Detlef Weigel

Biosynthetic gene clusters in Pseudomonas viridiflava have a fitness cost during Arabidopsis thaliana infection

The paper investigates biosynthetic gene clusters in Pseudomonas viridiflava and finds most reduce bacterial fitness during Arabidopsis thaliana infection, suggesting specialized metabolites may be more relevant for microbe-microbe interactions.

Centromeric origin of megabase-scale Arabidopsis interstitial telomeric repeat domains

The paper identifies centromeres as a source of telomeric sequences in Arabidopsis, showing ITR domains arise from centromeres through amplification and adopt a distinct chromatin state.

Dynamic co-existence of bacteriophages and their hosts in the Arabidopsis thaliana phyllosphere

This study tracks bacteriophage and bacterial community dynamics in Arabidopsis thaliana phyllosphere across growth stages, finding bacterial communities are more dynamic than their phages.

Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations

The paper examines transcriptome organization in wild Arabidopsis thaliana populations and finds that biotic-response networks are well conserved, while other networks are reorganized in natural settings.

Recruitment of SERK co-receptors determines signaling specificity within the systemin peptide family

The paper shows that different systemin peptides recruit specific SERK co-receptors, leading to distinct signaling responses in tomato plants.

Natural selection acting on the genetics of host response to commensal bacteria

This study identifies candidate genes and signatures of natural selection in Arabidopsis thaliana's response to commensal bacteria, revealing genetic architecture and adaptation mechanisms.

Multiple redundant mechanisms account for the majority of gene silencing downstream of DNA methylation

The paper shows that multiple redundant mechanisms account for most gene silencing downstream of DNA methylation, with loss of these pathways causing widespread derepression and genomic changes.

Cell-type specific gating of gene regulatory modules as a hallmark of early immune responses in Arabidopsis leaves

The paper examines cell-type specific gene regulatory responses in Arabidopsis during immune activation, identifying distinct defense strategies and regulatory modules.

Natural variation modifies centromere proximal meiotic crossover frequency and segregation distortion in Arabidopsis thaliana

The paper investigates how natural genetic variation in Arabidopsis thaliana affects centromere-proximal crossover frequency and segregation distortion during meiosis.

PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content

PanGene-O-Meter quantifies gene-content similarity between bacterial genomes, revealing hidden functional diversity and improving dereplication compared to ANI-based methods.

Pangenomic context reveals the extent of intraspecific plant NLR evolution

The paper analyzes NLR gene diversity in Arabidopsis thaliana using pangenomic methods to show that multiple mutational processes contribute to NLR variation without a single metric capturing all diversity.

Long-read detection of transposable element mobilization in the soma of hypomethylated Arabidopsis thaliana individuals

This study uses long-read sequencing to detect somatic transposable element mobilization in hypomethylated Arabidopsis thaliana mutants, revealing new mobile elements and variable activity within TE families.

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

The study shows that field conditions override the growth-defense tradeoff in Arabidopsis thaliana by modulating ACD6 activity, unlike greenhouse conditions.

Seasonality, land use, and host diversity shape microbiome-pathogen interactions in wild populations of Arabidopsis thaliana

The paper examines how seasonality, land use, and host diversity influence microbiome-pathogen interactions in wild Arabidopsis thaliana populations across different habitats.

Minimizing detection bias of somatic mutations in a highly heterozygous oak genome

The paper improves somatic mutation detection in a highly heterozygous oak genome by using a read assignment strategy, increasing the mutation rate estimate by fivefold.

Arabidopsis PRMT5 Buffers Pre-mRNA Splicing and Development Against Genetic Variation in Donor Splice Sites

Cryptic Variation in Adaptive Phenotypes Revealed by Panspecific flc Mutants

The paper investigates how genetic background modulates the effects of FLC mutants on flowering and other traits in Arabidopsis thaliana, revealing cryptic variation and pleiotropy.

The mutational dynamics of the Arabidopsis centromeres

This study defines the mutation spectrum in Arabidopsis thaliana centromeres, showing higher point mutation rates and homology-directed repair-driven indels.

Rapid adaptation and extinction across climates in synchronized outdoor evolution experiments of Arabidopsis thaliana

This study observes rapid genetic adaptation and population dynamics in Arabidopsis thaliana across diverse climates over 5 years, showing predictable adaptation trends linked to survival and extinction risks.

The structure of mitochondrial genomes is associated with geography in Arabidopsis thaliana

This study analyzes mitochondrial and chloroplast genomes of Arabidopsis thaliana to show that large repeats correlate with geography and phenotypes, and identify novel ORFs potentially from horizontal gene transfer.

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

The paper curates and presents a collection of long-read genome assemblies for Arabidopsis thaliana accessions to enhance plant genome research.

Gretl - Variation GRaph Evaluation TooLkit

Gretl evaluates genome graphs to identify genetic variation patterns and improve analysis of complex genomic data.

Gfa2bin enables graph-based GWAS by converting genome graphs to pan-genomic genotypes

Gfa2bin converts genome graphs to pan-genomic genotypes for GWAS, identifying additional associations with higher significance than SNP-based approaches in Arabidopsis thaliana.

The spliceosomal component GAMETOPHYTIC FACTOR 1 (GFA1) regulates a key photoperiodic switch

This study identifies GFA1 as a key photoperiodic switch regulating long-day flowering by affecting pre-mRNA splicing and photoreceptor signaling.

Building pangenome graphs

This paper introduces PGGB, a pipeline for building pangenome graphs that includes all variation without bias, enabling variation detection, conservation measurement, recombination event detection, and phylogenetic inference.

Widespread position-dependent transcriptional regulatory sequences in plants

The paper identifies position-dependent transcriptional regulatory sequences in plants, showing they differ from position-independent enhancers in animals.

Towards an unbiased characterization of genetic polymorphism

The paper analyzes whole-genome polymorphism data from 27 Arabidopsis thaliana genomes to highlight challenges and insights in unbiased genetic variation characterization.

Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

The paper presents a diploid genome assembly for Malbec grapevine, enabling haplotype-aware transcriptomic analysis to uncover molecular bases of clonal phenotypic variation.

TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data

TIPPo assembles organellar genomes using HiFi data without reference genomes or nuclear information, achieving complete chloroplast assemblies and improved mitochondrial results compared to existing tools.

Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis

The paper maps meiotic crossover landscapes near centromeres in Arabidopsis, showing suppression linked to structural variation and DNA methylation.