News Archive

March for Science - Earth Day April 22

Posted on February 17, 2017

Around the world - and also in Tübingen. read more

Launching of Genomics of rapid Evolution in Novel Environments network

Posted on February 13, 2017

Today, on Charles Darwin's 208th birthday, we announce the launch of GrENE-net read more

Today, on Charles Darwin’s 208th birthday, we announce the launch of GrENE-net. A coordinated distributed global evolution experiment to study the Genomics of rapid Evolution in Novel Environments, that will give clues about plant adaptation in a rapidly changing world.

In brief, the idea is to sow seed mixtures of ca. 200 Arabidopsis thaliana ecotypes (previously sequenced in the 1001 genomes project and phenotypically characterized) in a large number of sites around the globe, starting in autumn 2017. Participants will collect plant material during subsequent flowering seasons for pool sequencing to assess allele frequency changes genome-wide. This will be used to investigate rapid evolution by natural selection across space. Combining this data with previous knowledge of phenotypes as well as with records of environmental variables will help to understand natural selection in an ecological context.

You can also find more detailed information, including the latest version of the experimental protocol, on our project website on grene-net.org.
 

PhD opening to work on grain amaranths

Posted on February 06, 2017

Joint project with Karl Schmid, Univ. of Hohenheim ... read more

Research Associate (TV-L E13 65%)
Population and quantitative genomics of heterosis in cultivated Amaranth


The three species of grain amaranth are ancient crops whose grains have a high nutritional value. Their domestication history is characterized by hybridization and gene flow. Amaranth species are annual plants with small genomes and a short generation time, which makes them attractive model organisms for lab and field experiments. Based on genomic data sets and phenotypic data from intra- and interspecific segregating populations the specific project goals are to (1) identify genomic regions with high diversity and footprints of gene flow between species (2) investigate the effects of interspecific vs. intraspecific heterosis on phenotypic traits and environmental stability a nd (3) map heterosis-associated genomic regions.
 
We are looking for a highly motivated and creative Ph. D. student with a strong background in population genetics, quantitative genetics, bioinformatics, evolutionary biology or plant breeding to work on this project. The student will be co-advised by Dr. Karl Schmid (University of Hohenheim; evoplant.uni-hohenheim.de) and Dr. Detlef Weigel (MPI of Developmental Biology; www.weigelworld.org).
 
The project is part of the Hohenheim-Tübingen Regio Alliance, which offers very good opportunities for interaction and further training. The position is available immediately and is funded for three years according to the E13 TV-L government salary scale (65% part-time). Registration for the Ph.D. program of the Faculty of Agriculture to obtain a Ph.D. degree is expected. The University of Hohenheim is an equal opportunity employer. Women and members of minority groups are strongly encouraged to apply.

Application deadline: 21.02.2017

Please attach the following documents to your application: Please upload your application material (Cover letter, CV, publications, a short letter of motivation and research interests, addresses of at least two references) as a single PDF.

The University of Hohenheim accepts applications via a secure internet site. To the application

Offer to temporary bench or desk space

Posted on February 02, 2017

We are offering scientists temporary bench or desk space ... read more

We are offering scientists temporary bench or desk space, library access and will help with finding accommodation for US-based scientists who are stranded abroad due to the White House Executive Order 13769 "Protecting the Nation from Foreign Terrorist Entry into the United States" of 27 January, 2017.

New Marie Curie Fellowships to Anjar & future member Fernando Rabanal

Posted on January 27, 2017

Congratulations!

Former postdoc Ove Nilsson elected to Royal Swedish Academy

Posted on January 24, 2017

Ove Nilsson - director of the UPSC and professor at the Swedish University of Agricultural Sciences read more

Rules of epiallele switching

Posted on January 09, 2017

DNA sequence properties that predict susceptibility to epiallelic switching read more

Catoni, M., Griffiths, J., Becker, C., Zabet N. R., Bayon, C., Dapp, M., Liebermann-Lazarovich, M., Weigel, D., Paszkowski, J.

Transgenerationally heritable epialleles are defined by the stable propagation of alternative transcriptional states through mitotic and meiotic cell cycles. Given that the propagation of DNA methylation at CpG sites, mediated in Arabidopsis by MET1, plays a central role in epigenetic inheritance, we examined genomewide DNA methylation in partial and complete loss?of?function met1 mutants. We interpreted the data in relation to transgenerational epiallelic stability, which allowed us to classify chromosomal targets of epigenetic regulation into (i) single copy and methylated exclusively at CpGs, readily forming epialleles, and (ii) transposon?derived, methylated at all cytosines, which may or may not form epialleles. We provide evidence that DNA sequence features such as density of CpGs and genomic repetitiveness of the loci predispose their susceptibility to epiallelic switching. The importance and predictive power of these genetic features were confirmed by analyses of common epialleles in natural Arabidopsis accessions, epigenetic recombinant inbred lines (epiRILs) and also verified in rice.

 

 

easyGWAS paper in Plant Cell

Posted on December 21, 2016

A Cloud-based Platform for Comparing the Results of Genome-wide Association Studies read more

Grimm, D. G., Roqueiro, D., Salomé, P. A., Kleeberger, S., Greshake, B., Zhu, W., Liu, C., Lippert, C., Stegle, O., Schölkopf, B., Weigel, D., and Borgwardt, K. M. 

The ever-growing availability of high quality genotypes for a multitude of species has enabled researchers to explore the underlying genetic architecture of complex phenotypes at an unprecedented level of detail using genome-wide association studies (GWAS). The systematic comparison of results obtained from GWAS of different traits opens up new possibilities, including the analysis of pleiotropic effects. Other advantages that result from the integration of multiple GWAS are the ability to replicate GWAS signals and to increase statistical power to detect such signals through meta-analyses. In order to facilitate the simple comparison of GWAS results, we present easyGWAS, a powerful, speciesindependent online resource for computing, storing, sharing, annotating and comparing GWAS. The easyGWAS tool supports multiple species, the uploading of private genotype data and summary statistics of existing GWAS, as well as advanced methods for comparing GWAS results across different experiments and datasets in an interactive and user-friendly interface. easyGWAS is also a public data repository for GWAS data and summary statistics, and already includes published data and results from several major GWAS. We demonstrate the potential of easyGWAS with a case study of the model organism Arabidopsis thaliana, using flowering and growth-related traits. 

https://easygwas.ethz.ch/

Summer nights - 2016 WeigelWorld clip

Posted on December 19, 2016

Click to watch it... read more

EMBO fellowship awarded to Lei

Posted on December 07, 2016

Congrats to Lei for securing an EMBO Long Term Fellowship!

Methods for Genotyping-by-Sequencing

Posted on December 01, 2016

A guide to genotyping-by-sequencing, in Methods in Molecular Biology read more

Rowan, B. A., Seymour, D. K., Chae, E., Lundberg, D. S., & Weigel, D. (2017).

A major goal for biologists is to understand the connection between genes and phenotypic traits, and genetic mapping in experimental populations remains a powerful approach for discovering the causal genes underlying phenotypes. For genetic mapping, the process of genotyping was previously a major rate-limiting step. Modern sequencing technology has greatly improved the resolution and speed of genetic mapping by reducing the time, labor, and cost per genotyping marker. In addition, the ability to perform genotyping-by-sequencing (GBS) has facilitated large-scale population genetic analyses by providing a simpler way to survey segregating genetic variation in natural populations. Here we present two protocols for GBS, using the Illumina platform, that can be applied to a wide range of genotyping projects in different species. The first protocol is for genotyping a subset of marker positions genome-wide using restriction digestion, and the second is for preparing inexpensive paired-end whole-genome libraries. We discuss the suitability of each approach for different genotyping applications and provide notes for adapting these protocols for use with a liquid-handling robot.

Farewell to Claude

Posted on November 29, 2016

We’re saying farewell to Claude; read more

after a very successful time in Weigelworld, he will move South and establish his own group at the GMI in Vienna

We wish you all the best! 

With VIB colleagues: Variation in Gibberellin Responses

Posted on November 28, 2016

Natural Variation of Molecular and Morphological Gibberellin Responses read more

Nam, Y. J., Herman, D., Blomme, J., Chae, E., Kojima, M., Coppens, F., Storme, V., Van Daele, T., Dhondt, S., Sakakibara, H., Weigel, D., Inzé, D., Gonzalez, N.

Although phytohormones such as gibberellins are essential for many conserved aspects of plant physiology and development, plants vary greatly in their responses to these regulatory compounds. Here, we use genetic perturbation of endogenous gibberellin levels to probe the extent of intraspecific variation in gibberellin responses in natural accessions of Arabidopsis thaliana (Arabidopsis). We find that these accessions vary greatly in their ability to buffer the effects of overexpression of GA20ox1, encoding a rate-limiting enzyme for gibberellin biosynthesis, with substantial differences in bioactive gibberellin concentrations as well as transcriptomes and growth trajectories. These findings demonstrate a surprising level of flexibility in the wiring of regulatory networks underlying hormone metabolism and signalling.

Farewell to Wanyan

Posted on November 17, 2016

We're saying goodbye to Wanyan and wish her all the very best for her future. read more

Thank you for a wonderful three years in the lab, and we hope you find the time to visit us soon!

Detlef tells us why he loves Genetics

Posted on November 11, 2016

Essay on Occasion of having Been Awarded the GSA Medal 2016 read more

The Genetics Society of America (GSA) Medal is awarded to an individual for outstanding contributions to the field of genetics in the last 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics, and exemplify the ingenuity of GSA membership. This year’s recipient was Detlef, and in this personal essay he writes about how he fell in love with Genetics, and continues to think of himself first and foremost as a geneticist.

To the article

AraPheno is online

Posted on November 09, 2016

AraPheno: a public database for Arabidopsis thaliana phenotypes read more

Seren, Ü., Grimm, D. G., Fitz, J., Weigel, D., Nordborg, M., Borgwardt, K. M., and Korte, A.

Natural genetic variation makes it possible to discover evolutionary changes that have been maintained in a population because they are advantageous. To understand genotype–phenotype relationships and to investigate trait architecture, the existence of both high-resolution genotypic and phenotypic data is necessary. Arabidopsis thaliana is a prime model for these purposes. This herb naturally occurs across much of the Eurasian continent and North America. Thus, it is exposed to a wide range of environmental factors and has been subject to natural selection under distinct conditions. Full genome sequencing data for more than 1000 different natural inbred lines are available, and this has encouraged the distributed generation of many types of phenotypic data. To leverage these data for meta analyses, AraPheno (https://arapheno.1001genomes.org) provide a central repository of population-scale phenotypes for A. thaliana inbred lines. AraPheno includes various features to easily access, download and visualize the phenotypic data. This will facilitate a comparative analysis of the many different types of phenotypic data, which is the base to further enhance our understanding of the genotype–phenotype map. 

Genetics of heterosis

Posted on November 02, 2016

Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids read more

Seymour D.K., Chae E., Grimm D.G., Martín Pizarro C., Habring-Müller A., Vasseur F., Rakitsch B., Borgwardt K.M., Koenig D., Weigel D.

The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority, has interested biologists for over a century and is of considerable agricultural importance. Although examples of both phenomena have been subject to intense investigation, no general model for the molecular basis of nonadditive genetic variance has emerged, and prediction of hybrid phenotypes from parental information continues to be a challenge. Here we explore the genetics of hybrid phenotype in 435 Arabidopsis thaliana individuals derived from intercrosses of 30 parents in a half diallel mating scheme. We find that nonadditive genetic effects are a major component of genetic variation in this population and that the genetic basis of hybrid phenotype can be mapped using genome-wide association (GWA) techniques. Significant loci together can explain as much as 20% of phenotypic variation in the surveyed population and include examples that have both classical dominant and overdominant effects. One candidate region inherited dominantly in the half diallel contains the gene for the MADS-box transcription factor AGAMOUS-LIKE 50 (AGL50), which we show directly to alter flowering time in the predicted manner. Our study not only illustrates the promise of GWA approaches to dissect the genetic architecture underpinning hybrid performance but also demonstrates the contribution of classical dominance to genetic variance.

Congratulations, Dr. Patricia Lang!

Posted on October 24, 2016

Patricia successfully defended her PhD thesis entitled 'Identification and characterization of new factors in the framework of Arabidopsis thaliana miRNA function' read more

Congratulations, Patricia!

Congratulations! Detlef receiving honorary doctorate from ...

Posted on October 07, 2016

... Swedish University of Agriculture read more

Farewell to Patrick

Posted on September 30, 2016

Patrick just completed his Diploma thesis entitled ‘Specificity and natural variation in response to allelochemicals’. read more

He will soon move on to start a PhD with Claude Becker at the GMI in Vienna

Good luck!

ACD6 dependent hybrid necrosis in local populations

Posted on September 05, 2016

Novel allelic variants in ACD6 cause hybrid necrosis in local collection of Arabidopsis thaliana read more

Swiadek M, Proost S, Sieh D, Yu J, Todesco M, Jorzig C, Rodriguez Cubillos AE, Plötner B, Nikoloski Z, Chae E, Giavalisco P, Fischer A, Schröder F, Kim ST, Weigel D, Laitinen RA

Hybrid necrosis is a common type of hybrid incompatibility in plants. This phenomenon is caused by deleterious epistatic interactions, resulting in spontaneous activation of plant defenses associated with leaf necrosis, stunted growth and reduced fertility in hybrids. Specific combinations of alleles of ACCELERATED CELL DEATH 6 (ACD6) have been shown to be a common cause of hybrid necrosis in Arabidopsis thaliana. Increased ACD6 activity confers broad-spectrum resistance against biotrophic pathogens but reduces biomass production. We generated 996 crosses among individuals derived from a single collection area around Tübingen (Germany) and screened them for hybrid necrosis. Necrotic hybrids were further investigated by genetic linkage, amiRNA silencing, genomic complementation and metabolic profiling. Restriction site associated DNA (RAD)-sequencing was used to understand genetic diversity in the collection sites containing necrosis-inducing alleles. Novel combinations of ACD6 alleles found in neighbouring stands were found to activate the A. thaliana immune system. In contrast to what we observed in controlled conditions, necrotic hybrids did not show reduced fitness in the field. Metabolic profiling revealed changes associated with the activation of the immune system in ACD6-dependent hybrid necrosis. This study expands our current understanding of the active role of ACD6 in mediating trade-offs between defense responses and growth in A.  thaliana.

