Biology subjects

Paun, O.

Publications and source records attributed to Paun, O..

At least 19 recordsLinked to original sources

bioRxiv2025

Dark matter of an orchid: metagenome of the microbiome associated with the rhizosphere of Dactylorhiza traunsteineri

Plant microbiota forms complex co-associations with its host, promoting health in natural environments. Root-associated bacteria (RAB) colonize root compartments and can modulate plant functions by producing bioactive compounds as part of their secondary metabolism. We present an in-depth analysis of the rhizosphere-associated microbiome of the endangered marsh orchid Dactylorhiza traunsteineri. Using deep sequencing of 16S rRNA genes, we identified Proteobacteria, Actinobacteria, Myxococcota, Bacteroidota, and Acidobacteria as predominant phyla associated with the rhizosphere of D. traunsteineri. Using deep shotgun metagenomics and de novo assembly, we extracted high-quality metagenome-assembled genomes (MAGs), revealing significant metabolic and biosynthetic potentials of the D. traunsteineris RABs. Our study offers a comprehensive investigation into the microbial community of the D. traunsteineri rhizosphere, highlighting a potential novel source of critical bioactive substances. Our study offers novel insights and a robust platform for future investigations into D. traunsteineris rhizosphere, crucial for understanding plant-microbe interactions and aiding conservation efforts for endangered orchids.

microbiology↗

bioRxiv2024

Small RNAs regulation and genomic harmony: insights into allopolyploid evolution in marsh orchids (Dactylorhiza)

O_LIHybridization and polyploidy are major drivers of plant diversification, often accompanied by shifts in gene expression and genome composition. Small RNAs (smRNAs) are thought to influence such genomic changes, particularly through their interactions with transposable elements (TEs). C_LIO_LIWe comparatively quantified smRNAs in established sibling allopolyploids Dactylorhiza majalis and D. traunsteineri and their diploid progenitors to assess how independent allopolyploidization events shaped smRNA landscapes. C_LIO_LIDespite independent origins, the allotetraploids exhibited substantial overlap in smRNA composition, including transgressive accumulation of smRNA near genes related to transcriptional regulation, cell division and stress response. Consistently, TE-associated 24 nt smRNAs more closely resembled the paternal and larger genome, while shorter smRNAs typically reflected the maternal and smaller genome. Nevertheless, distinct patterns were also evident: the older D. majalis showed greater accumulation of smRNAs near genes involved in transcriptional and translational regulation, while the younger D. traunsteineri displayed stronger non-additive patterns, suggesting ongoing resolution of post-polyploid meiotic and mitotic instability. C_LIO_LIOur results reveal both convergence and divergence in smRNA landscapes among independently formed allopolyploids. Our study highlights the central role of smRNAs in resolving genomic conflict, with possible implications for functional divergence and ecological innovation during polyploid evolution. C_LI Plain-language summaryWe studied two sibling marsh orchid species that arose through hybridization and genome doubling. By comparing their small RNA molecules and how these associate with genes, we found both shared and species-specific patterns. These differences reflect how the orchids genomes have changed since formation, and may explain how repeated polyploidy events contribute to genetic and ecological diversity in plants.

evolutionary biology↗

bioRxiv2024

Recent speciation and adaptation to aridity in the ecologically diverse Pilbara region of Australia enabled the native tobaccos (Nicotiana; Solanaceae) to colonize all Australian deserts

