Claude Becker
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View article: Plant specialised metabolites modulate the molecular signatures of host-bacteria and bacteria-bacteria interactions
Plant specialised metabolites modulate the molecular signatures of host-bacteria and bacteria-bacteria interactions Open
Plants participate in intricate interactions with a multitude of microorganisms, many of which also influence each other. This holobiont is situated in a chemical soil environment that is defined, in parts, by the specialised metabolite le…
View article: A TNL receptor mediates microbiome feedbacks in Arabidopsis
A TNL receptor mediates microbiome feedbacks in Arabidopsis Open
Plant performance depends on the soil microbiome. While microbiome feedbacks are well documented, the mechanisms by which plants perceive and mediate these feedbacks remain unclear. We established a framework using two distinct microbiomes…
View article: Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster in <i>Solanaceae</i>
Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster in <i>Solanaceae</i> Open
Biosynthetic gene clusters (BGCs) are sets of often heterologous genes that are genetically and functionally linked. Among eukaryotes, BGCs are most common in plants and fungi and ensure the coexpression of the different enzymes coordinati…
View article: Evolution and diversification of the momilactone biosynthetic gene cluster in the genus <i>Oryza</i>
Evolution and diversification of the momilactone biosynthetic gene cluster in the genus <i>Oryza</i> Open
Summary Plants are master chemists and collectively are able to produce hundreds of thousands of different organic compounds. The genes underlying the biosynthesis of many specialized metabolites are organized in biosynthetic gene clusters…
View article: The 1001G+ project: A curated collection of <i>Arabidopsis thaliana</i> long-read genome assemblies to advance plant research
The 1001G+ project: A curated collection of <i>Arabidopsis thaliana</i> long-read genome assemblies to advance plant research Open
Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorp…
View article: Sub-functionalization and epigenetic regulation of a biosynthetic gene cluster in<i>Solanaceae</i>
Sub-functionalization and epigenetic regulation of a biosynthetic gene cluster in<i>Solanaceae</i> Open
Biosynthetic gene clusters (BGCs) are sets of often heterologous genes that are genetically and functionally linked. Among eukaryotes, BGCs are most common in plants and fungi, where they ensure the co-expression of the different enzymes c…
View article: High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar
High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive transposable element superfamilies in the clonal Lombardy poplar Open
DNA methylation is environment-sensitive and can mediate stress responses. In trees, changes in the environment might cumulatively shape the methylome landscape over time. However, because high-resolution methylome studies usually focus on…
View article: Comparative RNA-seq analysis of Arabidopsis thaliana response to AtPep1 and flg22, reveals the identification of PP2-B13 and ACLP1 as new members in pattern-triggered immunity
Comparative RNA-seq analysis of Arabidopsis thaliana response to AtPep1 and flg22, reveals the identification of PP2-B13 and ACLP1 as new members in pattern-triggered immunity Open
In this research, a high-throughput RNA sequencing-based transcriptome analysis technique (RNA-Seq) was used to evaluate differentially expressed genes (DEGs) in the wild type Arabidopsis seedlings in response to At Pep1, a well-known pept…
View article: Transposon dynamics in the emerging oilseed crop Thlaspi arvense
Transposon dynamics in the emerging oilseed crop Thlaspi arvense Open
Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspeci…
View article: Evolution and diversification of the momilactone biosynthetic gene cluster in the genus<i>Oryza</i>
Evolution and diversification of the momilactone biosynthetic gene cluster in the genus<i>Oryza</i> Open
Plants are master chemists and collectively are able to produce hundreds of thousands of different organic compounds. The genes underlying the biosynthesis of many specialized metabolites are organized in biosynthetic gene clusters (BGCs),…
View article: <scp>DNA</scp> methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (<i>Fragaria vesca</i>)
<span>DNA</span> methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (<i>Fragaria vesca</i>) Open
Summary Due to the accelerating climate change, it is crucial to understand how plants adapt to rapid environmental changes. Such adaptation may be mediated by epigenetic mechanisms like DNA methylation, which could heritably alter phenoty…
View article: Data from: High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive TE superfamilies in the clonal Lombardy poplar
Data from: High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive TE superfamilies in the clonal Lombardy poplar Open
The following dataset contains the processed data presented in the article "High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive TE superfamilies in the clonal Lombardy poplar" Supplementary_…
View article: Data from: High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive TE superfamilies in the clonal Lombardy poplar
