Biology subjects

Kersten, S.

Publications and source records attributed to Kersten, S..

18 recordsLinked to original sources

bioRxiv2026

Probing the transcriptome response to shivering in skeletal muscle using a multilayered bioinformatics approach

Cold acclimation holds therapeutic potential for improving metabolic health. We previously demonstrated that repeated cold-induced shivering enhances insulin sensitivity in humans. However, the molecular pathways that underlie the skeletal muscle shivering response, and how these relate to beneficial physiological effects, remain poorly understood. In this study, we combined complementary bioinformatics approaches to allow in-depth analysis of the transcriptomic response of human skeletal muscle to repeated shivering. We identified a robust transcriptional signature and show a sex-specific component in the shivering skeletal muscle response, which seemed to diminish following cold adaptation. Our findings provide mechanistic insights into cold-induced muscle adaptations, shed light on potential interesting molecular targets for further investigation, and emphasize the importance of including both sexes in future cold acclimation studies.

bioinformatics↗

bioRxiv2026

A Polygenic Route to Thermal Melanism and high-elevation adaptation in Honey Bees

Thermal melanism, whereby darker pigmentation occurs in colder environments, is a widespread adaptive pattern, yet its genetic and physiological basis in eusocial insects remains poorly understood. East African honey bees (Apis mellifera) occupy steep elevational gradients in which highland populations are darker, larger, and more cold tolerant than lowland conspecifics. Here, we integrated population genomics, structural variation, reciprocal translocations, and functional genomics to dissect the basis of elevational melanism in honey bees. 139 workers from five East African mountain systems were sampled and phenotyped, and whole-genome resequencing was performed. A genome-wide association study identified 977 SNPs significantly associated with abdominal pigmentation, with a single pronounced peak at the ebony ortholog AmEbony on chromosome CM009931.2. Allelic variation at AmEbony formed three genetic clusters that closely tracked a continuous pigmentation gradient, and 77 highly divergent SNPs (DXY = 1) almost perfectly discriminated dark from light bees. Two large inversions (r7, r9), previously linked to high-elevation adaptation, were detected across additional mountain systems and were enriched in dark, highland genomic backgrounds, but did not replace AmEbony as the primary pigmentation locus. Reciprocal highland-lowland translocations revealed lineage-specific yet convergent expression shifts along detoxification/immune, chemosensory, proteostasis, and cuticle axes. CRISPR/Cas9-mediated disruption of AmEbony in A. m. carnica altered pigmentation and induced coherent changes in head transcriptomes, notably in odorant-binding and redox-related modules. Our results demonstrate that thermal melanism in a eusocial pollinator is governed by a top-heavy polygenic architecture centered on AmEbony, linking mechanistically naturally segregating pigmentation alleles to gene regulatory reprogramming and high-elevation adaptation.

evolutionary biology↗

bioRxiv2025

Weight cycling-induced hypothalamic and metabolic tissue immune remodeling is uncoupled from metabolic dysfunctions

BackgroundObesity-induced insulin resistance is associated with white adipose tissue (WAT) and liver inflammation, which are both mitigated by weight loss. However, most individuals undergoing weight loss will regain lost weight, resulting in weight cycling (WC), which may exacerbate metabolic dysfunctions. Here, we studied the immunometabolic impact of WC in mice. MethodsC57BL/6J mice were exposed to two cycles of weight gain and weight loss by alternating between low (LFD) and high-fat diet (HFD) feeding. Animals were sacrificed when WC mice were weight stable for 10 weeks upon weight loss (WC-lean) and after a subsequent exposure to weight regain for 10 weeks (WC-obese), and compared to mice persistently fed LFD (LFD-lean) or HFD (HFD-obese). ResultsBody weight stabilized at a higher level in WC-lean mice after two weight gain/loss cycles compared to LFD-lean controls. While insulin resistance, metabolic tissue inflammation, and hepatic steatosis normalized between the two groups of lean mice, WC-lean mice exhibited features of WAT dysfunction. In the hypothalamus, inflammatory microglia were less abundant in WC-lean mice compared to LFD-lean mice, but mean individual microglial cell volume was larger. WC-obese mice stabilized at slightly lower weight compared with HFD-obese controls. Intriguingly, WC-obese mice exhibited increased WAT macrophages and reduced WAT and liver effector T cells compared to HFD-obese mice, whereas energy intake, body composition, whole-body insulin resistance and hepatic steatosis were similar. ConclusionsOur results suggest that WC in mice differently impacts animals in the weight-stable lean and obese states. WC-lean mice display features of a novel body weight settling point, associated with hypothalamic inflammatory changes. However, metabolic dysfunctions were uncoupled from WC-induced metabolic tissue inflammation in WC-obese mice.