For the last six million years, the arid Australian Eremaean Zone (EZ) has been as dry as today. An accepted hypothesis, applied to arid regions worldwide, suggests that flora and fauna were more broadly distributed before aridification began. In Australia, this aridification process started around 20 million years ago (Mya), leading to gradual speciation processes via vicariance as the climate became increasingly arid. Here, we use genomic data to investigate the biogeography and timing of divergence of native allotetraploid tobaccos, Nicotiana section Suaveolentes (Solanaceae), which putatively entered the EZ 5 Mya. The original allotetraploid migrants from South America were adapted to mesic areas of Australia and putatively radiated recently in the EZ, including sandy dune fields (only 1.2 My old), after developing drought adaptations. Based on coalescent and maximum likelihood analyses designed to corroborate timing of the Australian radiation independently, arrival of Nicotiana section Suaveolentes on the continent occurred approximately 6 Mya, and ancestors of the Pilbara (Western Australian) lineages radiated there at the onset of extreme aridity 5 Mya by locally adapting to these various ancient, highly stable habitats. The Pilbara thus served as both a mesic refugium and cradle for adaptations to harsher conditions. This dual role is due to its high topographical diversity, providing microhabitats with varying moisture levels, and its proximity to the ocean, which buffers against extreme aridity. Consequently, species like Nicotiana have been able to survive in mesic refugia during arid periods and subsequently adapt to more arid conditions. These results demonstrate that initially poorly adapted plant groups can develop novel adaptations in situ, permitting extensive and rapid wide dispersal despite the highly variable and unpredictable extremes of heat and drought in the EZ.

evolutionary biology↗

bioRxiv2024

Closely related facultative and constitutive CAM phenotypes show little transcriptomic overlap in the subgenus Tillandsia

Crassulacean acid metabolism (CAM) is a water-efficient photosynthetic strategy involving a coordinated suite of complex traits including metabolic, anatomical and regulatory aspects that shift across the diel cycle. While CAM has evolved repeatedly in land plants, the evolutionary routes enabling this convergence remain elusive. Whereas the same core CAM (de)carboxylation genes are consistently involved, a key question is whether distinct CAM phenotypes also depend on a shared set of auxiliary genes, reflecting a quantitative continuum of expression, or whether they can instead emerge through divergent or redundant peripheral solutions. The bromeliad subgenus Tillandsia, with diverse photosynthetic strategies, offers an ideal system to explore this question. Using physiological and transcriptomic analyses of well-watered and water-limited accessions of two closely related species, we characterized facultative and constitutive CAM. By comparing orthologous gene expression and orthogroup recruitment, we found that while both species performed CAM upon water-withholding, transcriptional shifts in pathways related to stomatal movement, sugar/malate transport, aquaporins and starch metabolism showed minimal overlap. Core enzymes involved in the CAM (de)carboxylation cycle exhibited broadly shared expression patterns, yet the facultative CAM species uniquely up-regulated PPC2 at night instead of the canonical CAM-related PEPC ortholog PPC1. Our study reveals that, while the expression of certain core CAM enzymes is conserved, the surrounding transcriptional architecture can differ substantially even between closely related species. This supports a model in which CAM evolves through a mosaic recruitment of functionally equivalent, yet non-orthologous genes - underscoring its flexible and modular genetic architecture. These insights advance our understanding of the mechanisms enabling the repeated evolution of CAM and its capacity to facilitate adaptive diversification.

evolutionary biology↗

bioRxiv2024

Ecological divergence is marked by specific plastic gene expression and distinct rhizosphere among sibling allopolyploid marsh orchids (Dactylorhiza)

Phenotypic plasticity, the dynamic adjustment of traits to environmental variations, is crucial for enabling species to exploit broader niches and withstand suboptimal conditions. This adaptability is particularly relevant for newly formed allopolyploids, which possess redundant gene copies and must become established in diverse environments distinct from their parents and other relatives. By evaluating gene expression and root mycobiome among two ecologically divergent sibling allopolyploid marsh orchids (Dactylorhiza majalis and D. traunsteineri) in reciprocal transplants at localities where both species are native, we aimed to understand the drivers of species persistence in the face of interspecific gene flow. Despite consistent abiotic differences characterising the alternative environments at each locality, the majority of gene expression differences between the allopolyploids appears to be plastic. Ecologically relevant processes, such as photosynthesis and transmembrane transport, include some genes that are differentially expressed between the two orchids regardless of the environment, while others change their activity plastically in one species or the other. This suggests that although plasticity helps define the specific ecological range of each sibling allopolyploid, it also mediates gene flow between them, thereby preventing differentiation. Extending our investigations to the root mycobiome, we uncover more diverse fungal communities for either species when grown in the environment with nutrient-poor soils, indicating that both abiotic and biotic factors drive the distribution of sibling marsh orchids. Altogether, our results indicate that plasticity can simultaneously promote diversification and homogenization of lineages, influencing the establishment and persistence of recurrently formed allopolyploid species. Significance statementThis study highlights the role of phenotypic plasticity in the persistence and distribution of sibling allopolyploid marsh orchids (Dactylorhiza majalis s.l.). By examining gene expression and the diversity of root mycobiome across reciprocal transplantations in native environments, we uncover high plasticity that facilitates adaptation and gene flow, thereby promoting both diversification and homogenization. These findings underscore the importance of plasticity in the establishment and long-term survival of allopolyploid species across the landscape.

