Biology subjects

Lesur, I.

Publications and source records attributed to Lesur, I..

8 recordsLinked to original sources

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The authors have withdrawn this manuscript because the sequenced individual was misidentified as Quercus canariensis following a label swap and was subsequently confirmed to be Quercus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

A higher load of deleterious mutations has a detrimental effect on tree growth in maritime pine

A high proportion of deleterious mutations in the genome is predicted to cause a reduction in fitness known as genetic load. In plants, most studies focus on how detrimental mutations increase as a consequence of population bottlenecks, for instance in cultivated species as a negative outcome of domestication or at the margin of species ranges. However, the actual adverse effect of genetic load on individual phenotypes remains little characterised, especially in wild plant species with large populations and long lifespans. We estimated genetic load based on genomic data in populations of the conifer maritime pine (Pinus pinaster, Ait.), and examined its association with phenotypic traits related to growth, phenology, and water-use efficiency measured under common garden conditions. Our results revealed a strong negative correlation between genetic load and tree height on the Mediterranean island of Corsica, thus suggesting a negative cumulative effect of deleterious mutations on tree growth at the regional scale. Our study is one of the first to experimentally demonstrate adverse phenotypic effects (reduced tree growth) of genetic load in a long-lived plant.

evolutionary biology↗

bioRxiv2023

Whole-genome screening for near-diagnostic genetic markers for white oak species identification in Europe

ContextIdentifying species in the European white oak complex has been a long standing concern in taxonomy, evolution, forest research and management. Quercus petraea, Q. robur, Q. pubescens and Q. pyrenaica are part of this species complex in western temperate Europe and hybridize in mixed stands, challenging species identification. AimsOur aim was to identify diagnostic single nucleotide polymorphisms (SNPs) for each of the four species that are suitable for routine use and rapid diagnosis in research and applied forestry. MethodsWe first scanned existing whole-genome and target-capture data sets in a reduced number of samples (training set) to identify candidate diagnostic SNPs, ie genomic positions being characterized by a reference allele in one species and by the alternative allele in all other species. Allele frequencies of the candidates SNPs were then explored in a larger, range-wide sample of populations in each species (validation step). ResultsWe found a subset of 38 SNPs (ten for Q. petraea, seven for Q. pubescens, nine for Q. pyrenaica and twelve for Q. robur) that showed near-diagnostic features across their species distribution ranges with Q. pyrenaica and Q. pubescens exhibiting the highest and lowest diagnosticity, respectively. ConclusionsWe provide a new, efficient and reliable molecular tool for the identification of the species Q. petraea, Q. robur, Q. pubescens and Q. pyrenaica, which can be used as a routine tool in forest research and management. This study highlights the resolution offered by whole-genome sequencing data to design diagnostic marker sets for taxonomic assignment, even for species complexes with relatively low differentiation.

plant biology↗

bioRxiv2021

Locally adapted oak populations along an elevation gradient display different molecular strategies to regulate bud phenology.

Research conductedWith the ongoing global warming, there are serious concerns about the persistence of locally adapted populations. Indeed, with the raising of temperature, the phenological cycle of tree species may be strongly affected since higher winter temperatures may have a negative impact on endodormancy release if chilling requirements are not fulfilled during winter and late frost in spring may expose trees if buds flush too early. Thus, Environmental gradients (showing continuous variations of environmental conditions) constitute a design of choice to analyze the effect of winter dormancy in locally adapted population. MethodsIn the present study, we used an elevation gradient in the Pyrenees to explore the gene expression network involved in dormancy regulation in natural populations of sessile oak locally adapted to temperature. Terminal buds were harvested during dormancy induction and release at different elevations. Then, gene expression was quantified using RNAseq and we used a likelihood ratio test to identify genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects. Key resultsOur results highlight molecular processes in locally adapted populations along this elevation cline, and made it possible to identify key dormancy-by-elevation responsive genes revealing that locally adapted populations have evolved distinct molecular strategies to adapt their bud phenology in response to environmental variation (i.e. temperature).