immunology↗

bioRxiv2025

Transcription-based identification of uncharacterized genes in the human immune response

Host-pathogen interactions are shaped by the nature of the pathogen and by host-related factors. The human host responses can be characterized in microbe-stimulated immune cells using transcriptomics. We set out to characterize gene expression changes as a result of microbial in vitro stimulation in RPMI-cultured human primary immune cells, using four pathogen ligands representing bacteria (LPS and S. aureus), viruses (Poly(I:C)) and fungi (C. albicans) for 4 and 24 hours, resulting in a total of 52 samples for analysis. We analyze the transcriptional changes on gene- and pathway level, highlighting common and distinct effects of pathogen stimulation. We highlight genes without a known function that were differentially expressed as a common effect of pathogen stimulation. We find uncharacterized genes such as KIAA0040 and CYRIA to be co-expressed with genes involved in innate immunity and downstream signaling from the PRRs, respectively. We identify 901 variants in uncharacterized genes in a cohort of patients with rare immune disorders, prioritizing 5 candidate variants in 4 genes that could underly these diseases. Our results therefore indicate the potential role of these genes the human immune response and provides candidate variants with potential relevance in rare immune-mediated diseases.

genomics↗

bioRxiv2024

Field conditions greatly modify a major growth-defense tradeoff in Arabidopsis thaliana

When plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off in the plant Arabidopsis thaliana is ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild plant populations maintain significant functional variation in the ACD6 gene, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactive ACD6 alleles are resistant to diverse pathogens, yet are of smaller stature, their leaves senesce earlier, and they set fewer seeds. We hypothesized that such hyperactive alleles would not only affect the growth of microbial pathogens, but also more generally leaf microbiome assembly in the wild. To test this, we grew plants with hyperactive, standard, and defective ACD6 alleles in the same field-collected soil, both in climate-controlled conditions and outdoors. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. To our surprise, we discovered that mature field plants, in stark contrast to greenhouse plants, were unaffected by their ACD6 genotype, suggesting that additional abiotic and/or microbial signals present outdoors - but not in the greenhouse - greatly modulate ACD6 activity.

plant biology↗

bioRxiv2023

Multi-omic profiling of pathogen-stimulated primary immune cells

We performed long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs) from healthy donors to discover new transcript and protein isoforms expressed during immune responses to diverse pathogens. Long-read transcriptome profiling reveals novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing. Widespread loss of intron retention occurs as a common result of all pathogen stimulations. We highlight novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms. RNA expression differences did not result in differences in the amounts of secreted proteins. Clustering analysis of secreted proteins revealed a correlation between chemokine (receptor) expression on the RNA and protein levels in C. albicans- and Poly(I:C)-stimulated PBMCs. Isoform aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.

immunology↗

bioRxiv2023

In-depth immunometabolic profiling by measuring single-cell protein translation inhibition via bioorthogonal noncanonical amino acid tagging (SCENITH-BONCAT)