evolutionary biology↗

bioRxiv2024

Decoupled genetic and epigenetic variation at local scale in an endemic and a widespread Erodium (Geraniaceae) species

Epigenetic states offer an additional layer of variation besides genetic polymorphism that contribute to phenotypic variation and may arise either randomly or in response to environmental factors. We hypothesize that closely related species with different life-histories and habitat requirements could show distinct patterns of intraspecific epigenetic variation. We used Restriction-site Associated DNA sequencing (RADseq) and its bisulfite-converted variant (bsRADseq) to investigate in Sierra de Cazorla (SE Spain) the genetic and epigenetic population structure of two congeneric species, the endemic woody perennial Erodium cazorlanum and the widely distributed annual herb E. cicutarium. Population genomics analyses revealed no structure in either E. cazorlanum and E. cicutarium, suggesting substantial gene flow between the study populations. In contrast, we found that the mean proportion of global DNA methylation was different between populations and species, with E. cazorlanum DNA showing higher methylation average and across-individuals variation. For each species, we searched for the loci with the strongest epigenetic differentiation between populations (differentially methylated cytosines, DMCs), and summarized them across regions (differentially methylated regions, DMRs). Multivariate analysis and hierarchical clustering of single cytosines methylation percentages did not group individuals by population, pointing to high epigenetic variation within populations. DMRs were enriched in Copia transposable elements, putatively associated with stress response in plants. Our results suggest that variation at both genetic and epigenetic levels in our study area occur mainly within natural populations of E. cazorlanum and E. cicutarium, with stronger population structure in E. cicutarium, and highlight the relevance of analyzing short distance spatial patterns.

genomics↗

bioRxiv2023

The explosive radiation of the Neotropical Tillandsia subgenus Tillandsia (Bromeliaceae) has been facilitated by pervasive hybridization

The recent rapid radiation of Tillandsia subgenus Tillandsia (Bromeliaceae) provides an attractive system to study the drivers and constraints of species diversification. This species-rich Neotropical monocot clade includes predominantly epiphytic species displaying vast phenotypic diversity. Recent in-depth phylogenomic work revealed that the subgenus originated within the last 7 MY, with one major expansion from South into Central America within the last 5 MY. However, disagreements between phylogenies and lack of resolution at shallow nodes suggest that hybridization may have occurred throughout the radiation, together with frequent incomplete lineage sorting and rapid gene family evolution. We used whole-genome resequencing data to explore the evolutionary history of representative ingroup species employing both tree-based and network approaches. Our results indicate that lineage co-occurrence does not predict relatedness and confirm significant deviations from a tree-like structure, coupled with pervasive gene tree discordance. Focusing on hybridization, ABBA-BABA and related statistics were used to infer the rates and relative timing of events, while topology weighting uncovered high heterogeneity of the phylogenetic signal along the genome. High rates of hybridization within and among subclades suggest that, contrary to previous hypotheses, the expansion of subgenus Tillandsia into Central America proceeded through several dispersal events, punctuated by episodes of diversification and gene flow. Network analysis revealed reticulation as a plausible propeller during radiation and establishment across different ecological niches. This work contributes a plant example of prevalent hybridization during rapid species diversification, supporting the hypothesis that interspecific gene flow facilitates explosive diversification.

evolutionary biology↗

bioRxiv2023

Short structural variation fuelled CAM evolution within an explosive bromeliad radiation

1.The subgenus Tillandsia (Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean Acid Metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of a Tillandsia species pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, TE dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution in Tillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes of Tillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species, but are no candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.

