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Besnard, G.

Publications and source records attributed to Besnard, G..

11 recordsLinked to original sources
bioRxiv2026

Utilising nuclear encoded plastid DNA to identify donors of grass-to-grass lateral gene transfer

Determining the correct donor species/lineages of grass-to-grass lateral gene transfer (LGT) is vital for deducing specific donor features that could help inform the mechanism of transfer. This requires a dataset spanning a broad range of species to achieve the phylogenetic resolution necessary for precise donor inference. As grass-to-grass LGT often involves the transfer of multi-gene DNA fragments, they can contain additional sequences that allow for accurate orthologous comparisons, such as nuclear DNA of plastid origin (NUPTs). Here we systematically scan for NUPTs in the genomes of four Alloteropsis semialata accessions, whose LGTs have previously been characterised. Using the abundant Panicoideae chloroplast sequences, we reconstruct NUPT phylogenies and infer two lateral acquisitions: one from Paniceae/Digitaria and another from Andropogoneae/Eremochloa adjacent to a previously identified LGT. We then assembled and included an additional 12 Eremochloa chloroplast genomes in the analysis and showed the likely donor was Eremochloa attenuata. Subsequent short-read mapping from E. attenuata to the nuclear region flanking this NUPT showed consistent coverage across the region, including the previously identified LGT, supporting co-transfer. Overall this study highlights the potential for NUPTs to better identify the donors of grass-to-grass LGT.

evolutionary biology↗
bioRxiv2025

Phylogenomics of Plasmopara halstedii reveals genomic regions associated with the breakdown of sunflower downy mildew resistance genes

O_LIUnderstanding the genetic diversity and evolutionary history of plant pathogens is crucial for effective disease management strategies. Sunflower downy mildew, caused by the oomycete Plasmopara halstedii, is a worldwide threat to the sunflower oil crop. We aimed to explain through phylogenomic studies how downy mildew resistance breakdown occurred recurrently in the last decades in France, leading to new virulence profiles. C_LIO_LIWe assembled high-quality genomes of three founder pathotypes of Pl. halstedii. Performing comparative genomic analyses, population genetics, and phylogenomic analyses, we studied the genomic structure among the 16 reference French pathotypes of Pl. halstedii. C_LIO_LIWe revealed a conserved genomic organisation among pathotypes and a strong synteny with other Peronosporales species. The history of Pl. halstedii invasion in France over the last 60 years was documented by identifying founder strains and their admixture patterns. The emergence of pathotypes with broader virulence spectra and therefore capable of overcoming host resistance was associated with genomic reshuffling. We highlighted genomic mosaicism in admixed pathotypes and identified regions associated with the breakdown of host resistance genes harbouring putative effector genes. C_LIO_LIOur findings provide insights into evolutionary mechanisms underlying plant pathogen host adaptation, which has implications for a sustainable deployment of multiple resistance genes. C_LI

plant biology↗
bioRxiv2025

Genomic rearrangements promote diversification of a facultative meiotic parthenogenetic nematode pest (Meloidogyne graminicola)

Meloidogyne graminicola (Mg), commonly known as the rice root-knot nematode, is a highly destructive pest that inflicts significant damage on rice crops worldwide. Mg is thought to reproduce primarily by meiotic parthenogenesis, but its success across diverse habitats and hosts raises important questions about its adaptation mechanisms, particularly those driving the evolution of its virulence. Documenting the origin of the pathogen, its reproductive strategies and other evolutionary processes shaping its genome are thus crucial to understand its recent, rapid expansion. In this study, we first improved gene annotations of the Mg genome to enhance identification of potential secreted parasitism genes. Next, comparative genomics analyses of 13 Mg isolates from diverse geographic locations revealed evolutionary changes in the genome, including single nucleotide variations (SNVs), loss of heterozygosity (LoH), and copy number variations (CNVs). These events affected a substantial number of genes, including those coding for secreted proteins, suggesting their roles in nematode adaptation. LoH, the reduction of linkage disequilibrium between SNPs with distance as well as the 4-gamete test all provide evidence for meiotic recombination, supporting some sexual reproduction in Mg. Clustering of populations, based on LoH profiles and SNVs, allowed the definition of groups of isolates not correlating with current geographic distribution. The low sequence divergence at the genome level and the lack of clear phylogeographic structure among isolates support the hypothesis of a recent, widespread dissemination of the parasite, especially across Southeast Asia. Overall, our study supports a dual reproductive mode (sexual/asexual) in Mg, which offers an evolutionary advantage by balancing clonal proliferation in favorable conditions with occasional sexual reproduction allowing generation of new allelic combinations in adverse environments.

genomics↗
bioRxiv2024

Nuclear phylogenomics of grasses (Poaceae) supports current classification and reveals repeated reticulation

