Biology subjects

Duchoslav, M.

Publications and source records attributed to Duchoslav, M..

4 recordsLinked to original sources

bioRxiv2026

A Global Genomic Resource for Outcrossing Arabidopsis lyrata and Arabidopsis arenosa

Genetic studies leveraging natural variation in Arabidopsis species have improved our understanding of evolutionary genetic processes underlying ecologically important and adaptive traits. Integrating the thorough functional knowledge accumulated in A. thaliana with the extensive natural variation in outcrossing Arabidopsis species is a powerful approach to study the basis of adaptation in natural evolutionary and ecological contexts. Here we present an integrated genomics database of sequenced genomes from several studies in A. lyrata (1018 genomes in total) and A. arenosa (736 genomes in total), spanning the geographic ranges of these two ploidy-variable, outcrossing taxa. We provide a searchable genome browser with population data mapped to respective reference genomes, an interactive geographic map of population structure clusters, and an efficient way to subsample the full dataset of genetic variation, available at arabidopsislyrata.org. To demonstrate its utility, we perform a genome-wide association study on a latitudinal cline of A. lyrata and find strong associations of several loci with latitude, including variants in key regulators of photoperiodic growth. This resource provides access to genetic diversity data in a single repository, enabling further studies of comparative genetics and local adaptation, as well as of individual genes of interest.

evolutionary biology↗

bioRxiv2025

Genomic basis of adaptation to serpentine soil in two Alyssum species shows convergence with Arabidopsis across 20 million years of divergence

Background and AimsSerpentine outcrops, characterized by low nutrient availability, high heavy metal concentrations, propensity to drought, and island-like distributions, offer valuable systems to study parallelisms in repeated adaptation to extreme environments. While shared phenotypic manifestation of adaptation to serpentine environments has been investigated in many species, it is still unclear whether there may be a common genetic basis underlying such responses. Here we assess local adaptation to serpentine soil and infer the parallel genetic signatures of local adaptation to serpentine environments in two thus far unexplored closely related species, Alyssum gmelinii and Alyssum spruneri (Brassicaceae). Then we measure gene- and function-level convergence with the previously explored Arabidopsis arenosa, to reveal candidate shared adaptive strategies within Brassicaceae. MethodsWe tested for adaptation using a reciprocal substrate-transplant experiment in A. gmelinii. Then, after assembling a reference genome, we generated population-level sequencing data of four population pairs and performed genome scans for directional selection to infer serpentine adaptive candidate genes in Alyssum. Finally, we compared candidate gene lists with those inferred in similar experiments in Arabidopsis arenosa and used protein-protein interaction networks to discern functional convergence in serpentine adaptation. Key ResultsIndependent colonization of serpentine environments by Alyssum populations is associated with footprints of selection on genes related to ion transport and homeostasis, nutrient and water uptake, and life-history traits related to germination and reproduction. Reciprocal transplant experiments demonstrated that adapted plants germinate sooner and exhibit better growth in serpentine conditions while excluding heavy metals and increasing Ca uptake in their tissues. Finally, a significant fraction of such genes and molecular pathways is shared with Arabidopsis arenosa. ConclusionsWe show that genetic adaptation to the multi-factorial challenge imposed by serpentine environments involves key pathways that are shared not only between closely related species, but also between Brassicaceae tribes of [~]20 Mya divergence.

evolutionary biology↗

bioRxiv2024

Plant kleptomaniacs: geographic genetic patterns in the amphi-apomictic Rubus ser. Glandulosi (Rosaceae) reveal complex reticulate evolution of Eurasian brambles

Rubus ser. Glandulosi represents a unique model of geographic parthenogenesis on a homoploid (4x) level. We employed double digest restriction-site associated DNA sequencing (ddRADseq) in 587 individuals of different Rubus taxa and modelling of suitable climate to characterize evolutionary and phylogeographic patterns and shed light on the geographic differentiation of apomicts and sexuals. Six ancestral species were identified that contributed to the contemporary gene pool of R. ser. Glandulosi. While sexuals were introgressed from R. dolichocarpus and R. moschus in West Asia and from R. ulmifolius agg., R. canescens and R. incanescens in Europe, apomicts were characterized by alleles of R. subsect. Rubus. Gene flow between sexuals and apomicts was also detected, as well as occasional hybridization with other taxa. We hypothesize that sexuals survived the last glacial period in several large southern refugia, whereas apomicts were mostly restricted to southern France from whence they quickly recolonized Central and Western Europe. The secondary contact of sexuals and apomicts was probably the principal factor that established geographic parthenogenesis in R. ser. Glandulosi. Sexual populations are not impoverished in genetic diversity along their borderline with apomicts and maladaptive population genetic processes likely did not shape the geographic patterns. HighlightsO_LIGeographic parthenogenesis in Rubus ser. Glandulosi is caused by secondary contact C_LIO_LIReticulate evolution in Eurasian brambles is more extensive than expected C_LIO_LIAt least six species contributed to the evolution of Rubus ser. Glandulosi C_LIO_LIExtinct ancestors gene pool is associated with apomixis C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/575855v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@a25ccforg.highwire.dtl.DTLVardef@17b1a5corg.highwire.dtl.DTLVardef@ffa036org.highwire.dtl.DTLVardef@6f6e0e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

evolutionary biology↗

bioRxiv2019

Plasticity of Medicago truncatula seed dormancy relates to large-scale environment variation

Seed dormancy and timing of its release is important developmental transition determining the survival of individual as well as population and species. We used Medicago truncatula as model to study legume seed dormancy in ecological and genomics context. The effect of oscillating temperatures as one of the dormancy release factor was tested over the period of 88 days on the set of 178 accessions originating from variable environmental conditions of Mediterranean basin. Phenotypic plasticity of final dormancy was significantly correlated with increased aridity, suggesting that plastic responses to external stimuli provide seeds with strong bet-hedging capacity and the potential to cope with high levels of environmental heterogeneity. Genome-wide association analysis identified candidate genes associated with dormancy release related to secondary metabolites synthesis, hormone regulation and modification of the cell wall likely mediating seed coat permeability and ultimately imbibition and germination. HighlightMedicago seed dormancy was correlated with increased aridity of the environment, suggesting that plastic responses provide seeds with a bet-hedging capacity. Genome-wide association analysis identified candidate genes associated with release from dormancy.

plant biology↗