Farewell to Ezgi and Jorge

Posted on August 31, 2016

We’re saying goodbye to Ezgi and Jorge - all the best for their new adventures! read more

Ezgi will start a PhD with former Weigelworld postdoc Chang Liu at the ZMBP in Tübingen, and Jorge will move to Leipzig and join Barbara Treutlein’s lab at MPI-EVA as a postdoc.

Graduation and farewell party!

Posted on August 08, 2016

On July 29, we said goodbye to George Wang, who will be heading the Computomics Corporation in Davis, CA. And .... read more

We also celebrated the three freshly minted PhD graduates, Diep Tran (starting as a postdoc with Lionel Navarro at the ENS in Paris), Jorge Kageyama (starting as a postdoc with Barbara Treutlein at the MPI-EVA in Leipzig) and Cris Zaidem (starting in 2017 as a postdoc with Michael Purugganan at NYU)

 

 

Congratulations, Dr. Maricris Zaidem!

Posted on July 29, 2016

Cris successfully defended her PhD thesis entitled 'Identification of genetic modifiers of ACCELERATED CELL DEATH 6 (ACD6) in natural Arabidopsis thaliana accessions' read more

Congratulations, Cris!

Complex history of Arabidopsis speciation

Posted on July 28, 2016

Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism read more

Polina Yu Novikova, Nora Hohmann, Viktoria Nizhynska, Takashi Tsuchimatsu, Jamshaid Ali, Graham Muir, Alessia Guggisberg, Tim Paape, Karl Schmid, Olga M Fedorenko, Svante Holm, Torbjörn Säll, Christian Schlötterer, Karol Marhold, Alex Widmer, Jun Sese, Kentaro K Shimizu, Detlef Weigel, Ute Krämer, Marcus A Koch & Magnus Nordborg

The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection.

Congratulations, Dr. Jorge Kageyama!

Posted on July 26, 2016

Jorge successfully defended his PhD thesis entitled 'Genome-wide analysis of organ-specific DNA methylation patterns in Arabidopsis thaliana' read more

Congratulations, Jorge!

Chromatin loops in Arabidopsis thaliana

Posted on July 25, 2016

Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution read more

Liu, C., Wang, C., Wang, G., Becker, C., Zaidem, M., Weigel, D.

The three-dimensional packing of the genome plays an important role in regulating gene expression. We have used Hi-C, a genome-wide chromatin conformation capture (3C) method, to analyze Arabidopsis thaliana chromosomes dissected into subkilobase segments, which is required for gene-level resolution in this species with a gene-dense genome. We found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage over long distances. In line with the globally dispersed distribution of RNA polymerase II in A. thaliana nuclear space, actively transcribed genes do not show a strong tendency to associate with each other. In general, there are often contacts between 5' and 3' ends of genes, forming local chromatin loops. Such self-loop structures of genes are more likely to occur in more highly expressed genes, although they can also be found in silent genes. Silent genes with local chromatin loops are highly enriched for the histone variant H3.3 at their 5' and 3' ends but depleted of repressive marks such as heterochromatic histone modifications and DNA methylation in flanking regions. Our results suggest that, different from animals, a major theme of genome folding in A. thaliana is the formation of structural units that correspond to gene bodies.

Congratulations, Dr. Diep Tran!

Posted on July 25, 2016

Diep successfully defended her PhD thesis entitled 'Biochemical Basis of Autoactivity of a Pair of Plant NLR Immune Receptors'. read more

Congratulations, Diep!

1001 Epigenomes: DNA methylation diversity in Arabidopsis thaliana

Posted on July 15, 2016

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions read more

Kawakatsu, T., Huang, S.-S. C., Jupe, F., Sasaki, E., Schmitz, R. J., Urich, M. A., Castanon, R, Nery., J. R., Barragan, C., He, Y., Chen, H., Dubin, M., Lee, C.-R., Wang, C., Bemm, F., Becker, C., O’Neil, R., O’Malley, R. C., Quarless, D. X., The 1001 Genomes Consortium, Schork, N. J., Weigel, D., Nordborg, M., Ecker, J. R. 

The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

Quantitative trait response in ETI: Genetics paper with Dangl lab

Posted on July 15, 2016

Effector Triggered Immune Response in Arabidopsis thaliana Is a Quantitative Trait read more

Iakovidis, M., Teixeira, P. J. P. L., Exposito-Alonso, M., Cowper, M. G., Law, T. F., Liu, Q., Vu, M. C., Dang, T. M., Corwin, J. A., Weigel, D., Dangl, J. L., Grant, S. R. 

We identified loci responsible for natural variation in Arabidopsis thaliana (Arabidopsis) responses to a bacterial pathogen virulence factor, HopAM1. HopAM1 is a type III effector protein secreted by the virulent Pseudomonas syringae strain Pto DC3000. Delivery of HopAM1 from disarmed Pseudomonas strains leads to local cell death, meristem chlorosis, or both, with varying intensities in different Arabidopsis accessions. These phenotypes are not associated with differences in bacterial growth restriction. We treated the two phenotypes as quantitative traits to identify host loci controlling responses to HopAM1. Genome Wide Association (GWA) of 64 Arabidopsis accessions identified independent variants highly correlated with response to each phenotype. Quantitative Trait Locus (QTL) mapping in a recombinant inbred population between Bur-0 and Col-0 accessions revealed genetic linkage to regions distinct from the top GWA hits. Two major QTL associated with HopAM1-induced cell death were also associated with HopAM1-induced chlorosis. HopAM1-induced changes in Arabidopsis gene expression showed that rapid HopAM1- dependent cell death in Bur-0 is correlated with effector-triggered immune responses. Studies of the effect of mutations in known plant immune system genes showed, surprisingly, that both cell death and chlorosis phenotypes are enhanced by loss of EDS1, a regulatory hub in the plant immune signaling network. Our results reveal complex genetic architecture for response to this particular type III virulence effector, in contrast to the typical monogenic control of cell death and disease resistance triggered by most type III effectors. 

2016 Campus Soccer Tournament

Posted on June 24, 2016

Two incredibly good department teams participated in this year’s Campus Soccer Tournament read more

Absolute winner spirit - we keep practicing to become next year’s champions! 

Thanks to our numerous fans for believing in us, and thanks to the PhD reps for organizing a fun event!

Teams SWAT (Swift Weigel Attack Team) and Darwin’s Posse: 

Temporal patterns of damage and decay of DNA from herbaria specimens

Posted on June 22, 2016

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens read more

Weiss, C. L., Schuenemann, V. J., Devos, J., Shirsekar, G., Reiter, E., Gould, B. A., Stinchcombe, J. R., Krause, J., Burbano, H. A.

Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66×10-4 per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

First major phase of 1001 Genomes Project concluded

Posted on June 10, 2016

1135 genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana read more

The 1001 Genome Consortium

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Epigenetic stress memory - elife paper with Gutierrez-Marcos lab

Posted on May 31, 2016

Hyperosmotic stress memory in Arabidopsis is mediated by distinct epigenetically labile sites in the genome and is restricted in the male germline by DNA glycosylase activity. read more

Wibowo, A., Becker, C., Marconi, G., Durr, J., Price, J., Hagmann, J., Papareddy, R., Putra, H., Kageyama, J., Becker, J., Weigel, D., Gutierrez-Marcos J.

Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal ‘short-term stress memory’ with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.

Congratulations, Dr. EunCheon Lim!

Posted on May 04, 2016

EunCheon successfully defended his PhD thesis entitled 'A large-scale computational framework for comparative analyses in population genetics and metagenomics' read more

Congratulations, EunCheon!

Congratulations, Dr. Danelle Seymour!

Posted on April 29, 2016

Danelle successfully defended her PhD thesis entitled 'On the Genetics and Genomics of Arabidopsis thaliana and its Relatives’ and received the exceptional summa cum laude grade. read more

Congratulations, Danelle!

Growth inhibition by allelochemicals - don't need much

Posted on April 26, 2016

Allelochemicals of the phenoxazinone class act at physiologically relevant concentrations. read more

Venturelli, S., Petersen, S., Langenecker, T., Weigel, D., Lauer, U. and Becker, C.

Plants compete with their neighbors via the release of chemical compounds into the rhizosphere. These phytotoxins originate from a series of secondary metabolites and can be processed further by soil-living microorganisms before exerting their activity on the target plant. To determine the molecular mode of action and the physiological relevance of potential phytotoxins, it is important to simulate true-to-life conditions in laboratory experiments, for example by applying physiologically relevant concentrations. Here, we report on an improved experimental setting to study the function of allelochemicals of the benzoxazolinone class. By adjusting the solvent and the application of the chemicals, we reduced by more than twenty-fold the concentration that is necessary to induce growth defects in the model plant Arabidopsis thaliana.

Farewell to Jane

Posted on March 24, 2016

We’re saying goodbye to Jane and wish her all the best for her new adventures in agroecology in France! read more

Collaborative paper with Oliver Mathieu's group

Posted on March 23, 2016

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in A. thaliana F1 epihybrids. read more

Rigal, M., Becker, C., Pélissier, T., Pogorelcnik, R., Devos, J., Ikeda, Z., Weigel, D., and Mathieu, O.

Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation.

Talia receives HFSP fellowship

Posted on March 18, 2016

Congratulations to Talia for receiving an HFSP post-doctoral fellowship!

Pearls review on plant immunity

Posted on March 17, 2016

Cooperation and conflict in the plant immune system. read more

Chae, E., Tran, D. T. N., and Weigel, D.

Plants have a sophisticated innate immune system with which they defend themselves against a myriad of pathogens. During the past two decades, work in a range of species has advanced our knowledge of the molecular and biochemical details of plant immunity. Many of these studies have focused on the action of nucleotide-binding domain/leucine-rich repeat (NB-LRR or NLR) immune receptors. NLR genes constitute the most diverse gene family in plants, reflecting their role in perceiving a very diverse set of molecules that are released by pathogens. There has also been progress in unraveling the forces that drive diversification of NLR and non-NLR immune receptors in wild species. A major recent insight from mechanistic and evolutionary studies is that there is both cooperation and conflict in the plant immune system. Here, we propose that these two antagonistic forces are inherently entangled, and that they are potentially fundamental to our understanding of growth-defense trade-offs.

How to validate the identity of genetic stocks - letter in Plant Cell

Posted on March 09, 2016

A proposal regarding best practices for validating the identity of genetic stocks and the effects of genetic variants read more

Bergelson, J., Buckler, E. S., Ecker, J. R., Nordborg, M., and Weigel, D.

Colleagues from the medical field have estimated that up to one third of cell lines are contaminated with other cell lines or are misidentified, and in addition, repeated passaging substantially changes cell line properties (reviewed in Hughes et al., 2007). The medical community has therefore begun to establish standards for verification of cell lines and genetic stocks, and NIH has announced efforts to require validation and to aid researchers in validating their biological material (Lorsch et al., 2014). Plant biologists should do the same. Even though the propagation of seed stocks cannot be directly compared to animal cell culture, contamination is a real possibility, and it is not uncommon that the same genetic stock produces different phenotypes in different laboratories. Confirming the genetic identity of research material is necessary to know whether such phenotypic differences reflect gene-by-environment (GxE) interactions, or whether they are simply due to apples being compared to oranges. 

Arabidopsis, Alter! - Leaf sampling completed

Posted on February 26, 2016

We harvested thousands of leaf samples from a large subset of the 1001G genotypes grown in challenging conditions in Madrid and Tübingen. read more

Winds and snow threatened the success of the experiment, but we verified how tough both Arabidopsis and researchers can be. We finished in good spirits, and more than 200 plates are ready for a systematic molecular analysis. 

Thanks to all who helped!

Join us as a Computational Biologist/ (Bio)Informatician

Posted on February 16, 2016

We are looking for motivated team players (PhD student or Postdoctoral level) to join our efforts in generating multi-reference plant and meta-genomes. read more

More information and the full ad is here.

Heavy winds challenge field experiment

Posted on February 11, 2016

A stormy night in Tübingen blew away the cover of our foil tunnel harboring hundreds of Arabidopsis accessions undergoing a fitness experiment. read more

Thanks to all who helped repairing it so quickly!
Special thanks to all the members from Oliver Bossdorf's lab at Uni Tübingen for their help!

Genetics Society of America awards Detlef the 2016 GSA Medal

Posted on February 08, 2016

Detlef has been awarded the GSA Medal for his outstanding contributions to the field of genetics in the last 15 years. read more

The society honors both seminar contributions to the understanding of flowering in Arabidopsis thaliana and the development of multiple community resources

Read the Public Release here.

And have a look at past recipients of the GSA medal here.

Genome-edited crops: regulatory framework proposal in Nature Genetics

Posted on January 27, 2016

A proposed regulatory framework for genome-edited crops read more

Huang, S., Weigel, D., Beachy, R. N., and Li, J.-y.