evolutionary biology↗

bioRxiv2023

Long-term methylome changes after experimental seed demethylation and their interaction with recurrent water stress in Erodium cicutarium (Geraniaceae)

O_LIThe frequency and length of drought periods are increasing in subtropical and temperate regions worldwide. Epigenetic responses to water stress could be key for plant resilience to this largely unpredictable challenge. Experimental DNA demethylation together with application of a stress factor stands as a suitable strategy to uncover the contribution of epigenetics to plant responses to stress. C_LIO_LIWe analysed leaf cytosine methylation changes in adult plants of the Mediterranean weed, Erodium cicutarium, after seed demethylation with 5-Azacytidine and/or recurrent water stress in a greenhouse. We used bisulfite RADseq (BsRADseq) and a newly reported reference genome for E. cicutarium to characterize methylation changes in a 2x2 factorial design, controlling for plant relatedness. C_LIO_LIIn the long-term, 5-Azacytidine treatment alone caused both hypo and hyper-methylation at individual cytosines, with substantial hypomethylation in CG contexts. In control conditions, drought resulted in a decrease in methylation level in all but CHH contexts. In contrast, the genome of plants that experienced recurrent water stress and had been treated with 5-Azacytidine increased DNA methylation level by ca. 5%. C_LIO_LISeed demethylation and recurrent drought exhibited a highly significant interaction in terms of global and context-specific cytosine methylation supporting an epigenetic contribution in response to stress at molecular level. C_LI

ecology↗

bioRxiv2022

ASCL1 interacts with the mSWI/SNF at distal regulatory elements to regulate neural differentiation

AO_SCPLOWBSTRACTC_SCPLOWPioneer transcription factors are thought to play pivotal roles in developmental processes by binding nucleosomal DNA to activate gene expression. The role of neurogenic pioneer factor ASCL1 in shaping chromatin landscape in human neurogenesis remains unclear. Here we show that ASCL1 acts as a pioneer transcription factor in a transient population of progenitors. Using an in vitro ASCL1 knockout model we show it drives progenitor differentiation by cis-regulation both as a classical pioneer factor and as a non-pioneer remodeler, where ASCL1 binds permissive chromatin to induce chromatin conformation changes. We find ASCL1 directly interacts with mammalian BAF SWI/SNF chromatin remodeling complexes, essential for neurogenesis and involved in multiple neurodevelopmental disorders. ASCL1 acts as a non-pioneer chromatin remodeler to regulate gene expression at a subset of loci, requiring mBAF SWI/SNFs ATPase activity for cis-regulation of gene expression. Our findings demonstrate that ASCL1 is a key chromatin remodeler in human neurogenesis, uncovering an alternative mechanism of remodeling function dependent on partner ATPase activity.

developmental biology↗

bioRxiv2022

Parallel adaptation to lower altitudes is associated with enhanced plasticity in Heliosperma pusillum (Caryophyllaceae)

High levels of phenotypic plasticity are thought to be inherently costly in stable or extreme environments, but enhanced plasticity may evolve as a response to novel environments and foster adaptation. Heliosperma pusillum forms pubescent montane and glabrous alpine ecotypes that diverged recurrently and polytopically (parallel evolution). The specific montane and alpine localities are characterized by distinct temperature conditions, available moisture and light. To disentangle the relative contribution of constitutive versus plastic gene expression to altitudinal divergence, we analyze the transcriptomic profiles of two parallely evolved ecotype pairs, grown in reciprocal transplantations at native altitudinal sites. In both ecotype pairs, only a minor proportion of genes appear constitutively differentially expressed between the ecotypes regardless of the growing environment. Both derived, montane populations bear comparatively higher plasticity of gene expression than the alpine populations that can be considered in this system as ancestor-proxies. Genes that change expression plastically and constitutively underlie similar ecologically relevant pathways, related to response to drought and trichome formation. Other relevant processes, such as photosynthesis, seem to rely mainly on plastic changes. The enhanced plasticity consistently observed in the montane ecotype likely evolved as a response to the newly colonized niche. Our findings confirm that directional changes in gene expression plasticity can shape initial stages of phenotypic evolution, likely fostering adaptation to novel environments. Significance StatementUnderstanding the importance of phenotypic plasticity for fast adaptation to stress is very timely for breeding and current environmental challenges. Our study of an alpine plant in the carnation family evidences an increased level of expression plasticity in early stages of adaptation to hotter and drier habitats.

