic variation on circadian-regulated traits, we investigated the relationship of the circadian clock and leaf senescence in hexaploid bread wheat. Phenotyping of a collection of elite wheat cultivars identified significant variation in circadian rhythms which was associated with timing of senescence and nutrient mobilisation efficiency. RNA sequencing revealed substantial reorganisation of the circadian-regulated transcriptome during senescence and a transcriptional sub-network representing a link between the circadian oscillator and regulators of leaf senescence. We used genotypes of multiple circadian clock genes to assign cultivars to chronotypes, which could be used to predict circadian-regulated phenotypes. This identified a deletion variant of EARLY FLOWERING 3-D1 (ELF3-D1) attributed to a phenology locus, Earliness per se (Eps-D1), and we used near-isogenic lines (NILs) to show that it affects timing of senescence and grain protein content (GPC). Thus, there are potential consequences of circadian clock genes selected for phenology on other valuable crop traits.

plant biology↗

bioRxiv2023

Comparative Genomics Points to Tandem Duplications of SAD Gene Clusters as Drivers of Increased ω-3 Content in S. hispanica Seeds

O_LIA high-quality chromosome-level reference genome of S. hispanica was assembled and analysed. C_LIO_LIAncestral whole-genome duplication events have not promoted the high -linolenic acid content in S. hispanica seeds C_LIO_LITandem duplication of six stearoyl-ACP desaturase genes is a plausible cause for high {omega}-3 content in chia seeds. C_LI Salvia hispanica L. (chia) is an abundant source of {omega}-3 polyunsaturated fatty acids (PUFAs) that are highly beneficial to human health. The genomic basis for this accrued PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica (321.5 Mbp). The highly contiguous 321.5Mbp genome assembly, which covers all six chromosomes enabled the identification of 32,922 protein coding genes. Two whole-genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high -linolenic acid (ALA, {omega}-3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl-acyl carrier protein (ACP) desaturase (ShSAD) gene family, is the main driver of the abundance of {omega}-3 PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help leveraging advanced genome editing techniques and will greatly support breeding efforts for improving {omega}-3 content in other oil crops.

genomics↗

bioRxiv2023

compare_genomes: a comparative genomics workflow to streamline the analysis of evolutionary divergence across genomes

SummaryThe dawn of cost-effective genome assembly is enabling deep comparative genomics to address fundamental evolutionary questions by comparing the genomes of multiple species. However, comparative genomics analyses often deploy multiple, often purpose-built frameworks, limiting their transferability and replicability. Here, we developed compare_genomes, a transferable and extensible comparative genomics workflow package which streamlines the identification of orthologous families within and across genomes and tests for the presence of several mechanisms of evolution (gene family expansion or contraction and substitution rates within protein-coding sequences). Availability and ImplementationThe workflow is available for Linux, written as a Nextflow workflow which calls established genomics and phylogenetics tools to streamline the analysis and visualisation of genome divergence. This workflow is freely available at https://github.com/jeffersonfparil/compare_genomes, distributed under the GNU General Public License version 3 (GPLv3). ContactCorresponding author: Jeff Paril jeff.paril@unimelb.edu.au. Queries and issues regarding the implementation can be submitted on the issue page of the github repository: https://github.com/jeffersonfparil/compare_genomes/issues. Supplementary informationSynonymous to non-synonymous (Ka/Ks) nucleotide substitution ratio plots for the example data set are found in the github repository.

bioinformatics↗

bioRxiv2022

Rounding up the annual ryegrass genome: high-quality reference genome of Lolium rigidum

The genome of the major agricultural weed species, annual ryegrass (Lolium rigidum) was assembled, annotated and analysed. Annual ryegrass is a major weed in wheat cropping, and has the remarkable capacity to evolve resistance to herbicides with various modes of action. The chromosome-level assembly was achieved using short- and long-read sequencing in combination with Hi-C mapping. The assembly size is 2.44Gb with N50=361.79Mb across 1,764 scaffolds where the seven longest sequences correspond to the seven chromosomes. Genome completeness assessed through BUSCO returned a 99.8% score for complete (unique and duplicated) and fragmented genes using the Viridiplantae set. We found evidence for the expansion of herbicide resistance-related gene families including detoxification genes. The reference genome assembly of L. rigidum is pivotal for the management of this highly problematic weed species which leverages genomic tools to devise new control options.

genomics↗

bioRxiv2019

The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations of Drosophila melanogaster

Imidacloprid, the worlds most utilised insecticide1, has raised considerable controversy due to its harmful effects on non-pest species2-6 and there is increasing evidence showing that insecticides have become the primary selective force in many insect species7-14. The genetic response to insecticides is heterogeneous across population and environment15-17, leading to more complex patterns of genetic variation than previously thought. This motivated the investigation of imidacloprid resistance at different temperatures in natural populations of Drosophila melanogaster originating from four climate extremes replicated across two continents. Population and quantitative genomic analysis, supported by functional tests, demonstrated a polygenic basis to resistance and a major trade-off with thermotolerance. Reduced genetic differentiation at resistance-associated loci indicate enhanced gene flow at these loci. Resistance alleles showed stronger evidence of positive selection in temperate populations compared to tropical populations. Polygenic architecture and ecological factors should be considered when developing sustainable management strategies for both pest and beneficial insects.

evolutionary biology↗

bioRxiv2017

Multiple P450s And Variation In Neuronal Genes Underpins The Response To The Insecticide Imidacloprid In A Population Of Drosophila melanogaster

Insecticide resistance is an economically important example of evolution in response to intense selection pressure. Here, the genetics of resistance to the neonicotinoid insecticide imidacloprid is explored using the Drosophila Genetic Reference Panel, a collection of inbred Drosophila melanogaster genotypes derived from a single population in North Carolina. Imidacloprid resistance varied substantially among genotypes, and more resistant genotypes tended to show increased capacity to metabolize and excrete imidacloprid. Variation in resistance level was then associated with genomic and transcriptomic variation, implicating several candidate genes involved in central nervous system function and the cytochrome P450s Cyp6g1 and Cyp6g2. CRISPR-Cas9 mediated removal of Cyp6g1 suggested that it contributed to imidacloprid resistance only in backgrounds where it was already highly expressed. Cyp6g2, previously implicated in juvenile hormone synthesis via expression in the ring gland, was shown to be expressed in metabolically relevant tissues of resistant genotypes. Cyp6g2 overexpression was shown to both metabolize imidacloprid and confer resistance. These data collectively suggest that imidacloprid resistance is influenced by a variety of previously known and unknown genetic factors.

genetics↗