Crop breeding is being revolutionized by rapid progress in DNA sequencing and targeted alteration of DNA sequences by genome editing. Here we propose a regulatory framework for precision breeding with 'genome-edited crops' (GECs) so that society can fully benefit from the latest advances in plant genetics and genomics.

Listen to an Interview with Detlef by Deutschlandfunk, a German radio station [in German].

Farewell to Danelle, Dan, Nacho, and Paula

Posted on December 14, 2015

We’re saying goodbye to Nacho, Danelle, Dan and Paula - all the best for their new adventures! read more

Here is where the new adventures will start: 

  • CRAG in Barcelona, Spain (Nacho; now Group Leader)
  • UC Riverside in California, USA (Dan; now Assistant Professor)
  • UC Irvine in California, USA (Danelle; now Postdoc with Brandon Gaut)

Shake it off - 2015 Weigelworld clip is out

Posted on December 09, 2015

See more in the 'About Us' section.... read more

or here.

EMBO fellowship awarded to Talia

Posted on December 08, 2015

Congrats to Talia for securing an EMBO Long Term Fellowship!

Congratulations, Dr. Dominik Grimm!

Posted on November 19, 2015

Dominik successfully defended his PhD thesis today. read more

Dominik worked with Karsten Borgwardt (now ETH Zürich) and among other things developed easyGWAS: https://easygwas.tuebingen.mpg.de

eLife paper on assessing ancient DNA authenticity from low-coverage da...

Posted on November 03, 2015

Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data read more

Weiss, C..L., Dannemann, M., Pruefer K., Burbano, H.A.

Contamination with exogenous DNA is a constant hazard to ancient DNA studies, since their validity greatly depend on the ancient origin of the retrieved sequences. Since contamination occurs sporadically, it is fundamental to show positive evidence for the authenticity of ancient DNA sequences even when preventive measures to avoid contamination are implemented. Recently the presence of wheat in the United Kingdom 8000 years before the present has been reported based on an analysis of sedimentary ancient DNA (Smith et al. 2015). Smith et al. did not present any positive evidence for the authenticity of their results due to the small number of sequencing reads that were confidently assigned to wheat. We developed a computational method that compares postmortem damage patterns of a test dataset with bona fide ancient and modern DNA. We applied this test to the putative wheat DNA and find that these reads are most likely not of ancient origin.

Read Nature News Article

Plant-plant competition through HDAC inhibitors

Posted on November 03, 2015

Plants release precursors of histone deacetylase inhibitors to suppress growth of competitors read more

Venturelli, S., Belz, R., Kämper, A., Berger, A., von Horn, K., Wegner, A.,  Böcker, A., Zabulon, G.,  Langenecker, T.,  Kohlbacher, O., Barneche, F.,  Weigel, D.,  Lauer, U., Bitzer, M, Becker, C.

To secure their access to water, light, and nutrients, many plant species have developed allelopathic strategies to suppress competitors. To this end, they release into the rhizosphere phytotoxic substances that inhibit the germination and growth of neighbors. Despite the importance of allelopathy in shaping natural plant communities and for agricultural production, the underlying molecular mechanisms are largely unknown. Here, we report that allelochemicals derived from the common class of cyclic hydroxamic acid root exudates directly affect the chromatin-modifying machinery in Arabidopsis thaliana. These allelochemicals inhibit histone deacetylases both in vitro and in vivo and exert their activity through locus-specific alterations of histone acetylation and associated gene expression. Our multilevel analysis collectively shows how plant-plant interactions interfere with a fundamental cellular process, histone acetylation, by targeting an evolutionarily highly conserved class of enzymes.

Read the Plant Cell Preview Article

Press Release

New paper connecting GA signaling and ambient-temperature mediated flo...

Posted on October 29, 2015

Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana read more

Galvão, V. C., Collani, S, Horrer, D., Schmid, M.

Distinct molecular mechanisms integrate changes in ambient temperature into the genetic pathways that govern flowering time in Arabidopsis thaliana. Temperature-dependent eviction of the histone variant H2A.Z from nucleosomes has been suggested to facilitate the expression of FT by PIF4 at elevated ambient temperatures. Here we show that, in addition to PIF4, PIF3 and PIF5, but not PIF1 and PIF6, can promote flowering when expressed specifically in phloem companion cells (PCC), where they can induce FT and its close paralog, TSF. However, despite their strong potential to promote flowering, genetic analyses suggest that the PIF genes seem to have only a minor role in adjusting flowering in response to photoperiod or high ambient temperature. In addition, loss of PIF function only partially suppressed the early flowering phenotype and FT expression of the arp6 mutant, which is defective in H2A.Z deposition. In contrast, the chemical inhibition of gibberellic acid (GA) biosynthesis resulted in a strong attenuation of early flowering and FT expression in arp6. Furthermore, GA was able to induce flowering at low temperature (15 degrees C) independently of FT, TSF, and the PIF genes, probably directly at the shoot apical meristem. Together, our results suggest that the timing of the floral transition in response to ambient temperature is more complex than previously thought and that GA signaling might play a crucial role in this process. This article is protected by copyright. All rights reserved.

In PNAS: Role of RCF as a HYL1 cofactor in miRNA biogenesis

Posted on October 28, 2015

The KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1 read more

Karlsson, P., Christie, M.D., Seymour, D., Wang, H., Wang, X., Hagmann, J., Kulcheski, F.R. and Manavella, P.A.

The biogenesis of microRNAs (miRNAs), which regulate mRNA abundance through posttranscriptional silencing, comprises multiple well-orchestrated processing steps. We have identified the Arabidopsis thaliana K homology (KH) domain protein REGULATOR OF CBF GENE EXPRESSION 3 (RCF3) as a cofactor affecting miRNA biogenesis in specific plant tissues. MiRNA and miRNA-target levels were reduced in apex-enriched samples of rcf3 mutants, but not in other tissues. Mechanistically, RCF3 affects miRNA biogenesis through nuclear interactions with the phosphatases C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 and 2 (CPL1 and CPL2). These interactions are essential to regulate the phosphorylation status, and thus the activity, of the double-stranded RNA binding protein and DICER-LIKE1 (DCL1) cofactor HYPONASTIC LEAVES1 (HYL1)

Markus officially installed as a professor in Umeå

Posted on October 22, 2015

Formal ceremony and public lecture on the occasion of the university’s 50th birthday. read more

Picture of Markus with Ove Nilsson (left), also former Weigelworld postdoc and now director of the Umeå Plant Science Centre

Congratulations, Dr. Jörg Hagmann!

Posted on October 19, 2015

Jörg successfully defended his PhD thesis today! read more

Its title: 'Characterizing short-term evolution of DNA methylation in A. thaliana using next-generation sequencing'
Congratulations, Jörg! 

Population genomics review in ARGG

Posted on October 09, 2015

Population genomics for understanding adaptation in wild plant species read more

Weigel, D., and Nordborg, M.

Darwin’s theory of evolution by natural selection is the foundation of modern biology. However, it has proven remarkably difficult to demonstrate at the genetic, genomic, and population level exactly how wild species adapt to their natural environments. We discuss how one can use large sets of multiple genome sequences from wild populations to understand adaptation, with an emphasis on the small herbaceous plant Arabidopsis thaliana. We present motivation for such studies; summarize progress in describing whole-genome, species-wide sequence variation; and then discuss what insights have emerged from these resources, either based on sequence information alone or in combination with phenotypic data. We conclude with thoughts on opportunities with other plant species and the impact of expected progress in sequencing technology and genome engineering for studying adaptation in nature.

Farewell to Chang and Silvio

Posted on September 28, 2015

We're saying goodbye to Chang and Silvio and wish them all the best for their personal and scientific future! read more

Chang moved over to the other side of the hill, and just started his own group at the Center for Plant Molecular Biology. Silvio follows Markus to Umeå and will continue his projects very far up North. 

Good luck!

Gordon and Betty Moore Foundation Award

Posted on September 28, 2015

Collaborative project on disease resistance gene diversity funded read more

The Gordon and Betty Moore Foundation awarded $2.3M to the Two Blades Foundation (2Blades), a charitable organization that supports the development of durable disease resistance in crop plants and their deployment in agriculture. Jeff Dangl (University of North Carolina at Chapel Hill), Brian Staskawicz (University of California, Berkeley), Jonathan Jones (Sainsbury Laboratory in Norwich, UK) and Detlef Weigel (Max Planck Institute for Developmental Biology in Tübingen, Germany) will collaborate to discover the variability of immune system receptors of the nucleotide-binding, leucine-rich repeat (NLR) class. The enormous diversity of NLR proteins has made their genes difficult to study with conventional genome sequencing techniques. These hurdles have recently been overcome, and using a new highly accurate, fast, and cost-efficient technique developed in the Jones lab, the teams will reveal the diversity of NLR proteins within and across plant species.

 

 

Congratulations, Dr. Subhashini Muralidharan!

Posted on September 21, 2015

Subu successfully defended per PhD thesis today! read more

Its title: 'Causes and Consequences of Hybrid Incompatibilities in Arabidopsis thaliana'

Congratulations, Subu!

 

Mendel Medal of the Leopoldina

Posted on September 18, 2015

The German National Academy of Sciences Leopoldina bestows the Mendel Medal upon Detlef Weigel read more

The Leopoldina honors his outstanding achievements in the fields of developmental and evolutionary genetics. Weigel has received the Mendel Medal on September 18, 2015, at the ceremonial opening of the Leopoldina's Annual Assembly, which is also attended by German Chancellor Angela Merkel.The Mendel Medal commemorates Gregor Mendel (1822-1884), the founder of genetics. It was established on occasion of the 100th anniversary of the first public presentation of Mendel’s seminal findings in 1865. With this award, the Leopoldina honors pioneering achievements in the field of general and molecular genetics. Previous winners include the Nobel laureates Max Delbrück and Sydney Brenner, both pioneers of modern genetics, the evolutionary biologist Ernst Mayr, and the microbiologist Regine Kahmann.

New Review on 3D Chromatin Packing

Posted on August 23, 2015

Chromatin in 3D: progress and prospects for plants read more

Liu, C. and Weigel, D. 

Methods that use high-throughput sequencing have begun to reveal features of the three-dimensional structure of genomes at a resolution that goes far beyond that of traditional microscopy. Integration of these methods with other molecular tools has advanced our knowledge of both global and local chromatin packing in plants, and has revealed how patterns of chromatin packing correlate with the genomic and epigenomic landscapes. This update reports recent progress made in this area in plants, and suggests new research directions.

Farewell to Noemi and Andrés

Posted on August 12, 2015

We’re saying goodbye to Noemi and wish her all the best for the second part of her PhD in Umeå, Sweden! read more

Andrés will go back to Argentina after a 3-months visit in the department - lots of luck! 

Current Opinion Review on Splicing and Temperature Signaling

Posted on August 07, 2015

Temperature dependent alternative splicing and its role in flowering time regulation read more

Developmental plasticity enables plants to respond rapidly to changing environmental conditions, such as temperature fluctuations. Understanding how plants measure temperature and integrate this information into developmental programs at the molecular level will be essential to breed thermo-tolerant crop varieties. Recent studies identified alternative splicing (AS) as a possible 'molecular thermometer', allowing plants to quickly adjust the abundance of functional transcripts to environmental perturbations. In this review, recent advances regarding the effects of temperature-responsive AS on plant development will be discussed, with emphasis on the circadian clock and flowering time control. The challenge for the near future will be to understand the molecular mechanisms by which temperature can influence AS regulation.

Farewell to Stefan

Posted on July 29, 2015

After a long time in Weigelworld, we say „Goodbye“ to Stefan and wish him all the luck in the world and lots of success in his new occupation!

Farewell to Verena

Posted on July 27, 2015

After a very successful time in Weigelworld - first as a diploma, then as a PhD student, Verena is moving on to a new adventure. read more

She will continue some of her work on guppy color patterns as a Postdoc in Würzburg. 

We wish her all the best for her future!

Weigelworld Soccer Talent

Posted on July 27, 2015

Team spirit inside and outside the lab - two teams participated in the Campus Soccer Tournament and one of them did not finish in last place! read more

Team S.W.A.T (Scientists with(out) athletic talent)

 

Team 6Flats

In Plant Journal: 20Gbp white spruce genomes

Posted on July 27, 2015

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer defense metabolism read more

Warren, R. L., Keeling, C. I., Yuen, M. M. S., Raymond, A., Taylor, G. A., Vandervalk, B. P., Paulino, D., Robertson, G., Yang, C., Hoffmann, M., Weigel, D., Ritland, C., Isabel, N., Jaquish, B., Yanchuk, A., Bousquet, J., Jone, S. J. M., MacKay, J., Birol, I., and Bohlmann, J.

White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

New paper on melanophore development in guppies

Posted on June 25, 2015

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

Kottler, V. A., Künstner, A., Koch, I., Flötenmeyer, M., Langenecker, T., Hoffmann, M., Sharma, E., Weigel, D., and Dreyer, C.

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 lifespan 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.

In Plant Journal: new microRNA paper on THO2

Posted on June 05, 2015

THO2, core member of the THO/TREX complex, is required for micro RNA production in Arabidopsis read more

Francisco-Mangilet A.G., Karlsson P., Kim M.H., Eo H.J., Oh S.A., Kim J.H., Kulcheski F.R., Park S.K., Manavella P.A.