Data from: High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive TE superfamilies in the clonal Lombardy poplar Open
The following dataset contains the processed data presented in the article "High-resolution methylome analysis uncovers stress-responsive genomic hotspots and drought-sensitive TE superfamilies in the clonal Lombardy poplar" Supplementary_…
View article: The lactonase BxdA mediates metabolic adaptation of maize root bacteria to benzoxazinoids
The lactonase BxdA mediates metabolic adaptation of maize root bacteria to benzoxazinoids Open
Root exudates contain secondary metabolites that affect the plant’s root microbiome. How microbes cope with these bioactive compounds, and how this ability shapes root microbiomes remain largely unknown. We investigated how maize root bact…
View article: Histone Deacetylases HD2A and HD2B Undergo Feedback Regulation by ABA and Modulate Drought Tolerance via Mediating ABA-Induced Transcriptional Repression
Histone Deacetylases HD2A and HD2B Undergo Feedback Regulation by ABA and Modulate Drought Tolerance via Mediating ABA-Induced Transcriptional Repression Open
Histone deacetylation catalyzed by histone deacetylase plays a critical role in gene silencing and subsequently controls many important biological processes. It was reported that the expression of the plant-specific histone deacetylase sub…
View article: Arabidopsis histone deacetylase HD2A and HD2B regulate seed dormancy by repressing DELAY OF GERMINATION 1
Arabidopsis histone deacetylase HD2A and HD2B regulate seed dormancy by repressing DELAY OF GERMINATION 1 Open
Seed dormancy is a crucial developmental transition that affects the adaption and survival of plants. Arabidopsis DELAY OF GERMINATION 1 (DOG1) is known as a master regulator of seed dormancy. However, although several upstream factors of …
View article: Transposon dynamics in the emerging oilseed crop<i>Thlaspi arvense</i>
Transposon dynamics in the emerging oilseed crop<i>Thlaspi arvense</i> Open
Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspeci…
View article: DNA methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (Fragaria vesca)
DNA methylation in the wild: epigenetic transgenerational inheritance can mediate adaptation in clones of wild strawberry (Fragaria vesca) Open
Due to the accelerating climate change, it is crucial to understand how plants adapt to rapid environmental changes. Such adaptation may be mediated by epigenetic mechanisms like DNA methylation, which could heritably alter phenotypes with…
View article: DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)
DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca) Open
Genome sequence and annotation of Fragaria vesca cv. Reine des Vallées In order to generate a reference genome for Fragaria vesca cv. Reine des Vallées, we used MinIon long-read sequencing data to substitute the F. vesca genome v.4.0.a2 ge…
View article: DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca)
DNA methylation dynamics during stress-response in woodland strawberry (Fragaria vesca) Open
Genome sequence and annotation of Fragaria vesca cv. Reine des Vallées In order to generate a reference genome for Fragaria vesca cv. Reine des Vallées, we used MinIon long-read sequencing data to substitute the F. vesca genome v.4.0.a2 ge…
View article: Epigenetic variation in the Lombardy poplar along climatic gradients is independent of genetic structure and persists across clonal reproduction
Epigenetic variation in the Lombardy poplar along climatic gradients is independent of genetic structure and persists across clonal reproduction Open
Summary - Environmental changes can trigger phenotypic variation in plants through epigenetic mechanisms, but strong genetic influences make it difficult to isolate and study epigenetic effects. Clonal trees with low genetic variation, suc…
View article: Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor
Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor Open
Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as som…
View article: High-resolution methylome analysis in the clonal<i>Populus nigra</i>cv. ‘Italica’ reveals environmentally sensitive hotspots and drought-responsive TE superfamilies
High-resolution methylome analysis in the clonal<i>Populus nigra</i>cv. ‘Italica’ reveals environmentally sensitive hotspots and drought-responsive TE superfamilies Open
/SUMMARY DNA methylation is environment-sensitive and can mediate plant stress responses. In long-lived trees, changing environments might cumulatively shape the methylome landscape over their lifetime. However, because high-resolution met…
View article: Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense
Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense Open
Natural plant populations often harbour substantial heritable variation in DNA methylation. However, a thorough understanding of the genetic and environmental drivers of this epigenetic variation requires large-scale and high-resolution da…
View article: Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense
Genetic and environmental drivers of large-scale epigenetic variation in Thlaspi arvense Open
This repository stores data produced from a genomic and epigenomic large-scale survey of natural populations of Thlaspi arvense, investigating the genetic and environmental bases of epigenetic variation. 207 lines from across Europe were g…