O_LIGrasses (Poaceae) comprise around 11,800 species and are central for human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. C_LIO_LIWe inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1,153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a 910-tip plastome tree. C_LIO_LIThe nuclear phylogeny matches that of the plastome at most deep branches, with only a few instances of incongruence. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly in the history of grasses. C_LIO_LIWe provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture. C_LI

plant biology↗
bioRxiv2023

African bush pigs exhibit porous species boundaries and appeared in Madagascar concurrently with human arrival

Several African mammals exhibit a phylogeographic pattern where closely related taxa are split between West/Central and East/Southern Africa, but their evolutionary relationships and histories remain controversial. Bushpigs (Potamochoerus larvatus) and red river hogs (P. porcus) are recognised as separate species due to morphological distinctions, a perceived lack of interbreeding at contact, and putatively old divergence times, but historically, they were considered conspecific. Moreover, the presence of Malagasy bushpigs as the sole large terrestrial mammal shared with the African mainland raises intriguing questions about its origin and arrival in Madagascar. Analyses of 67 whole genomes revealed a genetic continuum between the two species, with putative signatures of historical gene flow, variable FST values, and a recent divergence time (<500,000 years). Thus, our study challenges key arguments for splitting Potamochoerus into two species and suggests their speciation might be incomplete. Our findings also indicate that Malagasy bushpigs diverged from southern African populations and underwent a limited bottleneck 1,000-5,000 years ago, concurrent with human arrival in Madagascar. These results shed new light on the evolutionary history of an iconic and widespread African genus and provide insight into the longstanding biogeographic puzzle surrounding the bushpigs presence in Madagascar.

evolutionary biology↗
bioRxiv2023

Genetic variation in Loudetia simplex supports the presence of ancient grasslands in Madagascar