The THO/TREX complex mediates the transport of nascent mRNAs from the nucleus towards the cytoplasm in animals, and it has a role in small interfering RNA-dependent processes in plants. Here we describe five mutant alleles of Arabidopsis thaliana THO2, a core subunit of the plant THO/TREX complex. tho2 mutants present strong developmental defects resembling those in plants compromised in microRNA (miRNA) activity. In agreement, not only the levels of siRNAs, but also of mature miRNAs were reduced in tho2 mutants. As a consequence a feedback mechanism is triggered, increasing the amount of miRNA precursors, finally causing accumulation of miRNA-targeted mRNAs. Yeast two hybrid experiments and confocal microscopy showed that THO2 does not seem to interact with any of the known miRNA biogenesis components, but rather with the splicing machinery, implying an indirect role of THO2 in small RNA biogenesis. Using a RIP approach we found that THO2 is able to interact with miRNA precursors and that tho2 mutants fail to recruit such precursors into the miRNA-processing complex, explaining the reduction in the miRNA production in this mutant background. We also detected alterations in the splicing pattern of genes encoding Serine/Arginine-Rich (SR) proteins in tho2 mutants, supporting a previously unappreciated role of the THO/TREX complex in alternative splicing.

Congratulations, Dr. Verena Kottler!

Posted on May 22, 2015

Verena successfully defended per PhD thesis today! read more

Its title: 'Pigment cell organization and genetic analysis of color pattern formation in the guppy’

Congratulations, Verena!

Farewell to Markus

Posted on May 18, 2015

After 15 years in Weigelworld - first as a post-doc in San Diego, later as a group leader in Tübingen - Markus will move North and start his new lab at the Umeå Plant Science Center. We wish you all the best! read more

Read more about Markus' research here

Weigelworld Retreat 2015

Posted on May 11, 2015

We spent two days discussing future research directions - follow the link below to see some pictures. read more

Nature Review Genetics: Comparative genomics of Arabidopsis relatives

Posted on April 10, 2015

Beyond the thale: comparative genomics and genetics of Arabidopsis relatives. read more

Koenig D, Weigel D.

For decades a small number of model species have rightly occupied a privileged position in laboratory experiments, but it is becoming increasingly clear that our knowledge of biology is greatly improved when informed by a broader diversity of species and evolutionary context. Arabidopsis thaliana has been the primary model organism for plants, benefiting from a high-quality reference genome sequence and resources for reverse genetics. However, recent studies have made a group of species also in the Brassicaceae family and closely related to A. thaliana a focal point for comparative molecular, genomic, phenotypic and evolutionary studies. In this Review, we emphasize how such studies complement continued study of the model plant itself, provide an evolutionary perspective and summarize our current understanding of genetic and phenotypic diversity in plants.

Nature Plants: Reduced symmetric DNA methylation in Arabis alpina

Posted on February 25, 2015

Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation read more

 

Willing E. M., Rawat V., Mandáková T., Maumus F., James G. V., Nordström K., Becker C., Warthmann N., Chica C., Szarzynska B., Zytnicki M.,Albani M., Kiefer C., Bergonzi S., Castaings L., Mateos J. L., Berns M. C., Bujdoso N., Piofczyk T., de Lorenzo L., Barrero-Sicilia C., Mateos I.,Piednoël M., Hagmann J., Chen-Min-Tao R., Iglesias-Fernández R., Schuster S. C., Alonso-Blanco C., Roudier F., Carbonero P., Paz-Ares J.,Davis S. J., Pecinka A., Quesneville H., Colot V., Lysak M. A., Weigel D., Coupland G. and Schneeberger K. 

Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the low-recombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.



Plant Journal: Rapid divergence of miRNAs and miRNA targets

Posted on January 25, 2015

Rapid divergence and high diversity of miRNAs and miRNA targets in the Camelineae. read more

Smith LM, Burbano HA, Wang X, Fitz J, Wang G, Ural-Blimke Y, Weigel D.

MicroRNAs (miRNAs) are short RNAs involved in gene regulation through translational inhibition and transcript cleavage. After processing from imperfect fold-back structures, miRNAs are incorporated into RNA-induced silencing complexes (RISCs) before targeting transcripts with varying degrees of complementarity. Some miRNAs are evolutionarily deep-rooted, and sequence complementarity with their targets is maintained through purifying selection. Both Arabidopsis and Capsella belong to the tribe Camelineae in the Brassicaceae, with Capsella rubella serving as an outgroup to the genus Arabidopsis. The genome sequence of C. rubella has recently been released, which allows characterization of its miRNA complement in comparison with Arabidopsis thaliana and Arabidopsis lyrata. Through next-generation sequencing, we identify high-confidence miRNA candidates specific to the C. rubella lineage. Only a few lineage-specific miRNAs have been studied for evolutionary constraints, and there have been no systematic studies of miRNA target diversity within or divergence between closely related plant species. Therefore we contrast sequence variation in miRNAs and their targets within A. thaliana, and between A. thaliana, A. lyrata and C. rubella. We document a surprising amount of small-scale variation in miRNA-target pairs, where many miRNAs are predicted to have species-specific targets in addition to ones that are shared between species. Our results emphasize that the transitive nature of many miRNA-target pairs can be observed even on a relatively short evolutionary time-scale, with non-random occurrences of differences in miRNAs and their complements in the miRNA precursors, the miRNA* sequences.

G3: Inexpensive GBS, new algorithm for genetic mapping

Posted on January 14, 2015

Rapid and Inexpensive Whole-Genome Genotyping-by-Sequencing for Crossover Localization and Fine-Scale Genetic Mapping read more

Beth A. Rowan, Vipul Patel, Detlef Weigel, and Korbinian Schneeberger 

The reshuffling of existing genetic variation during meiosis is important both during evolution and in breeding. The re-assortment of genetic variants relies on the formation of crossovers (COs) between homologous chromosomes. The pattern of genome-wide CO distributions can be rapidly and precisely established by short read sequencing of individuals from F2 populations, which in turn are useful for quantitative trait locus (QTL) mapping. While sequencing costs have dropped precipitously in recent years, the costs of library preparation for hundreds of individuals have remained high. To enable rapid and inexpensive CO detection and QTL mapping using low-coverage whole-genome sequencing of large mapping populations, we have developed a new method for library preparation along with Trained Individual GenomE Reconstruction (TIGER), a probabilistic method for genotype and CO predictions for recombinant individuals. In an example case with hundreds of F2 individuals from two Arabidopsis thaliana accessions, we resolved most CO breakpoints to within 2 kb and reduced a major flowering time QTL to a 9-kb interval. In addition, an extended region of unusually low recombination revealed a 1.8-Mb inversion polymorphism on the long arm of chromosome 4. We observed no significant differences in the frequency and distribution of COs between F2 individuals with and without a functional copy of the DNA helicase gene RECQ4A. In summary, we present a new, cost efficient method for large-scale, high-precision genotyping-by-sequencing.

PLoS Genetics: Century-scale Methylomes in Arabidopsis

Posted on January 14, 2015

Century-scale Methylome Stability in a Recently Diverged Arabidopsis thaliana Lineage. read more

Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D.

There has been much excitement about the possibility that exposure to specific environments can induce an ecological memory in the form of whole-sale, genome-wide epigenetic changes that are maintained over many generations. In the model plant Arabidopsis thaliana, numerous heritable DNA methylation differences have been identified in greenhouse-grown isogenic lines, but it remains unknown how natural, highly variable environments affect the rate and spectrum of such changes. Here we present detailed methylome analyses in a geographically dispersed A. thaliana population that constitutes a collection of near-isogenic lines, diverged for at least a century from a common ancestor. Methylome variation largely reflected genetic distance, and was in many aspects similar to that of lines raised in uniform conditions. Thus, even when plants are grown in varying and diverse natural sites, genome-wide epigenetic variation accumulates mostly in a clock-like manner, and epigenetic divergence thus parallels the pattern of genome-wide DNA sequence divergence.

G3: Plant genetic archaeology: Pedigree of a trisomic line

Posted on December 18, 2014

Whole-Genome Sequencing Reveals the Pedigree of a Classical Trisomic Line read more

Patrice A. Salomé and Detlef Weigel

The circadian oscillator is astonishingly robust, to changes in the environment, but also to genomic changes that alter the copy number of its components through genome duplication, gene duplication and homeologous gene loss. While studying the potential effect of aneuploidy on the Arabidopsis thaliana circadian clock, we discovered that a line thought to be trisomic for chromosome 3 also bears the gi-1 mutation, resulting in a short period and late flowering. With the help of whole genome sequencing, we uncovered the unexpected complexity of this trisomic stock's history, as its genome shows evidence of past outcrossing with another A. thaliana accession. Our study indicates that while historical aneuploidy lines exist and are available, it might be safer to generate new individuals and confirm their genomes and karyotypes by sequencing.

PLoS Genet: Hybrid incom- patibility & R gene evolution

Posted on December 15, 2014

From collaboration with Alcázar, Koornneef and Parker labs: read more

Analysis of a Plant Complex Resistance Gene Locus Underlying Immune-Related Hybrid Incompatibility and Its Occurrence in Nature

Rubén Alcázar,  Marcel von Reth, Jaqueline Bautor, Eunyoung Chae, Detlef Weigel, Maarten Koornneef, Jane E. Parker

PLoS Genetics
Published: December 11, 2014DOI: 10.1371/journal.pgen.1004848


Mechanisms underlying speciation in plants include detrimental (incompatible) genetic interactions between parental alleles that incur a fitness cost in hybrids. We reported on recessive hybrid incompatibility between an Arabidopsis thaliana strain from Poland, Landsberg erecta (Ler), and many Central Asian A. thaliana strains. The incompatible interaction is determined by a polymorphic cluster of Toll/interleukin-1 receptor-nucleotide binding-leucine rich repeat (TNL) RPP1 (Recognition of Peronospora parasitica1)-like genes in Ler and alleles of the receptor-like kinase Strubbelig Receptor Family 3 (SRF3) in Central Asian strains Kas-2 or Kond, causing temperature-dependent autoimmunity and loss of growth and reproductive fitness. Here, we genetically dissected the RPP1-like Ler locus to determine contributions of individual RPP1-like Ler (R1–R8) genes to the incompatibility. In a neutral background, expression of most RPP1-like Ler genes, except R3, has no effect on growth or pathogen resistance. Incompatibility involves increased R3 expression and engineered R3 overexpression in a neutral background induces dwarfism and sterility. However, no individual RPP1-like Ler gene is sufficient for incompatibility between Ler and Kas-2 or Kond, suggesting that co-action of at least two RPP1-like members underlies this epistatic interaction. We find that the RPP1-like Ler haplotype is frequent and occurs with other Ler RPP1-like alleles in a local population in Gorzów Wielkopolski (Poland). Only Gorzów individuals carrying the RPP1-like Ler haplotype are incompatible with Kas-2 and Kond, whereas other RPP1-like alleles in the population are compatible. Therefore, the RPP1-like Ler haplotype has been maintained in genetically different individuals at a single site, allowing exploration of forces shaping the evolution of RPP1-like genes at local and regional population scales.

Current Biology:

Posted on November 22, 2014

miRNA networks & leaf complexity read more

Temporal Control of Leaf Complexity by miRNA-Regulated Licensing of Protein Complexes

Ignacio Rubio-Somoza, Chuan-Miao Zhou, Ana Confraria, Claudia Martinho, Patrick von Born, Elena Baena-Gonzalez, Jia-Wei Wang, Detlef Weigel

Current Biology 24, 2714–2719

Highlights

•miR319-targeted TCPs regulate the activity of miR164-(in)dependent CUC proteins
•miR156-targeted SPLs license active transcription factor complexes
•Changes in protein complex composition control age-dependent leaf shape

Summary


The tremendous diversity of leaf shapes has caught the attention of naturalists for centuries. In addition to interspecific and intraspecific differences, leaf morphologies may differ in single plants according to age, a phenomenon known as heteroblasty [ 1 ]. In Arabidopsis thaliana, the progression from the juvenile to the adult phase is characterized by increased leaf serration. A similar trend is seen in species with more complex leaves, such as the A. thaliana relative Cardamine hirsuta, in which the number of leaflets per leaf increases with age. Although the genetic changes that led to the overall simpler leaf architecture in A. thaliana are increasingly well understood [ 2–4 ], less is known about the events underlying age-dependent changes within single plants, in either A. thaliana or C. hirsuta. Here, we describe a conserved miRNA transcription factor regulon responsible for an age-dependent increase in leaf complexity. In early leaves, miR319-targeted TCP transcription factors interfere with the function of miR164-dependent and miR164-independent CUC proteins, preventing the formation of serrations in A. thaliana and of leaflets in C. hirsuta. As plants age, accumulation of miR156-regulated SPLs acts as a timing cue that destabilizes TCP-CUC interactions. The destabilization licenses activation of CUC protein complexes and thereby the gradual increase of leaf complexity in the newly formed organs. These findings point to posttranslational interaction between unrelated miRNA-targeted transcription factors as a core feature of these regulatory circuits.