MotivationExtracellular Flux (XF) analysis has been a key technique in immunometabolism research, measuring cellular oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) to determine immune cell metabolic profiles. However, XF analysis has several limitations, including the need for purified adherent cells, relatively high cell numbers, and specialized equipment. Recently, a novel flow cytometry-based technique called SCENITH (Single Cell Energetic metabolism by profiling Translation inhibition) was introduced, which measures the inhibition of cellular protein synthesis as a proxy for metabolic activity in single cells. A limitation of this technique is its reliance on fluorescent staining of intracellular puromycin, a toxic antibiotic. To address this, we propose an alternative approach using biorthogonal noncanonical amino acid tagging (BONCAT) to measure protein synthesis. SummaryThe field of immunometabolism has revealed that cellular energy metabolism significantly contributes to immune cell function. Disturbances in immune cell metabolism have been associated with various diseases, including obesity, atherosclerosis, and cancer. To further advance immunometabolic research, developing novel methods to study the metabolism of immune cells in complex samples is essential. Here, we introduce CENCAT (Cellular Energetics through Non-Canonical Amino acid Tagging). This technique utilizes click-labeling of alkyne-bearing non-canonical amino acids (ncAAs) to measure protein synthesis inhibition as a proxy of metabolic activity. CENCAT successfully reproduced known metabolic signatures of immune cell activation. Specifically, LPS/IFN{gamma}-induced classical activation increased glycolytic capacity, and IL-4-induced alternative activation enhanced mitochondrial dependence in human primary macrophages. The assays applicability was further explored in more complex samples, including peripheral blood mononuclear cells (PBMCs) from healthy volunteers, which revealed diverse metabolic rewiring in immune cell subsets upon stimulation with different activators. Finally, CENCAT was used to analyze the cellular metabolism of murine tissue-resident immune cells from various organs. Principal component analysis (PCA) revealed tissue-specific clustering based on metabolic profiles, likely driven by microenvironmental priming of tissue-resident immune cells. In conclusion, CENCAT offers valuable insights into immune cell metabolic responses and presents a powerful platform for studying immune cell metabolism in complex samples and tissue-resident immune populations in both human and murine studies.

immunology↗

bioRxiv2022

SUsPECT: A pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation

Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular in transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are predicted to be benign using the reference transcript annotation. In further support of SUsPECTs utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.

bioinformatics↗

bioRxiv2022

Deep haplotype analyses of target-site resistance locus ACCase in blackgrass enabled by pool-based amplicon sequencing

Rapid adaptation of weeds to herbicide applications in agriculture through resistance development is a widespread phenomenon. In particular, the grass Alopecurus myosuroides is an extremely problematic weed in cereal crops with the potential to manifest resistance in the course of only a few generations. Target-site resistances (TSRs), with their strong phenotypic response, play an important role in this rapid adaptive response. Recently, using PacBios long-read amplicon sequencing technology in hundreds of individuals, we were able to decipher the genomic context in which TSR mutations occur. However, sequencing individual amplicons is both costly and time consuming, thus impractical to implement for other resistance loci or applications. Alternatively, pool-based approaches overcome these limitations and provide reliable allele frequencies, albeit at the expense of not preserving haplotype information. In this proof-of-concept study, we sequenced with PacBio High Fidelity (HiFi) reads long-range amplicons (13.2 kb) encompassing the entire ACCase gene in pools of over hundred individuals, and resolved them into haplotypes using the clustering algorithm PacBio amplicon analysis (pbaa), a new application for pools and for plants. From these amplicon pools, we were able to recover most haplotypes from previously sequenced individuals of the same population. In addition, we analyzed new pools from a Germany-wide collection of A. myosuroides populations and found that TSR mutations originating from soft sweeps of independent origin were common. Forward-in-time simulations indicate that TSR haplotypes will persist for decades even at relatively low frequencies and without selection, pointing to the importance of accurate measurement of TSR haplotype prevalence for weed management.