plant biology↗

bioRxiv2021

Water stress-associated isolation barriers between two sympatric oak species

Drought and waterlogging impede tree growth and may even lead to tree death. With climate change, these environmental factors are a growing source of concern, particularly for temperate forests. Oaks, an emblematic group of tree species, have evolved a range of adaptations to cope with these constraints. The two most widely distributed European species -- pedunculate oak (PO) and sessile oaks (SO) -- have overlapping ranges, but are highly constrained locally by soil water content variation. These differences in local ecological requirements provide a powerful biological model for studying the role of ecological barriers in speciation. We used an experimental set-up mimicking the ecological preferences of these species, in which seedlings were subjected to waterlogging and drought. We studied gene expression in roots by RNA-seq and identified genes differentially expressed between treatments with different outcomes depending on species. These "species x environment"-responsive genes revealed adaptive molecular strategies involving adventitious and lateral root formation, aerenchyma formation in PO, and osmoregulation and ABA regulation in SO. With this experimental design, we also identified genes with expression profiles presenting a "species" effect regardless of imposed constraints with important roles in intrinsic reproductive barriers. Finally, we compared our findings with those for a genome scan of species divergence and found that the candidate genes were enriched in highly differentiated SNPs. This suggests that many of the genes involved in the contrasting transcriptomic responses are subject to natural selection and that gene regulation helps to maintain these two different oak species in sympatry.

plant biology↗

bioRxiv2021

Genome-wide evolutionary response of European oakssince the Little Ice Age

The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of convergent linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last three hundred years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. Our results therefore provide evidence of selection operating on long-lived species during recent climatic changes.

evolutionary biology↗

bioRxiv2021

Genetic signatures of divergent selection in European beech (Fagus sylvatica L.) are associated with the variation in temperature and precipitation across its distribution range

High genetic variation and extensive gene flow may help forest trees with adapting to ongoing climate change, yet the genetic bases underlying their adaptive potential remain largely unknown. We investigated range-wide patterns of potentially adaptive genetic variation in 64 populations of European beech (Fagus sylvatica L.) using 270 SNPs from 139 candidate genes involved either in phenology or in stress responses. We inferred neutral genetic structure and processes (drift and gene flow) and performed differentiation outlier analyses and gene-environment association (GEA) analyses to detect signatures of divergent selection. Beech range-wide genetic structure was consistent with the species previously identified postglacial expansion scenario and recolonization routes. Populations showed high diversity and low differentiation along the major expansion routes. A total of 52 loci were found to be putatively under selection and 15 of them turned up in multiple GEA analyses. Temperature and precipitation related variables were equally represented in significant genotype-climate associations. Signatures of divergent selection were detected in the same proportion for stress response and phenology-related genes. The range-wide adaptive genetic structure of beech appears highly integrated, suggesting a balanced contribution of phenology and stress-related genes to local adaptation, and of temperature and precipitation regimes to genetic clines. Our results imply a best-case scenario for the maintenance of high genetic diversity during range shifts in beech (and putatively other forest trees) with a combination of gene flow maintaining within-population neutral diversity and selection maintaining between-population adaptive differentiation.

evolutionary biology↗

bioRxiv2019

Genomic landscape of the global oak phylogeny

O_LIThe tree of life is highly reticulate, with the history of population divergence buried amongst phylogenies deriving from introgression and lineage sorting. In this study, we test the hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly informative about phylogeny and investigate global patterns of oak diversity.\nC_LIO_LIWe utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the worlds oaks. We use reversible-jump MCMC to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20,000 RAD-seq loci back to a recently published oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny.\nC_LIO_LIOak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification due to climatic transitions or ecological opportunity.\nC_LIO_LIThe support we find for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.\nC_LI

evolutionary biology↗