Cell: NLRs as hotspots of deleterious epistasis

Posted on November 21, 2014

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis read more

Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hot Spots of Deleterious Epistasis

Eunyoung Chae, Kirsten Bomblies, Sang-Tae Kim, Darya Karelina, Maricris Zaidem, Stephan Ossowski, Carmen Martín-Pizarro, Roosa A.E. Laitinen, Beth A. Rowan, Hezi Tenenboim, Sarah Lechner, Monika Demar, Anette Habring-Müller, Christa Lanz, Gunnar Rätsch, Detlef Weigel

Cell, published online November 20, 2014


Highlights

  • A species-wide genetic analysis identifies incompatibility hot spots in the genome
  • Antagonistic epistasis involving plant NLR immune receptors is a common cause
  • Polymorphic NLR tandem arrays can generate multiple incompatibility alleles
  • Deleterious epistasis limits the accessible space of immune receptor combinations


Summary
Intraspecific genetic incompatibilities prevent the assembly of specific alleles into single genotypes and influence genome- and species-wide patterns of sequence variation. A common incompatibility in plants is hybrid necrosis, characterized by autoimmune responses due to epistatic interactions between natural genetic variants. By systematically testing thousands of F1 hybrids of Arabidopsis thaliana strains, we identified a small number of incompatibility hot spots in the genome, often in regions densely populated by nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes. In several cases, these immune receptor loci interact with each other, suggestive of conflict within the immune system. A particularly dangerous locus is a highly variable cluster of NLR genes, DM2, which causes multiple independent incompatibilities with genes that encode a range of biochemical functions, including NLRs. Our findings suggest that deleterious interactions of immune receptors limit the combinations of favorable disease resistance alleles accessible to plant genomes.

PLoS Genet: Evolution of DNA Methylation Patterns

Posted on November 14, 2014

Evolution of DNA Methylation Patterns in the Brassicaceae is Driven by Differences in Genome Organization read more

Danelle K. Seymour, Daniel Koenig, Jörg Hagmann, Claude Becker, Detlef Weigel

PLoS Genetics Published: November 13, 2014; DOI: 10.1371/journal.pgen.1004785

DNA methylation is an ancient molecular modification found in most eukaryotes. In plants, DNA methylation is not only critical for transcriptionally silencing transposons, but can also affect phenotype by altering expression of protein coding genes. The extent of its contribution to phenotypic diversity over evolutionary time is, however, unclear, because of limited stability of epialleles that are not linked to DNA mutations. To dissect the relative contribution of DNA methylation to transposon surveillance and host gene regulation, we leveraged information from three species in the Brassicaceae that vary in genome architecture, Capsella rubella, Arabidopsis lyrata, and Arabidopsis thaliana. We found that the lineage-specific expansion and contraction of transposon and repeat sequences is the main driver of interspecific differences in DNA methylation. The most heavily methylated portions of the genome are thus not conserved at the sequence level. Outside of repeat-associated methylation, there is a surprising degree of conservation in methylation at single nucleotides located in gene bodies. Finally, dynamic DNA methylation is affected more by tissue type than by environmental differences in all species, but these responses are not conserved. The majority of DNA methylation variation between species resides in hypervariable genomic regions, and thus, in the context of macroevolution, is of limited phenotypic consequence.

Genome Res: Hi-res Hi-C analysis in Arabidopsis

Posted on November 10, 2014

Genome Res. 2014 Nov 3. pii: gr.170332.113. read more

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana.

Wang C, Liu C, Roqueiro D, Grimm D, Schwab R, Becker C, Lanz C, Weigel D.

Genome Res. 2014 Nov 3. pii: gr.170332.113.

The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intra-chromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1 and H3.3. We also identify over 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found over 1,000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks, and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.

Dissection of miRNA pathways using protoplasts

Posted on October 26, 2014

Mol Plant. 2014 Oct 24. pii: ssu119. [Epub ahead of print] read more

 

Dissection of miRNA pathways using Arabidopsis mesophyll protoplasts.

Martinho C, Confraria A, Elias CA, Crozet P, Rubio-Somoza I, Weigel D, Baena-González E.

microRNAs (miRNAs) control gene expression mostly post-transcriptionally by guiding transcript cleavage and/or translational repression of complementary mRNA targets, thereby regulating developmental processes and stress responses. Despite the remarkable expansion of the field, the mechanisms underlying miRNA activity are not fully understood. In this paper, we describe a transient expression system in Arabidopsis mesophyll protoplasts that is highly amenable for the dissection of miRNA pathways. We show that by transiently overexpressing primary miRNAs and target mimics, we can manipulate miRNA levels and consequently impact on their targets. Furthermore, we developed a set of luciferase-based sensors for quantifying miRNA activity that respond specifically to both endogenous and overexpressed miRNAs and target mimics. We demonstrate that these miRNA sensors can be used to test the impact of putative components of the miRNA pathway on miRNA activity, as well as the impact of specific mutations, either by overexpression or by the use of protoplasts from the corresponding mutants. We further show that our miRNA sensors can be used for investigating the effect of chemicals on miRNA activity. Our cell-based transient expression system is fast and easy to set up and generates quantitative results, being a powerful tool for assaying miRNA activity in vivo.

SPP1529 Adaptomics projects renewed

Posted on October 26, 2014

Our two projects in the SPP1529 (Research Focus Program of the German Research Council DFG) have been renewed read more

One on variation in Capsella, with Magnus Nordborg and Barbara Neuffer, and one on adaptation of various Brassicaceae along a steep rainfall cline in Israel, with Katja Tielbörger and Christian Schlötterer.

 

Read more here:

Starting from scratch: adaptation to variable environments after an extreme bottleneck

Phenotypic and genetic variation in Biscutella didyma and adaptation to environmental change - a combined ecological-genomic approach

 

 

CHM: Convergence of pathogens on common host proteins

Posted on October 26, 2014

We were able to contribute analyses based on 1001 Genomes data to his exciting project describing how a common set of host proteins is convergently targeted by effectors from pathogens representing three kingdoms of life,... read more

Weßling R et al.: Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life.
Cell Host Microbe. 2014 Sep 10;16(3):364-75. doi: 10.1016/j.chom.2014.08.004.

 

While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.

Trowel: superior error correction module for Illumina

Posted on October 03, 2014

Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D. Bioinformatics. 2014 Jul 29. pii: btu513. [Epub ahead of print] read more

Trowel: a fast and accurate error correction module for Illumina sequencing reads.
Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D.
Bioinformatics. 2014 Jul 29. pii: btu513. [Epub ahead of print]

MOTIVATION:
The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections.

RESULT:
We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k-mer spectrum. With high-quality k-mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. Availability and implementation: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at trowel-ec.sourceforge.net.

CONTACT:
euncheon.lim@tue.mpg.de or weigel@tue.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

In Nature Genetics: Solanum pennellii genome

Posted on July 31, 2014

The genome of the stress-tolerant wild tomato species Solanum pennellii read more

Anthony Bolger, … , Christa Lanz, … , Korbinian Schneeberger, … Daniel Koenig, … , Detlef Weigel, Björn Usadel & Alisdair R Fernie

Nature Genetics (2014) doi:10.1038/ng.3046

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.

Taking over the eLife Twitter account

Posted on June 10, 2014

Tomorrow (Friday, June 13), we are taking over the eLife Twitter account. read more

We'll give you a glimpse of what our lab does, what we are excited about, and what new initiatives we are thinking about. Follow us under #elifetakeover.

Team Weigelworld on collection trip in US

Posted on April 12, 2014

Jane Devos and Gautam Shirsekar are in the US for two months, collecting Arabidopsis thaliana along the Eastern Seaboard and in the Midwest. read more

This is part of a project where we are following a lineage of A. thaliana that was introduced in historic times in the US. We are interested in adaptation to pathogens as well as epigenetic diversification. In addition, we are using herbarium specimens to look at local evolution and study genome-wide mutation rates in ecological time.

New group in herbarium genomics

Posted on April 01, 2014

Dr. Hernán Burbano has been appointed project group leader in herbarium genomics. read more

Read more about this work here.

In Plant Cell: How the FLOWERING works in FT

Posted on February 17, 2014

A very large scale mutagenesis study points to surface charge being an important determinant of flower promoting activity of FT protein. Rare to have a paper with only two authors these days! read more

William Wing Ho Ho and Detlef Weigel:

Structural Features Determining Flower-Promoting Activity of Arabidopsis FLOWERING LOCUS T

Open access in Plant Cell.



Modeling surface charge in FT, its antagonist TFL1, and in FT mutant proteins.

With Parcy lab: LEAFY evolution paper in Science

Posted on January 17, 2014

Very proud to have another collaborative paper with former postdoc read more

François Parcy (who left the lab in 1997), on the evolution of LEAFY DNA binding specificity. This is sort of a follow-up study on a paper by Alexis Maizel, published 2005, also in Science.

eLife paper on gene conversions in Arabidopsis thaliana

Posted on December 19, 2013

The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana read more

In eLife, with the Schneeberger, Keurentjes and Koornneef labs


Lisa Smith starting as Lecturer @ Univ. Sheffield

Posted on October 29, 2013

Lisa Smith left at the end of October to start as a Lecturer/Research Fellow at the University of Sheffield read more

After a very productive time in WeigelWorld, Lisa Smith left at the end of October to start as a Lecturer/Research Fellow at the University of Sheffield - good luck, Lisa!

Manavella lab: Max Planck Partner Group in Argentina

Posted on October 29, 2013

Pablo Manavella had a very successful postdoc career in WeigelWorld, making important contributions to our knowledge of miRNA processing and action. read more

He now won a grant that will support his new lab in Santa Fe, Argentina, as a Max Planck Partner Group. Congratulations, Pablo!

Nature: FLM splice form antagonism in flowering

Posted on October 26, 2013

How two splice forms of the FLM transcription factor antagonize each other to control temperature dependent flowering read more

Markus Schmid's group, with help from Detlef Weigel's PhD student Felix Ott (who was responsible for the bioinformatic analyses), in collaboration with Richard Immink and Gerco Angenent from Wageningen, show how two splice forms of the FLM transcription factor antagonize each other to control temperature dependent flowering.

Temperature-dependent regulation of flowering by antagonistic FLM variants

David Posé, Leonie Verhage, Felix Ott, Levi Yant, Johannes Mathieu, Gerco C. Angenent, Richard G. H. Immink & Markus Schmid

Nature (2013) doi:10.1038/nature12633
   
The appropriate timing of flowering is crucial for plant reproductive success. It is therefore not surprising that intricate genetic networks have evolved to perceive and integrate both endogenous and environmental signals, such as carbohydrate and hormonal status, photoperiod and temperature1, 2. In contrast to our detailed understanding of the vernalization pathway, little is known about how flowering time is controlled in response to changes in the ambient growth temperature. In Arabidopsis thaliana, the MADS-box transcription factor genes FLOWERING LOCUS M (FLM) and SHORT VEGETATIVE PHASE (SVP) have key roles in this process3, 4. FLM is subject to temperature-dependent alternative splicing3. Here we report that the two main FLM protein splice variants, FLM-? and FLM-?, compete for interaction with the floral repressor SVP. The SVP–FLM-? complex is predominately formed at low temperatures and prevents precocious flowering. By contrast, the competing SVP–FLM-? complex is impaired in DNA binding and acts as a dominant-negative activator of flowering at higher temperatures. Our results show a new mechanism that controls the timing of the floral transition in response to changes in ambient temperature. A better understanding of how temperature controls the molecular mechanisms of flowering will be important to cope with current changes in global climate5, 6.

WeigelWorld retreat

Posted on October 16, 2013

Summer 2013 read more

Follow this link to see photos from our retreat in June.

WeigelWorld also most highly cited dev biol lab in DE/CH/AT

Posted on October 12, 2013

We lead the list, with almost 5000 citations for articles published in 2007 to 2010. read more

The Laborjournal has released its ranking of developmental biologists active in one of the German speaking countries (Germany, Switzerland, Austria). We lead the list, with almost 5000 citations for articles published in 2007 to 2010. Notably, our h-index for these papers, 41, is 7 points higher than of the colleague with the second highest ranking. We are proud to do so well, especially with the heavy competition from the mammalian stem cell and microRNA fields.

ERC funding for Detlef Weigel

Posted on September 26, 2013

ERC Advanced Grant proposal IMMUNEMESIS is funded read more

it's official: our ERC Advanced Grant proposal IMMUNEMESIS is funded. The proposal text is here.

IMMUNEMESIS: The Plant Immune System: Epistasis and Fitness-Tradeoffs

A fundamental question in biology is how multicellular organisms distinguish self and non-self. The requirement to specifically recognize only foreign cells and molecules constrains the diversification of the immune system, resulting in conflicts between effective detection of enemies, adaptive changes in the cellular machinery and mating with divergent genotypes from the same species. In plants, there is generally a trade-off between immunity and growth, and immune system activation is often associated with impaired development. There are many examples of autoimmunity in hybrids, caused by a gene product from one parent erroneously interpreting a gene product from the other parent as foreign. This is not surprising, given the extraordinary diversity of many immune genes. On the other hand, hybrid vigor, or heterosis, is commonly observed in F1 progeny from two inbred parents, and this is widely exploited in breeding. Thus, it is also of practical importance to understand how outcrossing affects the plant immune system. We hypothesize that overt hybrid autoimmunity represents only the tip of the iceberg, and that there are many more subtle non-additive genetic interactions that affect both the plant immune system and growth. We therefore propose a comprehensive research program to dissect epistatic interactions with effects on plant growth and health. Specifically, we will conduct genomics-enabled, systematic forward genetic studies with natural genotypes of the model plant Arabidopsis thaliana and its outcrossing sister species A. lyrata. This will be complemented by experiments that will link diversity of microbial communities with that of the immune system in natural plant populations. The systematic understanding of forces that shape the distribution of immune gene alleles in the wild will have important implications for engineering disease resistance in crops, by helping to chose the best ensembles of resistance genes.

Temperature dependent flowering in Science

Posted on September 12, 2013

The Schmid group collaborated with Ji Hoon Ahn, former WeigelWorld postdoc and now professor at Korea University, on this beautiful study on temperature dependent flowering. read more

Published today in Science.

In PLoS: A miRNA network regulating flower maturation

Posted on July 24, 2013

Rubio-Somoza I, Weigel D (2013) read more

Coordination of Flower Maturation by a Regulatory Circuit of Three MicroRNAs.

