Biology subjects

Lipanova, V.

Publications and source records attributed to Lipanova, V..

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

Arabidopsis arenosa influences its microbiome as a serpentine soil adaptation strategy

There is growing evidence that microbes can facilitate plant growth in metal-rich soils. However, our current understanding of how plants recruit their microbiomes under abiotic stress remains incomplete. Serpentine soils are elementally skewed, with high concentrations of magnesium and nickel, often accompanied by other heavy metals, which can limit calcium availability and present unique challenges to plant growth. These soils are also nutrient-poor, prone to erosion, and have low water-holding capacity. To date, the mechanisms by which plants adapt to serpentine soils remain poorly understood and the role of plant-associated microbiomes in this process has not been described. Here, we focus on Arabidopsis arenosa populations adapted to serpentine conditions and investigate their bacterial and fungal microbiomes to better understand the role of plant-associated microbes in serpentine adaptation. We show that serpentine soils harbour distinct plant-associated microbiomes across different plant niches and that the plant genetic background plays a key role in shaping microbial community composition. Finally, we identify serpentine-specific bacterial and fungal variants that may contribute to plant adaptation under these challenging soil conditions.

ecology↗

bioRxiv2025

Soil heterogeneity and pleiotropy contribute to polygenic soil adaptation during postglacial range expansion in an alpine plant

1) Plants colonized new abiotic environments during postglacial range expansions. Little is known about whether populations adapt to different soil conditions during range expansion and, if so, which mechanisms underlie presumably polygenic adaptation. It remains unclear how pleiotropy and soil heterogeneity contribute to such adaptation. 2) We studied 43 populations of Dianthus sylvestris with characterized soil conditions along its postglacial range expansion in the Alps. We leveraged genome-wide data and variation in multiple soil variables to identify polygenic signatures of selection in soil-associated alleles using environmental association analysis, generalized dissimilarity models, and polygenic scores. 3) We found signatures of selection in 814 single nucleotide polymorphisms (SNPs) and the largest magnitude of allele frequency change in candidate SNPs associated with K, Mg, and Al. Candidate genes showed higher pleiotropy than randomly sampled genes. We found soil heterogeneity shaping the populations adaptive genetic variation in the landscape. 4) Our results suggest that populations of D. sylvestris adapted to contrasting soil chemical properties during postglacial range expansion through polygenic adaptation. Pleiotropy likely plays an important role in polygenic adaptation to novel selective pressures and soil heterogeneity is an important factor contributing to the maintenance of adaptive genetic variation.

evolutionary biology↗

bioRxiv2025

Whole-genome duplication reshapes adaptation: autotetraploid Arabidopsis arenosa leverages its high genetic variation to compensate for selection constraints.

Whole-genome duplication (WGD), a widespread macromutation across eukaryotes, is predicted to affect the tempo and modes of evolutionary processes. By theory, the additional set(s) of chromosomes present in polyploid organisms may reduce the efficiency of selection while, simultaneously, increasing heterozygosity and buffering deleterious mutations. Despite the theoretical significance of WGD, empirical genomic evidence from natural polyploid populations is scarce and a direct comparisons of selection footprints between autopolyploids and closely related diploids remains completely unexplored. We therefore combined locally sampled soil data with resequenced genomes of 76 populations of diploid-autotetraploid Arabidopsis arenosa and tested whether the genomic signatures of adaptation to distinct siliceous and calcareous soils differ between the ploidies. Leveraging multiple independent transitions between these soil types in each ploidy, we identified a set of genes associated with ion transport and homeostasis that were repeatedly selected for across the species range. Notably, polyploid populations have consistently retained greater variation at candidate loci compared to diploids, reflecting lower fixation rates. In tetraploids, positive selection predominantly acts on such a large pool of standing genetic variation, rather than targeting de novo mutations. Finally, selection in tetraploids targets genes that are more central within the protein- protein interaction network, potentially impacting a greater number of downstream fitness-related traits. In conclusion, both ploidies thrive across a broad gradient of substrate conditions, but WGD fundamentally alters the ploidies adaptive strategies: tetraploids leverage their greater genetic variation and redundancy to compensate for the predicted constraints on the efficacy of positive selection.

evolutionary biology↗