genomics↗

bioRxiv2021

Caveolae mediated endocytosis of VLDL particles in macrophages requires NPC1 and STARD3 for further lysosomal processing

Macrophages accumulate triglycerides under certain pathological conditions such as atherosclerosis. Triglycerides are carried in the bloodstream as part of very low-density lipoproteins (VLDL) and chylomicrons. How macrophages take up and process VLDL-lipids is not very well known. Here, using VLDL-sized triglyceride-rich emulsion particles, we aimed to study the mechanism by which VLDL-triglycerides are taken up, processed, and stored in macrophages. Our results show that macrophage uptake of emulsion particles mimicking VLDL (VLDLm) is dependent on lipoproteins lipase (LPL) and requires the lipoprotein-binding C-terminal domain of LPL but not the catalytic N-terminal domain. Subsequent internalization of VLDLm-triglycerides by macrophages is carried out by caveolae-mediated endocytosis, followed by triglyceride hydrolysis catalyzed by lysosomal acid lipase. Transfer of lysosomal fatty acids to the ER for subsequent storage as triglycerides is mediated by Stard3, whereas NPC1 was found to promote the extracellular efflux of fatty acids from lysosomes. Our data provide novel insights into how macrophages process VLDL-derived triglycerides and suggest that macrophages have the remarkable capacity to excrete part of the internalized triglycerides as fatty acids. SummaryTriglyceride-rich lipoproteins and their remnants contribute to atherosclerosis, possibly by carrying remnant cholesterol and/or by exerting a pro-inflammatory effect on macrophage. Nevertheless, little is known about how macrophages process triglyceride-rich lipoproteins. We show that uptake by macrophages of VLDL-like particles is dependent on the enzyme lipoproteins lipase via its C-terminal domain. Subsequent internalization of VLDL-triglycerides by macrophages is carried out by caveolae-mediated endocytosis, followed by hydrolysis by lysosomal acid lipase. Transfer of lysosomal fatty acids to the ER for lipid storage is mediated by Stard3, while NPC1 promotes the extracellular efflux of fatty acids. Our data provide novel insights into how macrophages process VLDL-derived triglycerides and suggest that macrophages have the remarkable capacity to excrete internalized triglycerides as fatty acids. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

cell biology↗

bioRxiv2021

Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.

evolutionary biology↗

bioRxiv2021

Transcriptomic analysis reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes

Various forms of fasting, including time-restricted feeding, alternate day fasting, and periodic fasting have shown promise in clinical and pre-clinical studies to normalize body weight, improve metabolic health, and protect against disease. Recent studies suggest that {beta}-hydroxybutyrate ({beta}OHB), a characteristic ketone body of the fasted metabolic state, acts as a potential signaling molecule mediating the beneficial effects of the various forms of fasting, potentially by acting as a histone deacetylase inhibitor. In the first part we investigated whether {beta}OHB, in comparison to the well-established histone deacetylase inhibitor butyrate, influences cellular differentiation in vitro. In C2C12 myotubes, 3T3-L1 adipocytes, and THP-1 monocytes, millimolar concentrations of {beta}OHB did not alter differentiation, as determined by gene expression and histological assessment, whereas equimolar concentrations of butyrate potently impaired differentiation in all cell types. RNA-sequencing revealed that unlike butyrate, {beta}OHB minimally impacted gene expression in adipocytes, macrophages, and hepatocytes. However, in myocytes, {beta}OHB upregulated genes involved in the TCA cycle and oxidative phosphorylation, while downregulating genes belonging to cytokine and chemokine signal transduction. Overall, our data do not support the notion that {beta}OHB serves as a powerful signaling molecule regulating gene expression in adipocytes, macrophages and hepatocytes, but suggest that {beta}OHB may act as a niche signaling molecule in muscle.

molecular biology↗

bioRxiv2020

Hypoxia-inducible lipid droplet-associated interacts with DGAT1 to promote lipid storage in hepatocytes