PLoS Genet 9(3): e1003374. doi:10.1371/journal.pgen.1003374

The development of multicellular organisms relies on interconnected genetic programs that control progression through their life cycle. MicroRNAs (miRNAs) and transcription factors (TFs) play key roles in such regulatory circuits. Here, we describe how three evolutionary conserved miRNA-TF pairs interact to form multiple checkpoints during reproductive development of Arabidopsis thaliana. Genetic, cellular, and physiological experiments show that miR159- and miR319-regulated MYB and TCP transcription factors pattern the expression of miR167 family members and their ARF6/8 targets. Coordinated action of these miRNA-TF pairs is crucial for the execution of consecutive hormone-dependent transitions during flower maturation. Cross-regulation includes both cis- and trans-regulatory interactions between these miRNAs and their targets. Our observations reveal how different miRNA-TF pairs can be organized into modules that coordinate successive steps in the plant life cycle.

Congratulations, Dr. William Ho!

Posted on July 24, 2013

William received a magna cum laude for his dissertation and public defence read more

of "Structural and Functional Analysis of FLOWERING LOCUS T in Arabidopsis thaliana"

WeigelWorld most highly cited plant lab in Europe

Posted on July 22, 2013

According to the Labtimes, WeigelWorld leads Europe in citation rankings for papers published 2005-2011. read more

An important contributor was our gene expression atlas paper published in 2005.Click  here for more details

In PLoS Genet: Autoimmunity caused by ACD6 alleles

Posted on July 12, 2013

Activation of the Arabidopsis thaliana Immune System by Combinations of Common ACD6 Alleles read more

Marco Todesco, Sang-Tae Kim, Eunyoung Chae, Kirsten Bomblies, Maricris Zaidem, Lisa M. Smith, Detlef Weigel, Roosa A. E. Laitinen

PLoS Genet 10, e1004459

A fundamental question in biology is how multicellular organisms distinguish self and non-self. The ability to make this distinction allows animals and plants to detect and respond to pathogens without triggering immune reactions directed against their own cells. In plants, inappropriate self-recognition results in the autonomous activation of the immune system, causing affected individuals to grow less well. These plants also suffer from spontaneous cell death, but are at the same time more resistant to pathogens. Known causes for such autonomous activation of the immune system are hyperactive alleles of immune regulators, or epistatic interactions between immune regulators and unlinked genes. We have discovered a third class, in which the Arabidopsis thaliana immune system is activated by interactions between natural alleles at a single locus, ACCELERATED CELL DEATH 6 (ACD6). There are two main types of these interacting alleles, one of which has evolved recently by partial resurrection of a pseudogene, and each type includes multiple functional variants. Most previously studies hybrid necrosis cases involve rare alleles found in geographically unrelated populations. These two types of ACD6 alleles instead occur at low frequency throughout the range of the species, and have risen to high frequency in the Northeast of Spain, suggesting a role in local adaptation. In addition, such hybrids occur in these populations in the wild. The extensive functional variation among ACD6 alleles points to a central role of this locus in fine-tuning pathogen defenses in natural populations.

User guide for mutation identification by sequencing

Posted on June 21, 2013

Just published in Genome Biology, collaboration with former grad student Korbinian Schneeberger: read more

User guide for mapping-by-sequencing in Arabidopsis

Geo Velikkakam James, Vipul Patel, Karl JV Nordstrom, Jonas R Klasen, Patrice A Salome, Detlef Weigel and Korbinian Schneeberger

Genome Biology 2013, 14:R61
doi:10.1186/gb-2013-14-6-r61

Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.

Causal mutations for two guppy color variants identified

Posted on June 16, 2013

by Kottler et al. read more

Published in Genetics on May 11, 2013, by Kottler et al.:

Pigment pattern formation in the guppy, Poecilia reticulata, involves the Kita and Csf1ra receptor tyrosine kinases.

Males of the guppy (Poecilia reticulata) vary tremendously in their ornamental patterns, which are thought to have evolved in response to a complex interplay between natural and sexual selection. Although the selection pressures acting onthe color patterns of the guppy have been extensively studied, little is known about the genes that control their ontogeny. Over 50 years ago, two autosomal color loci, blue and golden, have been described, which both play a decisive role in the formation of the guppy color pattern. Orange pigmentation is absent in the skin of guppies with a lesion in blue, suggesting a defect in xanthophore development. In golden mutants, the development of the melanophore pattern during embryo-genesis and after birth is affected. Here, we show that blue and golden correspond to guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra;previously called fms) and kita. Most excitingly, we found that both genes are required for the development of the black ornaments of guppy males, which in thecase of csf1ra might be mediated by xanthophore-melanophore interactions. Furthermore, we provide evidence that two temporally and genetically distinct melanophore populations contribute to the adult camouflage pattern expressed in both sexes: one early-appearing and kita-dependent, and the other late-developing and kita-independent. The identification of csf1ra and kita mutants provides thefirst molecular insights into pigment pattern formation in this important model species for ecological and evolutionary genetics.


The genomic consequences of rapid mating system evolution

Posted on June 10, 2013

Slotte et al. read more

Just out in Nature Genetics:

Slotte et al.

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

The shift from outcrossing to selfing is common in flowering plants1, 2, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.

Commentary: Sixty years of genome biology

Posted on May 12, 2013

Sixty years after Watson and Crick published the double helix model of DNA's structure read more

Thirteen members of Genome Biology's Editorial Board, including Detlef Weigel, comment in Genome Biology on key advances in the field of genome biology subsequent to that discovery.

EMBO | EMBL Symposium on Evolution & Ecology starts today

Posted on May 01, 2013

New Model Systems for Linking Evolution and Ecology read more

Organized by D. Tautz & D. Weigel

EMBL Heidelberg, Germany
Wednesday 1 May - Saturday 4 May 2013

Online program.

A major obstacle in linking evolution and ecology has been that for many of the preferred models for genetic and genomic research, ecological information has been lacking. Conversely, the preferred models for evolutionary ecology have generally not been amenable to genetic experiments and have had poorly developed genomic resources. The ongoing revolution in sequencing technologies is rapidly changing this. Large-scale sequencing-based studies have become affordable for individual labs and support population genomics, investigation of regulatory landscapes of the genomes as well as in situ genetics in a wide range of species. Importantly, such analyses can now be performed with hundreds or even thousands of individuals.

This meeting will present the latest advances with satellite systems, that is, species that are closely related to conventional genetic model organisms, and with entirely new models for evolutionary and ecological genetics and genomics. Special emphasis will be placed on the interaction between organisms as a basis for understanding ecological adaptation. If you want to bring a new species into the genomic era, this meeting is for you.

WeigelWorld most highly cited plant biology lab

Posted on April 23, 2013

in Germany, Austria and Switzerland read more

According to a just published publication analysis in the Laborjournal, WeigelWorld is by the far the most highly cited plant biology lab in German speaking countries. 74 articles published in 2007-2010 were cited a total of 4,440 times, with an h-index of 39 (39 articles that were cited at least 39 times).

“Whodunnit” of Irish potato famine solved

Posted on April 21, 2013

Weigelworld teamed up with colleagues from Germany, the UK and the US to reveal that a unique strain of potato blight they call HERB-1 triggered the Irish potato famine of the mid-nineteenth century. read more

It is the first time scientists have decoded the genome of a plant pathogen and its plant host from dried herbarium samples. This opens up a new area of research to understand how pathogens evolve and how human activity impacts the spread of plant disease.

Phytophthora infestans changed the course of history. Even today, the Irish population has still not recovered to pre-famine levels. “We have finally discovered the identity of the exact strain that caused all this havoc”, says Hernán Burbano from the Max Planck Institute for Developmental Biology.

For research to be published in eLife, a team of molecular biologists from Europe and the US reconstructed the spread of the potato blight pathogen from dried plants. Although these were 170 to 120 years old, they were found to have many intact pieces of DNA.

"Herbaria represent a rich and untapped source from which we can learn a tremendous amount about the historical distribution of plants and their pests - and also about the history of the people who grew these plants," according to Kentaro Yoshida from The Sainsbury Laboratory in Norwich.

The researchers examined the historical spread of the fungus-like oomycete Phytophthora infestans, known as the Irish potato famine pathogen. A strain called US-1 was long thought to have been the cause of the fatal outbreak. The current study concludes that a strain new to science was responsible. While more closely related to the US-1 strain than to other modern strains, it is unique. "Both strains seem to have separated from each other only years before the first major outbreak in Europe," says Burbano.

The researchers compared the historic samples with modern strains from Europe, Africa and the Americas as well as two closely related Phytophthora species. The scientists were able to estimate with confidence when the various Phytophthora strains diverged from each other during evolutionary time. The HERB-1 strain of Phytophthora infestans likely emerged in the early 1800s and continued its global conquest throughout the 19th century. Only in the twentieth century, after new potato varieties were introduced, was HERB-1 replaced by another Phytophthora infestans strain, US-1.

The scientists found several connections with historic events. The first contact between Europeans and Americans in Mexico in the sixteenth century coincides with a remarkable increase in the genetic diversity of Phytophthora. The social upheaval during that time may have led to a spread of the pathogen from its center of origin in Toluca Valley, Mexico. This in turn would have accelerated its evolution.

The international team came to these conclusions after deciphering the entire genomes of 11 historical samples of Phytophthora infestans from potato leaves collected over more than 50 years. These came from Ireland, the UK, Europe and North America and had been preserved in the herbaria of the Botanical State Collection Munich and the Kew Gardens in London.

"Both herbaria placed a great deal of confidence in our abilities and were very generous in providing the dried plants," said Marco Thines from the Senckenberg Museum and Goethe University in Frankfurt, one of the co-authors of this study. "The degree of DNA preservation in the herbarium samples really surprised us," adds Johannes Krause from the University of Tübingen, another co-author. Because of the remarkable DNA quality and quantity in the herbarium samples, the research team could evaluate the entire genome of Phytophthora infestans and its host, the potato, within just a few weeks.

Crop breeding methods may impact on the evolution of pathogens. This study directly documents the effect of plant breeding on the genetic makeup of a pathogen. "Perhaps this strain became extinct when the first resistant potato varieties were bred at the beginning of the twentieth century," speculates Yoshida. “What is for certain is that these findings will greatly help us to understand the dynamics of emerging pathogens. This type of work paves the way for the discovery of many more treasures of knowledge hidden in herbaria.”


The following authors contributed to the publication: Kentaro Yoshida, Liliana M. Cano, Marina Pais and Sophien Kamoun of the Sainsbury Laboratory in Norwich (UK); Verena J. Schuenemann and Johannes of the University of Tuebingen (Germany); Bagdevi Mishra, Rahul Sharma and Marco Thines of the Goethe University and Senckenberg Museum in Frankfurt (Germany); Frank N. Martin of the U.S. Department of Agriculture in California (US); Christa Lanz, Detlef Weigel and Hernán A. Burbano of the Max Planck Institute for Developmental Biology in Tuebingen (Germany).

The study was funded by the European Research Council, the Gatsby Charitable Foundation, the Biotechnology and Biological Sciences Research Council of the UK, the Campaign for the Development of Scientific and Economic Excellence in Hesse (LOEWE), the Deutsche Forschungsgemeinschaft and the Max- Planck Society.


Source:
Kentaro Yoshida et al.

Rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

eLife 2:e00731 doi 10.7554/elife.00731e

Detlef Weigel at Keystone Conference on Plant Immunity

Posted on April 14, 2013

Detlef Weigel will present the work of this team on natural variation in the plant immune system at the Keystone Conference on Plant Immunity in Big Sky, Montana, April 7-12, 2013. read more

The Plant Immune System at the Nexus of Trade-offs Affecting Fitness and Gene Flow

We are investigating three main questions of evolution: (i) How, and how frequently, do new genetic variants arise? (ii) Why do some variants increase in frequency? (iii) And why are some combinations of variants incompatible with each other? Through research directed at answering the third question we have become interested in the analysis of fitness tradeoffs in immunity. A while ago, we developed Arabidopsis thaliana as a model for hybrid necrosis, a syndrome that is characterized by inappropriate activation of the immune system due to self-recognition (Bomblies et al., PLoS Biol 5:e236  [2007]). We have identified dozens of hybrid necrosis cases in A. thaliana and have cloned the causal loci underlying four genetically distinct interactions. Most encode highly polymorphic immune receptors, and I will report on our efforts to describe species- and genome-wide variation at NB-LRR immune receptor genes.

While most hybrid necrosis systems involve two loci, autoimmunity can also be caused by inter-allelic interactions at a single locus, ACCELERATED CELL DEATH 6 (ACD6). We have previously shown that ACD6 is involved in a major fitness tradeoff between growth and pathogen resistance in inbred strains (Todesco et al., Nature 465:632 [2010]). The ACD6 case is particularly interesting, because necrosis is relatively mild, and naturally occurring hybrids survive in the field. Thus, while divergence of pathogen recognition systems can potentially result in reproductive isolation, hyperactivation of the immune system in hybrids may in other cases promote outcrossing in a species that is otherwise predominantly selfing.

Supported by the Max Planck Society and a Gottfried Wilhelm Leibniz Award of the DFG.

In Science: A sugar derivative regulating flowering

Posted on February 12, 2013

Just out in Science: New paper from Markus Schmid's group and collaborators at the Max Planck Institute for Molecular Plant Physiology in Golm: read more

In PLoS Genetics:

Posted on February 08, 2013

Intraspecific variation in TEs and their effects read more

By Xi Wang, Detlef Weigel and Lisa Smith: Transposon Variants and Their Effects on Gene Expression in Arabidopsis

Abstract

Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA–mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants.