O_LIResearch Aims -- The extent of Madagascars grasslands prior to human colonization is unresolved. We used population genetic analyses of a broadly dominant C4 fire-adapted grass, Loudetia simplex, as a proxy for estimating grassland change through time. We carefully examined the utility of target-enrichment data for population genetics to make recommendations for conservation genetics. We explored the potential of estimating individual ploidy levels from target-enrichment data and how assumptions about ploidy could affect analyses. C_LIO_LIMethods -- We developed a novel bioinformatic pipeline to estimate ploidy and genotypes from target-enrichment data. We estimated standard population genetic summary statistics in addition to species trees and population structure. Extended Bayesian skyline plots provided estimates of population size through time for empirical and simulated data. C_LIO_LIKey Result -- All Malagasy Loudetia simplex individuals sampled in this study formed a clade and possibly indicated an ancestral Central Highland distribution of 800m in altitude and above. Demographic models suggested grassland expansions occurred prior to the Last Interglacial Period and supported extensive grasslands prior to human colonization. Though there are limitations to target-enrichment data for population genetic studies, we find that analyses of population structure are reliable. C_LIO_LIKey Point --Genetic variation in Loudetia simplex supports widespread grasslands in Madagascar prior to the more recent periods of notable paleoclimatic change. However, the methods explored here could not differentiate between paleoclimatic change near the Last Glacial Maximum and anthropogenic effects. Target-enrichment data can be a valuable tool for analyses of population structure in the absence a reference genome. C_LI Societal Impact StatementRecognizing Loudetia dominated grasslands were widespread prior to human colonization highlights that open ecosystems were and continue to be an important component of Madagascars biodiversity. Urgently required are biodiversity inventories and integrative taxonomic treatments of grassland flora and fauna to asses risks to understudied ecosystems historically regarded as wastelands. Substantial financial and logistical barriers exist to implementing conservation studies using contemporary genomic tools. We ameliorated some of the challenges for population genetic analyses of non-model polyploids lacking reference genomes by developing computational resources to leverage a cost-effective data generation strategy that requires no prior genetic knowledge of the target species. ResumeO_LILes objectifs de la recherche -- Letendue des ecosystemes ouverts de Madagascar avant la colonisation humaine reste a eclaircir. Nous avons utilise une analyse de la population genetique dune graminee C4 adaptee au feu, largement dominante, Loudetia simplex, comme reference pour estimer les changements au niveau de ces biomes au fil du temps. Nous avons examine attentivement lutilite des donnees denrichissement cible pour la genetique de population afin de formuler des recommandations pour la conservation genetique. Nous avons explore le potentiel de lestimation du niveau des ploidies individuelles a partir des donnees denrichissement cible et comment les hypotheses a propos de ces ploidies pourraient affecter les analyses. C_LIO_LILes methodes -- Nous avons developpe un nouveau canal bioinformatique pour estimer les ploidies et les genotypes a partir des donnees denrichissement cible. Nous avons estime les statistiques standard de la population genetique, en plus des arbres des especes et de la structure de la population. Lutilisation des traces etendus du ciel bayesien a fourni une estimation de la taille de la population au fil du temps pour des donnees empiriques et simulees. C_LIO_LIResultat cle -- Tous les individus Malagasy de Loudetia simplex echantillonnes dans cette etude ont forme un clade, indiquant une eventuelle ancienne distribution dans les hauts plateaux. Les modeles demographiques suggerent une expansion des prairies bien avant la derniere periode interglaciaire et soutiennent lexistence dune vaste distribution avant la colonisation humaine. Bien quil y ait des limites a lenrichissement des donnees cibles pour letude de la genetique des populations, nous constatons que lanalyse des structures des populations est fiable. C_LIO_LILes points cles -- La variation genetique de Loudetia simplex soutient lexistence de vastes prairies a Madagascar avant les periodes plus recentes de changements paleoclimatiques notables. Cependant, les methodes explorees ici nont pas permis de faire la difference entre les changements paleoclimatiques pres du dernier maximum glaciaire et les effets anthropogenes. Les donnees denrichissement cible peuvent etre un outil precieux pour les analyses de la structure des populations en labsence dun genome de reference. C_LI Declaration dimpact societalReconnaitre que les prairies dominees par Loudetia etaient repandues avant la colonisation humaine souligne que les ecosystemes ouverts etaient et continuent detre un composant important de la biodiversite de Madagascar. Il est urgent de realiser des inventaires de la biodiversite et une taxonomie integree pour le traitement de la flore et de la faune des ecosystemes ouverts afin devaluer les risques pour les ecosystemes sous-etudies consideres historiquement comme des terres en friches. Des barrieres financieres et logistiques existent pour mettre en uvre letude de la conservation en utilisant les outils genomiques contemporains. Nous avons ameliore certains des defis lies aux analyses genetiques de populations de polyploides non modeles, sans genomes de reference, en developpant des ressources informatiques pour exploiter une strategie pouvant generer des donnees rentables ne necessitant aucune connaissance genetique prealable de lespece cible. FamintinanaO_LINy tanjonny fikarohana -- Mbola tsy fantatra mazava tsara ny fivelaranny hivoka teto Madagasikara talohanny fahatongavany olombelona. Mba ahafantarana ny fihovana nitranga nandritra ny fotoana naharitra teo aminireo hivoka ireo dia nanao famakafakahana ara-genetika aminny ahitra C4 miompana aminny afo iray antsoina Loudetia simplex ara-tsiantifika na Berambo na Hara aminny teny malagasy izahay. Nandinika tsara ny maha-zava-dehibe ny fampitomboana ny antotan-kevitra mba ahafahana manolo-kevitra momba ny fiarovana ny fototarazo genetika. Nandinika ny mety mampiavaka ny fanombanana anny ploidy tsirairay aminny fampitomboana antotan-kevitra sy ny mety ho fiantraikanny fiheverana momba ireo ploidy ireo aminny fikarohana. C_LIO_LIFomba Fiasa -- Namorona fantsona bioinformatika vaovao mba ahafahana manombana ny ploidy sy ny << genotypes >> avy aminny antotan-kevitra nokendrena izahay. Notombanana ny antontanisa famintinana ny fototarazo ara-genetikanireo vondronahitra ireo, miampy ny karazana hazo sy ny firafitry ny vondrona na koa hoe mponina. Nanome tombantombana ny habenny mponina aminny alalanny fotoana ny antontan-kevitra voavinavina azo taminny fikarohana. Fikarohana izay azo taminny alalanny << Bayesina Skuline Plots >>. C_LIO_LIVokam-pikarohana fototra -- Ny vondrona Loudetia simplex eto Madagasikara izay niasana dia namorona << clade >> na fikambanana iray, izay manondro ny mety maha ela netezana sy tranainy anio ahitra io eny aminny faritra avo. Ny modely demografika dia manoro hevitra aminny naha be velarana ny hivoka izay efa ela talohanny vanim-potoana << interglacial >> farany ary manohana ny fivelarana midadasika anireo kijana ireo alohanny fonenanny olombelona. Na dia misy fetrany aza ny fampitomboana ny antotan-kevitra kendrena aminny fandalinana ny fototarazo genetika mombanny mponina, dia hita fa azo itokisana ny fikarohana natao mombanny firafitry ny mponina. C_LIO_LIHevi-dehibe -- Ny fahasamihafana ara-genetika ao aminny Loudetia simplex dia manohana ny fisianny hivoka na kijana midadasika eto Madagasikara talohanny vanim-potoananny fiovana paleoclimatika nisongadina. Na izany aza, ny fombam-pikarohana nampiasana teto dia tsy nahavita nanavaka ny fiovanny paleoclimatika akaikinny vanim-potoana lehibe nangatsiaka farany sy ny vokatry ny fitrandrahana nataonny olombelona. Mety ho fitaovana manan-danja aminny famakafakana ny firafitry ny mponina ny antotan-kevitra nampitombona na dia tsy misy fitaovana genomika iangaina aza. C_LI Fanambarana fiantraika ara-tsosialyNy fanekena fa niely patrana ny hivoka itoeranny Loudetia talohanny fanjanahanny olombelona dia manamarika fa ireo hivoka ireo dia singa manan-danja aminny zavamananaina eto Madagasikara. Ilaina maika ny fahafantarana ara biolojika sy taxononomique ny zavamaniry sy ny biby aminny hivoka mba hanombanana ny loza mety hitranga aminny hivoka izay tsy ananana fahalalana maro sady heverina ho tany maina. Misy sakana ara-bola sy ara-pitaovana aminny fampiharana ny fandalinana momba ny fiarovana izay nampiasana fitaovana genomika ankehitriny. Nohatsarainay ny sasany aminireo fanamby mifandraika aminny famakafakana ara-genetika ny mponina manana ploidy maro tsy modely, izay tsy misy fitaovana genomika iaingana, aminny alalanny fampivoarana loharanon-kevitra kajy mba hitrandrahana paikady izay mety hiteraka angon-drakitra mahomby tsy mitaky fahalalana mahakasika ny fototarazo ara-genetika ny zava-maniry izay tiana karohina.

