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.

Leafy Controls Meristem Identity in Arabidopsis

Abstract: Flower development can be broken down into at least five steps: (1) Upon floral induction, the vegetative shoot meristem is converted into an inflorescence meristem. (2) The inflorescence meristem starts to generate floral meristems, or is itself transformed into a floral meristem. This step can be preceded by the generation of a limited number of secondary inflorescence meristems by the primary inflorescence meristem. (3) The floral meristems produce floral organ primordia. (4) The floral organ primordia adopt different fates according to their position within the developing flower. (5) The floral organ primordia differentiate into floral organs. Despite many efforts, very little is known about the molecules directing these processes. Since classical physiological approaches toward understanding flower development have met only with limited success, a genetic-molecular approach has recently been chosen by several groups (e.g., Komaki et al., 1988; Bowman et al., 1989, 1991, 1992; Hill and Lord, 1989; Kunst et al., 1989; Sommer et al., 1990; Yanofsky et al., 1990; Irish and Sussex, 1990; Carpenter and Coen, 1990; Coen et al., 1990; Martinez-Zapater and Somerville, 1990; Drews et al., 1991; Goto et al., 1991; Koornneef et al., 1991; Schultz and Haughn, 1991; Schultz et al. 1991; Shannon and Meeks-Wagner, 1991; Alvarez et al., 1992; Schwarz-Sommer et al., 1992; Jack et al., 1992; Huijser et al., 1992; Weigel et al., 1992; Huala and Sussex, 1992). The underlying rationale is to first identify mutations that specifically affect different steps of flower development, then to analyze these mutations at the genetic level, and finally to clone the corresponding genes to determine their function at the molecular level.

Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies

Abstract: Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signalling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.

An ultra high-density Arabidopsis thaliana crossover map that refines the influences of structural variation and epigenetic features

Abstract: Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of over 17,000 COs between the Col-0 and Ler accessions of Arabidopsis thaliana. COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders, and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large and small-scale SVs, representing influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.

Adenylate cyclase 5 is required for melanophore and male pattern development in the guppy (Poecilia reticulata)

Abstract: Summary Guppies (Poecilia reticulata) are colorful fish that have attracted the attention of pigmentation researchers for almost a century. Here, we report that the blond phenotype of the guppy is caused by a spontaneous mutation in the guppy ortholog of adenylate cyclase 5 (adcy5). Using double digest restriction site-associated DNA sequencing (ddRADseq) and quantitative trait locus (QTL) mapping, we linked the blond phenotype to a candidate region of 118 kb, in which we subsequently identified a 2-bp deletion in adcy5 that alters splicing and leads to a premature stop codon. We show that adcy5, which affects life span and melanoma growth in mouse, is required for melanophore development and formation of male orange pigmentation traits in the guppy. We find that some components of the male orange pattern are particularly sensitive to loss of Adcy5 function. Our work thus reveals a function for Adcy5 in patterning of fish color ornaments.

Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere

Abstract: Pseudomonas and Sphingomonas are among the most abundant bacterial genera in the phyllosphere of wild Arabidopsis thaliana. Relative to Pseudomonas, the ecology of Sphingomonas and its interaction with plants remains elusive, despite its global ubiquity and known representatives of plant-beneficial strains. We analyzed the genomic features of over 400 endophytic Sphingomonas isolates collected from A. thaliana and neighboring plants, revealing high intergenomic diversity compared to much more homogenous Pseudomonas populations on the same plants. Variation in plasmid complement and additional genomic features suggest high adaptability, and the widespread presence of protein secretion systems hints at frequent biotic interactions. While some of the isolates showed plant-protective properties, this was a rare trait. To begin to understand the bacterial populations at the investigated A. thaliana sites and the alternate hosts of these strains when A. thaliana becomes limiting, we employed amplicon sequencing and a novel bulk-culturing metagenomics approach on A. thaliana and neighboring plants, both in spring when A. thaliana was flowering and in late summer before the emergence of the A. thaliana winter cohort. Our data reveal that Sphingomonas and Pseudomonas strains from A. thaliana not only survive, but also thrive on other diverse local plant hosts, suggesting that leaf-to-leaf transmission from these biotic reservoirs may be a major source of microbes to the next generation.

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.