evolutionary biology↗

bioRxiv2022

Variation of the Rdr1 gene insertion in wild populations of Nicotiana benthamiana (Solanaceae) and insights into recent species divergence

O_LIOne of the most commonly encountered and frequently cited laboratory organisms worldwide is classified taxonomically as Nicotiana benthamiana (Solanaceae), an accession of which, typically referred to as LAB, is renowned for its unique susceptibility to a wide range of plant viruses and hence capacity to be transformed using a variety of methods. However, the origin and age of LAB and the evolution of N. benthamiana across its wide distribution in Australia remains relatively underexplored. C_LIO_LIHere, we have used multispecies coalescent methods on genome-wide single nuclear polymorphisms (SNPs) to assess species limits, phylogenetic relationships and divergence times within N. benthamiana. C_LIO_LIOur results show that the previous taxonomic concept of this species in fact comprises five geographically, morphologically and genetically distinct species, one of which includes LAB. C_LIO_LIRemarkably, we provide clear evidence that LAB is closely related to accessions collected further north in the Northern Territory; this species split much earlier from their common ancestor than the other four in this clade and is morphologically the most distinctive. Furthermore, this long-isolated species typically grows in sheltered sites in subtropical/tropical monsoon areas of northern Australia, contradicting the previously advanced hypothesis that this species is an extremophile that has traded viral resistance for precocious development. C_LI

evolutionary biology↗

bioRxiv2021

Recurrent allopolyploidization events diversify eco-physiological traits in marsh orchids

Whole-genome duplication, in particular allopolyploidy, has shaped the evolution of angiosperms and other organisms. Structural reorganization of chromosomes and repatterning of gene expression is frequently observed in early generation allopolyploids, with potential ecological consequences. The relative contributions of environmental and intrinsic drivers to these changes are unknown. We show here that in marsh orchids (Dactylorhiza, Orchidaceae), recurrently-formed allopolyploids are characterized by distinct eco-physiologies matching their respective environments, providing us with an excellent study system to address this question. Here we integrate eco-physiological and transcriptomic comparative studies to reveal a complex suite of intertwined, pronounced differences between sibling allopolyploids. We show that Dactylorhiza majalis that is distributed in Central and Southern Europe favors meadows with mesic soils. Its sibling allopolyploid D. traunsteineri occurs in fens, characterized by soils depleted by macro- and micronutrients, mainly in previously glaciated European areas. We further uncover distinct features in their nutrient transport, leaf elemental chemistry, light-harvesting, photoprotection, and stomata activity, that appear all linked to their distinct ecologies, in particular soil chemistry differences at their native sites. Recurrent polyploidization hence enriches biodiversity through eco-physiological diversification, providing the opportunity for sibling allopolyploids to evolve as distinct evolutionary units, despite pervasive interspecific gene flow. Significance StatementWhole-genome duplication resulting in polyploidy has underpinned the evolution of flowering plants and other organisms, and is important for many crops. However, the ecological implications of polyploidy remain little understood. Here, we demonstrate that two sibling allopolyploid marsh orchid species prefer distinct habitats, and have evolved a suite of distinctive ecophysiological characters (e.g. nutrient transport, energy harvesting and photoprotection). We argue that the divergence of these characters in the nascent polyploids drove adaptation into distinct ecological niches (low nutrient fens versus meadows with mesic soils), generating ecological barriers that maintains distinct, independent lineages, even in the presence of interspecific gene flow.

evolutionary biology↗

bioRxiv2021

Conserved genomic landscapes of differentiation across Populus speciation continuum