evolutionary biology↗
bioRxiv2021

Hybridisation boosts dispersal of two contrasted ecotypes in a grass species

O_LIIn the absence of strong reproductive barriers, genetic exchanges between closely related groups of organisms with different adaptations have well-documented beneficial and detrimental consequences. In plants, pollen-mediated exchanges affect the sorting of alleles across physical landscapes, and influence rates of hybridisation. How these dynamics affect the emergence and spread of novel ecological strategies remains only partially understood. C_LIO_LIWe use phylogenomics and population genomics to retrace the origin of two geographically overlapping ecotypes of the African grass Alloteropsis angusta. C_LIO_LIWe report the existence of a previously undescribed ecotype inhabiting miombo woodlands and grasslands. The two ecotypes have divergent nuclear genomes. However, the seed-transported chloroplast genomes are consistently shared by distinct ecotypes inhabiting the same region. These patterns suggest that the nuclear genome of one ecotype can reach the seeds of the other via pollen movements, with strong selection subsequently sorting nuclear alleles by habitat. C_LIO_LIThe contrasting ecotypes of A. angusta can use each other as a gateway to new locations across a large part of Africa. Coupled with newly discovered hybridisation with the sister species A. semialata, our results show that hybridisation can facilitate the geographical dispersal of distinct ecotypes of the same grass species. C_LI

evolutionary biology↗
bioRxiv2020

How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a micro-endemic Malagasy tree

Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exceptions in areas like the Loky-Manambato region (North) raise questions. Such regions also harbor a rich and endemic flora, whose evolutionary origin remains poorly understood. We assessed the genetic diversity of an endangered microendemic Malagasy olive species (Noronhia spinifolia Hong-Wa) to better understand the vegetation dynamic in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction associated sequencing data (RADseq) and chloroplast microsatellites (cpSSR). Combined population and landscape genetics analyses indicate that N. spinifolia diversity is largely explained by the current forest cover, highlighting a long-standing habitat mosaic in the region. This sustains a major and long-term role of riparian corridors in maintaining connectivity across those antique mosaic-habitats, calling for the study of organismal interactions that promote gene flow.

genomics↗
bioRxiv2020

Physiological diversity enhanced by recurrent divergence and secondary gene flow within a grass species

O_LIC4 photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this single species encompasses C4 and non-C4 populations. C_LIO_LIUsing phylogenomics and population genomics, we infer the history of dispersal and secondary exchanges before, during, and after photosynthetic divergence in A. semialata. We further establish the genetic origins of polyploids in this species. C_LIO_LIOrganelle phylogenies indicate limited seed dispersal within the Central Zambezian region of Africa, where the species originated [~] 2-3 Ma. Outside this region, the species spread rapidly across the paleotropics to Australia. Comparison of nuclear and organelle phylogenies and analyses of whole genomes reveal extensive secondary gene flow. In particular, the genomic group corresponding to the C4 trait was swept into seeds from distinct geographic regions. Multiple segmental allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. C_LIO_LILimited dispersal and isolation allowed lineage divergence, while episodic secondary exchanges led to the pollen-mediated, rapid spread of the derived C4 physiology. Overall, our study suggests that local adaptation followed by recurrent secondary gene flow promoted physiological diversification in this grass species. C_LI

evolutionary biology↗
bioRxiv2019

Phylogenomics supports a Cenozoic rediversification of the "living fossil" Isoetes

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

evolutionary biology↗
bioRxiv2016

Evolutionary forces affecting synonymous variations in plant genomes

Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic datasets based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.

evolutionary biology↗