Lipid droplets (LD) are dynamic organelles that can expand and shrink, driven by fluctuations in the rate of triglyceride synthesis and degradation. Triglyceride synthesis, storage in LD, and degradation are governed by a complex set of LD-associated proteins. One of these LD-associated proteins, hypoxia-inducible lipid droplet-associated (HILPDA), was found to impair LD breakdown by inhibiting adipose triglyceride lipase. Here we characterized the physiological role and mechanism of action of HILPDA in hepatocytes. Expression of HILPDA was induced by fatty acids in several hepatoma cell lines. Hepatocyte-specific deficiency of HILPDA in mice modestly but significantly reduced hepatic triglycerides in mice with non-alcoholic fatty liver disease. Similarly, deficiency of HILPDA in mouse precision-cut liver slices and primary hepatocytes reduced lipid storage and accumulation of fluorescently-labelled fatty acids in LD, respectively, which was independent of adipose triglyceride lipase. Fluorescence microscopy showed that HILPDA partly colocalizes with LD and with the endoplasmic reticulum, is especially abundant in perinuclear areas, and mainly associates with newly added fatty acids. Real-time fluorescence live-cell imaging further revealed that HILPDA preferentially localizes to LD that are being remodelled. Mechanistically, HILPDA overexpression increased lipid storage in human hepatoma cells concomitant with an increase in DGAT activity and DGAT1 protein levels. Finally, confocal microscopy and Forster resonance energy transfer-fluorescence lifetime imaging microscopy analysis indicated that HILPDA colocalizes and physically interacts with DGAT1. Overall, our data indicate that HILPDA physically interacts with DGAT1 and increases DGAT activity. These findings suggest a novel mechanism in hepatocytes that links elevated fatty acid levels to stimulation of triglyceride synthesis and storage.

biochemistry↗

bioRxiv2019

The relationship between microbial biomass and disease in the Arabidopsis thaliana phyllosphere

A central goal in microbiome research is to learn what distinguishes a healthy from a dysbiotic microbial community. Shifts in diversity and taxonomic composition are important indicators of dysbiosis, but a full understanding also requires knowledge of absolute microbial population sizes. In addition to the number of microbial cells, information on taxonomic composition can provide important insight into microbiome function and disease state. Here we use shotgun metagenomics to simultaneously assess microbiome composition and microbial load in the phyllosphere of wild populations of the plant Arabidopsis thaliana. We find that wild plants vary substantially in the load of colonizing microbes, and that high loads are typically associated with the proliferation of single taxa, with only a few putatively pathogenic taxa achieving high abundances in the field. Our results suggest (i) that the inside of a plant leaf is on average sparsely colonized with an estimated two bacterial genomes per plant genome and an order of magnitude fewer eukaryotic microbial genomes, and (ii) that higher levels of microbial cells often indicate successful colonization by pathogens. Lastly, our results show that load is a significant explanatory variable for loss of estimated Shannon diversity in phyllosphere microbiomes, implying that reduced diversity may be a significant predictor of microbial dysbiosis in a plant leaf.

plant biology↗

bioRxiv2019

Combining whole genome shotgun sequencing and rDNA amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves

Microorganisms from all domains of life establish associations with plants. Although some harm the plant, others antagonize pathogens or prime the plant immune system, acquire nutrients, tune plant hormone levels, or perform additional services. Most culture-independent plant microbiome research has focused on amplicon sequencing of 16S rDNA and/or the internal transcribed spacer (ITS) of rDNA loci, but the decreasing cost of high-throughput sequencing has made shotgun metagenome sequencing increasingly accessible. Here, we describe shotgun sequencing of 275 wild Arabidopsis thaliana leaf microbiomes from southwest Germany, with additional bacterial 16S rDNA and eukaryotic ITS1 amplicon data from 176 of these samples. The shotgun data were dominated by bacterial sequences, with eukaryotes contributing only a minority of reads. For shotgun and amplicon data, microbial membership showed weak associations with both site of origin and plant genotype, both of which were highly confounded in this dataset. There was large variation among microbiomes, with one extreme comprising samples of low complexity and a high load of microorganisms typical of infected plants, and the other extreme being samples of high complexity and a low microbial load. We use the metagenome data, which captures the ratio of bacterial to plant DNA in leaves of wild plants, to scale the 16S rDNA amplicon data such that they reflect absolute bacterial abundance. We show that this cost-effective hybrid strategy overcomes compositionality problems in amplicon data and leads to fundamentally different conclusions about microbiome community assembly.

