Detlef Weigel

Bio: Detlef Weigel is an academic researcher from Max Planck Society. The author has contributed to research in topics: Arabidopsis & Arabidopsis thaliana. The author has an hindex of 142, co-authored 516 publications receiving 84670 citations. Previous affiliations of Detlef Weigel include Ludwig Maximilian University of Munich & California Institute of Technology.

The rate and effect of de novo mutations in natural populations of Arabidopsis thaliana

Abstract: Like many other species, the plant Arabidopsis thaliana has been introduced in recent history from its native Eurasian range to North America, with many individuals belonging to a single lineage. We have sequenced 100 genomes of present-day and herbarium specimens from this lineage, covering the time span from 1863 to 2006. Within-lineage recombination was nearly absent, greatly simplifying the genetic analysis, allowing direct estimation of the mutation rate and an introduction date in the early-17th century. The comparison of substitution rates at different sites throughout the genome reveals that genetic drift predominates, but that purifying selection in this rapidly expanding population is nevertheless evident even over short historical time scales. Furthermore, an association analysis identifies new mutations affecting root development, a trait important for adaptation in the wild. Our work illustrates how mutation and selection rates can be observed directly by combining modern genetic methods and historic samples.

On epigenetics and epistasis: hybrids and their non-additive interactions.

Abstract: Hybrid seeds have been a key component of greatly increasing the yield of many important crops, foremost of maize. If the parents are properly chosen, non-additive interactions between diverged genomes can lead to strongly superior performance of the F1 progeny, known as heterosis. While many different explanations have been advanced, a consensus for the causes of genome-wide positive epistasis in hybrids has not emerged. In this issue of The EMBO Journal, Shivaprasad and colleagues describe a new mechanism that can account for heterosis often being a genome-wide phenomenon. These authors show that small RNA (sRNA) loci of tomato can exhibit transgressive activity, which can in turn lead to epigenetic and gene expression changes within hybrid progeny. This is particularly exciting because many sRNAs are produced from non-coding regions or transposable elements (TEs), which diverge more quickly than protein-coding genes and thus provide more opportunity for unexpected genetic interactions. Epistasis is defined as a non-additive genetic interaction, where the interaction may be described as transgressive if the hybrid progeny is in some way either superior to the better or inferior to the worse parent. Transgression has been previously suggested to facilitate hybrid niche specialization and is particularly important in crop breeding (i.e., when hybrid yields are higher than those of either parent). sRNAs play an important role in gene and genome regulation. MicroRNAs (miRNAs) and trans-acting small interfering RNAs (tasiRNAs) regulate coding transcript levels, while small interfering RNAs (siRNAs) guide DNA methylation and stable chromatin modifications predominantly at TEs and other repeat sequences. These epigenetic marks keep TEs repressed, thereby limiting potentially detrimental transposition events. Epigenetic and sRNA differences between and within species are relatively poorly described compared with genetic and transcriptome variation. Nonetheless, since genomic differences are overrepresented within TEs and repeat elements, which are controlled by siRNAs, one might expect that divergent epigenetic modifications could make major contributions to hybrid phenotypes. In agreement, TEs can be activated in interspecific hybrids, accompanied by changes in DNA methylation (Michalak, 2009), and TEs have been proposed to contribute to transgressive phenotypes

Musterbildung bei Drosophila

Abstract: Drosophila proved an excellent system to study molecular processes in establishing the body pattern of an embryo. Genes which are active during oogenesis provide localized cues which regulate a cascade of zygotic genes that determines the developmental fate of the blastoderm cells along the longitudinal axis of the embryo.

MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data

Abstract: Abstract Abstract Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype–epigenotype associations .

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

Human biochemical genetics

Abstract: So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

Abstract: The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans--the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.