Speciation, the continuous process by which new species form, is often investigated by looking at the variation of nucleotide diversity and differentiation across the genome (hereafter genomic landscapes). A key challenge lies in how to determine the main evolutionary forces at play shaping these patterns. One promising strategy, albeit little used to date, is to comparatively investigate these genomic landscapes as a progression through time by using a series of species pairs along a divergence gradient. Here, we resequenced 201 whole-genomes from eight closely related Populus species, with pairs of species at different stages along the divergence gradient to learn more about speciation processes. Using population structure and ancestry analyses, we document extensive introgression between some species pairs, especially those with parapatric distributions. We further investigate genomic landscapes, focusing on within-species (nucleotide diversity and recombination rate) and among-species (relative and absolute divergence) summary statistics of diversity and divergence. We observe highly conserved patterns of genomic divergence across species pairs. Independent of the stage across the divergence gradient, we find support for signatures of linked selection (i.e., the interaction between natural selection and genetic linkage) in shaping these genomic landscapes, along with gene flow and standing genetic variation. We highlight the importance of investigating genomic patterns on multiple species across a divergence gradient and discuss prospects to better understand the evolutionary forces shaping the genomic landscapes of diversity and differentiation.

evolutionary biology↗

bioRxiv2021

Polygenic routes lead to parallel altitudinal adaptation in Heliosperma pusillum (Caryophyllaceae)

Understanding how organisms adapt to the environment is a major goal of modern biology. Parallel evolution - the independent evolution of similar phenotypes in different populations - provides a powerful framework to investigate the evolutionary potential of populations, the constraints of evolution, its repeatability and therefore its predictability. Here, we quantified the degree of gene expression and functional parallelism across replicated ecotype formation in Heliosperma pusillum (Caryophyllaceae), and gained insights into the architecture of adaptive traits. Population structure analyses and demographic modelling support a previously formulated hypothesis of parallel polytopic divergence of montane and alpine ecotypes. We detect a large proportion of differentially expressed genes (DEGs) underlying divergence within each replicate ecotype pair, with a strikingly low amount of shared DEGs across pairs. Functional enrichment of DEGs reveals that the traits affected by significant expression divergence are largely consistent across ecotype pairs, in strong contrast to the non-shared genetic basis. The remarkable redundancy of differential gene expression indicates a polygenic architecture for the diverged adaptive traits. We conclude that polygenic traits appear key to opening multiple routes for adaptation, widening the adaptive potential of organisms.

evolutionary biology↗

bioRxiv2021

Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

Target capture has emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family, however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

evolutionary biology↗

bioRxiv2021

Spatial and ecological drivers of population structure in Alkanna tinctoria (Boraginaceae), a polyploid medicinal herb

Background and AimsQuantifying genetic variation is fundamental to understand a species demographic trajectory and its ability to adapt to future changes. In comparison to diploids, however, genetic variation and factors fostering genetic divergence remains poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies. MethodsWe collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing (RAD-seq). As an outgroup, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables. Key ResultsWe found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modelling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria. ConclusionsCurrent findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.

genomics↗

bioRxiv2020

Wnt/beta-catenin signalling is dispensable for adult neural stem cell homeostasis and activation.

Adult mouse hippocampal neural stem cells (NSCs) generate new neurons that integrate into existing hippocampal networks and modulate mood and memory. These NSCs are largely quiescent and are stimulated by niche signals to activate and produce neurons. Wnt/{beta}-catenin signalling acts at different steps along the hippocampal neurogenic lineage and has been shown to promote the proliferation of intermediate progenitor cells. However, whether it has a direct role in the regulation of NSCs still remains unclear. Here we used Wnt/{beta}-catenin reporters and transcriptomic data from in vivo and in vitro models to show that both active and quiescent adult NSCs respond to Wnt/{beta}-catenin signalling. Wnt/{beta}-catenin stimulation instructed neuronal differentiation of active NSCs and promoted the activation or differentiation of quiescent NSCs in a dose-dependent manner. However, we found that inhibiting NSCs response to Wnt, by conditionally deleting {beta}-catenin, did not affect their activation or maintenance of their stem cell characteristics. Together, our results indicate that whilst NSCs do respond to Wnt/{beta}-catenin stimulation in a dose-dependent and state-specific manner, Wnt/{beta}-catenin signalling is not cell-autonomously required to maintain NSC homeostasis, which could reconcile some of the contradictions in the literature as to the role of Wnt/{beta}-catenin signalling in adult hippocampal NSCs.

developmental biology↗