genomics↗

bioRxiv2019

HILPDA uncouples lipid storage in adipose tissue macrophages from inflammation and metabolic dysregulation

Obesity promotes accumulation of lipid-laden macrophages in adipose tissue. Here, we determined the role of macrophage lipid accumulation in the development of obesity-induced adipose tissue inflammation, using mice with myeloid-specific deficiency of the lipid-inducible HILPDA protein. HILPDA deficiency in bone marrow-derived macrophages markedly reduced intracellular lipid levels and accumulation of fluorescently-labeled fatty acids in lipid droplets. Decreased lipid storage in HILPDA-deficient macrophages could be almost completely rescued by inhibition of adipose triglyceride lipase (ATGL) and was associated with increased oxidative metabolism. In diet-induced obese mice, HILPDA deficiency did not alter inflammatory or metabolic parameters, despite markedly reducing lipid storage in adipose tissue macrophages. Our data indicate that HILPDA is a lipid-induced physiological inhibitor of ATGL-mediated lipolysis that uncouples lipid storage in adipose tissue macrophages from inflammation and metabolic dysregulation. Overall, our data question the importance of lipid storage in adipose tissue macrophages in obesity-induced inflammation and metabolic dysregulation.

physiology↗

bioRxiv2018

Arabidopsis thaliana populations support long-term maintenance and parallel expansions of related Pseudomonas pathogens

Crop disease outbreaks are often associated with clonal expansions of single pathogenic lineages. To determine whether similar boom-and-bust scenarios hold for wild plant pathogens, we carried out a multi-year multi-site survey of Pseudomonas in the natural host Arabidopsis thaliana. The most common Pseudomonas lineage corresponded to a pathogenic clade present in all sites. Sequencing of 1,524 Pseudomonas genomes revealed this lineage to have diversified approximately 300,000 years ago, containing dozens of genetically distinct pathogenic sublineages. These sublineages have expanded in parallel within the same populations and are differentiated both at the level of gene content and disease phenotype. Such coexistence of diverse sublineages indicates that in contrast to crop systems, no single strain has been able to overtake these A. thaliana populations in the recent past. Our results suggest that the selective pressures acting on a plant pathogen in wild hosts may be more complex than those in agricultural systems.

microbiology↗

bioRxiv2017

A rainfall-manipulation experiment with 517 Arabidopsis thaliana accessions

The gold standard for studying natural selection and adaptation in the wild is to quantify lifetime fitness of individuals from natural populations that have been grown together in a common garden, or that have been reciprocally transplanted. By combining fitness values with species traits and genome sequences, one can infer selection coefficients at the genetic level. Here we present a rainfall-manipulation experiment with 517 whole-genome sequenced natural accessions of the plant Arabidopsis thaliana spanning the global distribution of the species. The experiments were conducted in two field stations in contrasting climates, in the Mediterranean and in Central Europe, where we built rainout shelters and simulated high and low rainfall. Using custom image analysis we quantified fitness- and phenology-related traits for 23,154 pots, which contained about 14,500 plants growing independently, and over 310,000 plants growing in small populations (max. 30 plants). This large field experiment dataset, which associates fitness and ecologically-relevant traits with genomes, will provide an important resource to test eco-evolutionary genetic theories and to understand the potential evolutionary impacts of future climates on an important plant model species.

evolutionary biology↗