In EMBO J:

Posted on December 16, 2012

Iron and the plant circadian clock read more

In EMBO Journal (Open Access)

Circadian clock adjustment to plant iron status depends on chloroplast and phytochrome function

Patrice A Salomé, Michele Oliva, Detlef Weigel and Ute Krämer

Plant chloroplasts are not only the main cellular location for storage of elemental iron (Fe), but also the main site for Fe, which is incorporated into chlorophyll, haem and the photosynthetic machinery. How plants measure internal Fe levels is unknown. We describe here a new Fe-depen- dent response, a change in the period of the circadian clock. In Arabidopsis, the period lengthens when Fe becomes limiting, and gradually shortens as external Fe levels increase. Etiolated seedlings or light-grown plants treated with plastid translation inhibitors do not respond to changes in Fe supply, pointing to developed chloroplasts as central hubs for circadian Fe sensing. Phytochrome- deficient mutants maintain a short period even under Fe deficiency, stressing the role of early light signalling in coupling the clock to Fe responses. Further mutant and pharmacological analyses suggest that known players in plastid-to-nucleus signalling do not directly participate in Fe sensing. We propose that the sensor governing circa- dian Fe responses defines a new retrograde pathway that involves a plastid-encoded protein that depends on phyto- chromes and the functional state of chloroplasts.

In Plant Phys:

Posted on November 30, 2012

Tissue-specific silencing by miRNA* read more

In Plant Physiology:

Tissue-specific silencing of Arabidopsis thaliana SUVH8 by miR171a star

Pablo Manavella, Daniel Koenig, Ignacio Rubio-Somoza, Hernán A Burbano, Claude Becker, and Detlef Weigel

MicroRNAs (miRNAs) are produced from double stranded precursors, from which a short duplex is excised. The strand of the duplex that remains more abundant is usually the active form, the miRNA, while steady-state levels of the other strand, the miRNA*, are generally lower. The executive engines of miRNA-directed gene silencing are RNA-induced silencing complexes (RISCs). During RISC maturation, the miRNA/miRNA* duplex associates with the catalytic subunit, an AGO protein. Subsequently, the guide strand, which directs gene silencing, is retained, while the passenger strand is degraded. Under certain circumstances, the miRNA*s can be retained as guide strands. MiR170 and miR171 are prototypical miRNAs in Arabidopsis thaliana, with well-defined targets. We found that the corresponding star molecules, the sequence-identical miR170* and miR171a* have several features of active miRNAs, such as sequence conservation and AGO1 association. We confirmed that active AGO1-miR171a* complexes are common in A. thaliana and that they trigger silencing of SUVH8, a new miR171a* target that was acquired very recently in the A. thaliana lineage. Our study demonstrates that each miR171a strand can be loaded onto RISC, with separate regulatory outcomes.

EMBO Symposium: New Models for Evolution & Ecology

Posted on November 28, 2012

New Model Systems for Linking Evolution and Ecology read more

Organized by D. Tautz & D. Weigel

EMBL Heidelberg, Germany
Wednesday 1 May - Saturday 4 May 2013

Registration for this event is now live.

A major obstacle in linking evolution and ecology has been that for many of the preferred models for genetic and genomic research, ecological information has been lacking. Conversely, the preferred models for evolutionary ecology have generally not been amenable to genetic experiments and have had poorly developed genomic resources. The ongoing revolution in sequencing technologies is rapidly changing this. Large-scale sequencing-based studies have become affordable for individual labs and support population genomics, investigation of regulatory landscapes of the genomes as well as in situ genetics in a wide range of species. Importantly, such analyses can now be performed with hundreds or even thousands of individuals.

This meeting will present the latest advances with satellite systems, that is, species that are closely related to conventional genetic model organisms, and with entirely new models for evolutionary and ecological genetics and genomics. Special emphasis will be placed on the interaction between organisms as a basis for understanding ecological adaptation. If you want to bring a new species into the genomic era, this meeting is for you.

In Genome Biology:

Posted on November 12, 2012

Review on plant epialleles read more

Plant epialleles

Detlef Weigel and Vincent Colot review the role of epialleles in plant biology and evolution

Genome Biology 2012, 13:249

In Cell: fast-forward genetics miRNA screen

Posted on November 09, 2012

Just published: Using fast-forward genetics methods pioneered in the Weigel lab for rapid identification of a new regualtor of miRNA biogenesis. read more

Detlef Weigel plenary lecture at IPMB 2012 in Jeju

Posted on October 22, 2012

"Origin and consequences of genetic and epigenetic variation in Arabidopsis thaliana" read more

Detlef Weigel is giving a plenary lecture at the International Plant Molecular Biology (IPMB) Congress 2012 in Jeju, Korea, today.

Congratulations to Dr. Norman Warthmann!

Posted on October 09, 2012

Norman Warthmann defended his PhD thesis today: "Finding the Causal Genes: Developing Tools for Natural Variation Research" read more

He passed with a magna cum laude. Congratulations, Norman!

Review on epigenetic variation published

Posted on August 30, 2012

Epigenetic variation: origin and transgenerational inheritance. read more

In Current Opinion in Plant Biology

Epigenetic variation: origin and transgenerational inheritance.

Becker C, Weigel D.

Recent studies have revealed that epigenetic variation in plant populations exceeds genetic diversity and that it is influenced by the environment. Nevertheless, epigenetic differences are not entirely independent of shared ancestry. Epigenetic modifications have gained increasing attention, because one can now study their patterns across the entire genome and in many different individuals. Not only do epigenetic phenomena modulate the activity of the genome in response to environmental stimuli, but they also constitute a potential source of natural variation. Understanding the emergence and heritability of epigenetic variants is critical for understanding how they might become subject to natural selection and thus affect genetic diversity. Here we review progress in characterizing natural epigenetic variants in model and nonmodel plant species and how this work is helping to delineate the role of epigenetic changes in evolution.

Congratulations, Dr. Anusha Srikanth!

Posted on August 20, 2012

Today she defended her thesis read more

Anusha Srikanth, PhD student in the Schmid group, today defended her thesis, "Dissection of the role of FT and FD in the regulation of flowering in Arabidopsis thaliana". Congratulations, Anusha!

Launching eLife, Part 1

Posted on August 15, 2012

Editorial in eLife read more

Read our editorial in new top-flight journal eLife, on publishing our first articles.

Parallel evolution of flowering time in Capsella and Arabidopsis

Posted on August 03, 2012

Just out in Genetics: read more

Independent FLC Mutations as Causes of Flowering Time Variation in Arabidopsis thaliana and Capsella rubella.

Guo YL, Todesco M, Hagmann J, Das S, Weigel D.

Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering time variation in A. thaliana. Here we document flowering time under different conditions in 20 C. rubella accessions from across the species' range. Similar to A. thaliana, vernalization, long photoperiods and elevated ambient temperature generally promote flowering. In this collection of C. rubella accessions, we did not find any obvious loss-of-function FRI alleles. Using mapping-by-sequencing with two strains that have contrasting flowering behaviors, we identified a splice-site mutation in FLC as the likely cause of early flowering in accession 1408. However, other similarly early C. rubella accessions did not share this mutation. We conclude that the genetic basis of flowering time variation in C. rubella is complex, despite this very young species having undergone an extreme genetic bottleneck when it split from C. grandiflora a few tens of thousands of years ago.

D. Weigel giving plenary lecture at FESPB 2012

Posted on August 01, 2012

Detlef Weigel is delivering today, August 1, a plenary lecture entitled "Arabidopsis thaliana as a model system for the study of evolutionary questions", at the joint EPSO-FESPB Plant Biology 2012 meeting in Freiburg. read more

This is what he will discuss:

We are investigating three main questions of evolution: (i) How, and how frequently, do new genetic variants arise? (ii) Why do some variants increase in frequency? (iii) And why are some combinations of variants incompatible with each other? To this end, we are employing bottom-up and top-down approaches that rely heavily on large-scale sequencing. Whole-genome sequencing supports a detailed description of the pan-genome of A. thaliana (http://1001genomes.org; Schneeberger et al., PNAS 108:10249 [2011]; Cao et al., Nat Genet 43:956 [2011]), it reveals mutational biases shaping the genome (Ossowski et al. Science 327:92 [2010]), and it allows for rapid mapping of genes with major phenotypic effects (Schneeberger et al., Nat Methods 6:550 [2009]). We have also investigated spontaneous epigenetic variation. Our results suggest that most epialleles are unlikely to contribute to long-term evolution (Becker et al., Nature 480:245).

A major interest in the lab is the analysis of fitness tradeoffs in immunity. Arabidopsis thaliana is an excellent model for hybrid necrosis, a widespread syndrome of hybrid failure in plants (Bomblies et al., PLoS Biol 5:e236  [2007]). Several causal loci encode highly polymorphic immune receptors. While most hybrid necrosis systems involve two loci, autoimmunity can also be caused by inter-allelic interactions at a single locus that is involved in a major fitness tradeoff between growth and pathogen resistance in inbred strains (Todesco et al., Nature 465:632 [2010]). Thus, divergence of pathogen recognition systems can potentially result in reproductive isolation and subsequent speciation.

New department members: C. Wang, E. Lim, S. Collani

Posted on July 18, 2012

We were joined in July by three new scientists read more

Physicist Congmao Wang from Shanghai Jiao Tong University joined the Weigel group, and plant biologist Silvio Collani from the University of Padua joined the Schmid group. In addition, informatician Euncheon Lim from Seoul joined us as a potential graduate student.

eLife website news

Posted on June 21, 2012

website open for submissions! read more

eLife website online (Deputy Editor: Detlef Weigel)

Posted on May 02, 2012

eLife is a new high-level journal in the life sciences, supported by the Max Planck Society, Howard Hughes Medical Institute and the Wellcome Trust. read more

eLife is a researcher-driven initiative for the very best in science and science communication. eLife promotes rapid, fair, and more constructive review. It will use digital media and open access to increase the influence of published works. eLife is committed to serving authors and advancing careers in science.

eLife will launch at the end of this year; you can follow news and announcements at the eLife website.



No genome needed: synteny- based precision mapping

Posted on March 13, 2012

Mapping-by-sequencing, “SHOREmapping”, is greatly accelerating the identification of causal mutations. read more

Current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms, however, do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. As a proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, which has a genome with several large scale rearrangements relative to A. thaliana. Our approach outlines an alternative roadmap for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available.

See our paper in Plant Journal.

MiRNA duplex structure controls secondary siRNA formation

Posted on February 10, 2012

Plant secondary siRNA production determined by microRNA-duplex structure. read more

Out in PNAS by Manavella and colleagues: Plant secondary siRNA production determined by microRNA-duplex structure. In plants, miRNA-mediated cleavage of a target triggers in some cases the production of secondary small interfering RNAs (siRNAs), which in turn can silence other genes in trans, a phenomenon called transitivity. Several groups reported in 2010 that 22-nt miRNAs are sufficient, but not essential for generating secondary siRNAs. In this paper, we show that transitivity can be triggered when the small RNA that is not retained in AGO is 22-nt long. Moreover, we demonstrate that asymmetrically positioned bulged bases in the miRNA:miRNA* duplex, regardless of miRNA or miRNA* length, are sufficient for the initiation of transitivity. We propose that the RNA-induced silencing complex reprogramming occurs during the early steps of miRNA loading, before the miRNA duplex is disassembled and the guide strand is selected.

PNAS paper on evolution of epigenetic variants published

Posted on January 21, 2012

by Hollister, Smith, Guo, Ott, Weigel & Gaut. read more

Just out in PNAS: Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata, by Hollister, Smith, Guo, Ott, Weigel & Gaut.

New gene silencing method published: MIGS

Posted on January 15, 2012

Virus-induced gene silencing (VIGS) and hairpin RNA interference (hpRNAi), both of which rely on small interfering RNAs, together with artificial microRNAs (amiRNA), are amongst the most popular methods for reduction of gene... read more

However, all three approaches have limitations. In a paper published in Plant Journal, we introduce miRNA-induced gene silencing (MIGS). This method exploits a special 22-nucleotide miRNA of Arabidopsis thaliana, miR173, which can trigger production of another class of small RNAs called trans-acting small interfering RNAs (tasiRNAs). We show that fusion of gene fragments to an upstream miR173 target site is sufficient for effective silencing of the corresponding endogenous gene. MIGS can be reliably used for the knockdown of a single gene or of multiple unrelated genes. In addition, we show that MIGS can be applied to other species by co-expression of miR173.

Last paper of 2011: Natural variation in A. thaliana miRNAs

Posted on January 03, 2012

Another paper from the Todesco/Balasubramanian duo, in collaboration with the Altmann lab read more

Just published online in Current Biology

In this paper, we demonstrate that a naturally occurring polymorphism in the MIR164A gene affects leaf shape and shoot architecture in Arabidopsis thaliana, with the effects being modified by additional loci in the genome. A single base pair substitution in the miRNA complementary sequence alters the predicted stability of the miRNA:miRNA(?) duplex. It thereby greatly reduces miRNA accumulation, probably because it interferes with precursor processing. We demonstrate that this is not a rare exception and that natural strains of Arabidopsis thaliana harbor dozens of similar polymorphisms that affect processing of a wide range of miRNA precursors. Our results suggest that natural variation in miRNA biogenesis resulting from cis mutations is a common contributor to phenotypic variation in plants.

Last paper of 2010 published: non-autonomy of small RNAs

Posted on December 11, 2011

Comparative analysis of non-autonomous effects of tasiRNAs in miRNAs in Arabidopsis thaliana. read more

By Felippe Felippes, Felix Ott and Detlef Weigel, published online December 5, in Nucleic Acids Research.

Authorative review on natural variation in Arabidopsis thaliana

Posted on December 11, 2011

Just published in Plant Physiology read more

A Founders Review covering the history of natural variation research in Arabidopsis thaliana, an overview of genetic and genomic tools, current challenges and research directions, and opportunities for future research.

Most detailed analysis of recombination landscape in Arabidopsis publi...

Posted on November 09, 2011

Salomé et al read more

Now in Heredity by Salomé et al.: The recombination landscape in Arabidopsis thaliana F2 populations Recombination partitions alleles segregating in the progeny of hybrids, and thus has important consequences for the distribution of phenotypic variation in a population. We examined genome-wide recombination events in over 7000 plants from 17 F2 populations derived from crosses between 18 Arabidopsis thaliana accessions. We observed segregation distortion between parental alleles in over half of our populations. Most plants carry only one or two XOs per chromosome pair, and therefore inherit very large, non-recombined genomic fragments from each parent. Recombination frequencies vary between populations but consistently increase adjacent to the centromeres.

Plant Phys papers on NB-LRR and S-locus evolution out

Posted on August 29, 2011

Two papers by Yalong Guo et al. out in Plant Physiology read more

On S-locus evolution in A. thaliana and relatives and genome wide comparison of NB-LRR genes in A. thaliana and A. lyrata.

First major 1001 Genomes paper out in Nature Genetics

Posted on August 29, 2011

We just published its first major phase, based on 80 accessions representing much of the native range of the species read more

Finally -- after several previous papers in which we developed the tools and vision for the A. thaliana 1001 Genomes project, we just published its first major phase, based on 80 accessions representing much of the native range of the species. Among the major findings are that regions differ substantially in the numbers of sequence variants and deleterious mutations. In addition, we find that the mutation spectrum in the wild differs the more from the one in the laboratory, the older the mutations are. Find out more here.

This paper complements the publicaton of whole-genome assemblies by others and by us.

Out in Dev Cell: Impact of NGS on non-model genetics

Posted on July 25, 2011

Developmental Cell is celebrating its 10th anniversary. read more

Beth Rowan, Detlef Weigel and Dan Koenig are discussing how next-generation sequencing is leveling the playing field for forward genetics in many different species. Read more here.

Severe single-locus heterozygous disadvantage in PLoS Genetics

Posted on July 25, 2011

Our latest work on hybrid incompatibility read more

Out in PLoS Genetics. Our work provides insights into how tandem arrays, which are particularly prone to frequent, complex rearrangements, can produce genetic novelty.

Whole-genome assemblies of four A. thaliana accessions in PNAS

Posted on June 07, 2011

We have developed a new approach to whole-genome assembly that exploits the high-quality reference genome of Arabidopsis thaliana. read more

In PNAS, we just published genome assemblies for four strains, including the popular Ler (Landsberg erecta) and C24 strains.

State Research Prize to Detlef Weigel and Rupert Handgretinger

Posted on May 30, 2011

Detlef Weigel and his colleague Rupert Handgretinger from the university hospital Tübingen read more

They share this year's State Research Prize of Baden Württemberg, the highest such award given out by any of the 16 German states. The award ceremony was held in Tübingen on July 6. Detlef Weigel will use the prize money of 100,000 Euros to create a stipend for the training of Asian or African PhD students in modern genetic technology.


MiRNA regulates development, anthocyanin biosynthesis...

Posted on April 28, 2011

MiR156-controlled SPL transcription factors not only regulate leaf size, speed of leaf initiation, phase change, flowering and trichome formation, but also anthocyanin biosynthesis read more

Just out in Plant Cell: MiR156-controlled SPL transcription factors not only regulate leaf size, speed of leaf initiation, phase change, flowering and trichome formation, but also anthocyanin biosynthesis. Stay tuned, there will likely be more biological processes revealed to be under miR156 control.

Finally! Arabidopsis lyrata genome published

Posted on April 12, 2011

How one can lost a major part of its genome in just 10 million years? read more

If you want to find out how one can lost a major part of its genome in just 10 million years or so, and to live to tell the tale, read more here.


Marco Todesco wins Otto Hahn Medal

Posted on April 12, 2011

Marco Todesco will receive the Otto Hahn Medal of the Max Planck Society for this PhD dissertation. read more

Marco Todesco will receive the Otto Hahn Medal of the Max Planck Society for this PhD dissertation. It comes with the medal shown below and a cash prize, and will be awarded at the Annual Meeting of the Max Planck Society in Berlin on June 8, 2011.


TIPS review on miRNA networks in development published

Posted on April 08, 2011

Although there are relatively few miRNAs in Arabidopsis, they are more highly connected than one would expect by chance, and form regulatory networks with many direct interactions. read more

These networks in turn have important roles in the control of development. Read more here.

TIPS review on fast-forward genetics published

Posted on April 04, 2011

Implications of next-generation sequencing enabled genetic approaches for plant biology and plant breeding read more

In this review, we discuss the implications of next-generation sequencing enabled genetic approaches for plant biology and plant breeding.

Genetics paper on flowering time architecture published

Posted on March 17, 2011

In maize, many genes of small effects explain variation in flowering time. read more

In contrast, we report in this paper here that a large portion of flowering-time variation in A. thaliana can be explained by large-effect loci, but that these tend to map to only a small number of regions in the genome, which include the locations of the entire clade of FLC/MAF transcription factor genes.

PLoS Genetics:

Posted on March 12, 2011

Paper on phase change in trees published read more

Out in PLoS Genetics: MiRNA-mediated control of vegetative phase change in trees -- collaboration across three continents (Asia, Europe, North America)!

Heidelberg Academy of Sciences

Posted on February 26, 2011

Detlef Weigel has been elected a corresponding member of the Heidelberg Academy of Sciences and Humanities: read more

Detlef Weigel elected as Fellow of AAAS

Posted on January 06, 2011

Detlef Weigel has been elected a Fellow of the American Association for the Advancement of Science (AAAS) read more

An honor accorded to distinguished members of the Association, the world's largest scientific society and publisher of Science magazine. Fellows are elected annually by the AAAS Council. The Association has awarded fellowships since 1874.

Marco Todesco receives dissertation prize

Posted on December 10, 2010

Dissertation prize of the Reinhold-und-Maria-Teufel-Stiftung read more

Marco Todesco received the dissertation prize of the Reinhold-und-Maria-Teufel-Stiftung today.

Felipe Felippes graduates magna cum laude

Posted on December 10, 2010

Felipe Felippes is the sixth student to graduate with a PhD this year. read more

He is also first author on the last paper of 2010 published by the department (out of 34 total!):

Comparative analysis of non-autonomous effects of tasiRNAs in miRNAs in Arabidopsis thaliana. By Felippe Felippes, Felix Ott and Detlef Weigel, published online December 5, in Nucleic Acids Research.

The next decade of genetics and genomics

Posted on October 10, 2010

Perspective by Detlef Weigel and nine other leading geneticists published in Nature Reviews Genetics read more

Inaugural paper published in PNAS

Posted on September 27, 2010

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome. read more

Laubinger, S., Zeller, S., Henz, S. R., Buechel, S., Sachsenberg, T., Wang, J.-W., Rätsch, G., and Weigel, D.

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome.

Published online September 21, 2010

Beautiful miR172 and AP2 in situs published in Development

Posted on July 30, 2010

On reconciling the interactions between APETALA2, miR172 and AGAMOUS with the ABC model of flower development. read more

Wollmann H, Mica E, Todesco M, Long JA, Weigel D.Development. 2010 Sep 28. [Epub ahead of print]

MiRNA target mimicry collection published

Posted on July 22, 2010

In a paper just out in PLoS Genetics, we report the generation of a large-scale collection of knockdowns for Arabidopsis thaliana miRNA families. read more

This has been achieved using artificial miRNA target mimics, a recently developed technique fashioned on an endogenous mechanism of miRNA regulation. Morphological defects in the aerial part were observed for about 20% of analyzed families, all of which are deeply conserved in land plants. In addition, we find that non-cleavable mimic sites can confer translational regulation in cis.

The target mimic constructs have all been submitted to the European Arabidopsis Stock Centre, and should be available from there soon.

 

Two papers on GWAS and fitness trade-off published in Nature

Posted on June 03, 2010

In collaboration with several groups from around the world, we have recently discovered a locus that underlies a major fitness trade-off between growth and disease resistance in Arabidopsis thaliana. read more

This work was published today in Nature. An allele at the ACD6 locus that slows plant growth but at the same time makes plants resistant to a raft of pathogens is found in aobut 20% of all individuals throughout the world. Because it is so ubiquitous, it is easily picked up by genome wide association, as shown in the companion paper, also published in Nature.

Detlef Weigel elected to the Royal Society of London

Posted on May 21, 2010

Detlef Weigel is one of eight Foreign Members who have been elected to the Royal Society of London this year. read more

The Royal Society was founded in 1660 and is the oldest continuously existing scientific academy in the world. Among its Foreign Members is a small circle of German scientists, which apart from several Nobel laureates such as Christiane Nüsslein-Volhard includes only the former president of the Max Planck Society, Hubert Markl.

 

 

 

Collection of 80 sequenced accessions available from ABRC

Posted on May 03, 2010

A collection of 80 A. thaliana accessions sequenced as part of the 1001 Genomes Project is available from ABRC. read more

Each of the accessions is an inbred line that can be ordered as an individual line or as a set (CS76427). These stocks can be found using the ABRC catalog. For more details, please go to the 1001 Genomes Project homepage.

New paper: finding mutations in non-reference strains

Posted on April 14, 2010

Last year, we demonstrated that short-read sequencing is very useful to hunt down mutations causal for phenotypes in lines isolated from EMS mutant screens (Schneeberger et al., 2009). read more

However, this was for mutations induced in the Col-0 reference background, for which a very high-quality reference genome is available.

In a paper that just appeared online in Plant Physiology, we now show that we can reliably distinguish even rare new mutations from a sea of background SNPs in non-reference lines. Find the paper here.

Genome-wide association study published in Nature

Posted on March 28, 2010

Based on the Arabidopsis thaliana haplotype map that we published in 2007, 1200 accessions are currently genotyped with a 250,000 SNP chip by the Bergelson, Borevitz and Nordborg labs read more

The data can be found here. The results from performing genome-wide association scans (GWAS) with the first set of lines have just been published in Nature, including several phenotypes analyzed at the Max Planck Institute.

Atwell, S, Huang, YS, Vilhjalmsson, BJ, Willems, G, Horton, M, Li, Y, Meng, D, Platt, A, Tarone, AM, Hu, TT, Jiang, R, Muliyati, NW, Zhang, X, Amer, MA, Baxter, I, Brachi, B, Chory, J, Dean, C, Debieu, M, de, Me, Ecker, JR, Faure, N, Kniskern, JM, Jones, JD, Michael, T, Nemri, A, Roux, F, Salt, DE, Tang, C, Todesco, M, Traw, MB, Weigel, D, Marjoram, P, Borevitz, JO, Bergelson, J, and Nordborg, M (2010).
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.
Nature, published online March 24, 2010.

80 A. thaliana genome sequences released

Posted on March 17, 2010

The Weigel lab has released the first 80 A. thaliana genome sequences from the 1001 Genomes project. read more

See the project homepage for details.

Incoming postdoc Dan Koenig wins prestigious HFSP Fellowship

Posted on March 12, 2010

Dan Koenig has won one of the highly competitive Long-Term Fellowships from the Human Frontier Science Program Organization (HFSPO). Dan is finishing his PhD work with Neelima Sinha at UC Davis and join Team Natural Variation in... read more

Dan Koenig has won one of the highly competitive Long-Term Fellowships from the Human Frontier Science Program Organization (HFSPO). Dan is finishing his PhD work with Neelima Sinha at UC Davis and join Team Natural Variation in the Weigel lab in summer of this year. Congratulations, Dan!


See this link for a list of the company

Presentation of Otto Bayer Award in Berlin

Posted on February 12, 2010

Today, the Otto Bayer Award was presented at an impressive event at the E-werk in Berlin. read more

Present were, among others, the chairman of the board of Bayer, Dr. Manfred Schneider, the CEO of Bayer, Werner Wenning, Dr. Wolfgang Plischke, member of the Management Board responsible for innovation and technology, as well as high-level colleagues from other companies active in plant science such as KWS and BASF. The event was attended by in the Weigel lab, many academic colleagues from Tübingen and elsewhere, the extended Weigel family and many friends of the family.

Collaboration with Freiburg results in cover of Cell

Posted on January 07, 2010

A very interesting story on Physcomitrella miRNAs guiding DNA methylation at target genes has just been published in Cell, with a cover image. read more

Stephan Ossowski designed artificial miRNAs, which turned out to provide a small, but useful piece of the puzzle.

 

Science paper on spontaneous mutations published

Posted on January 02, 2009

A collaborative paper with the Lynch lab on the rate and spectrum of spontaneous mutations in Arabidopsis thaliana has been published on January 1, 2010, in Science. read more

The paper provides important information for understanding the longer-term effects of mutation and selection on the evolution of plant genomes. It also highlights the power of short read sequencing, as we were able to find 1 mutation in 5 million base pairs--harder than finding a needle in a haystack.

Read the original paper here.

Detlef Weigel receives Otto Bayer Award 2010

Posted on December 14, 2009

Detlef Weigel will receive the Otto Bayer Award 2010 of the Bayer Science and Education Foundation. read more

The award, one of the most important scientific prizes  in the German speaking countries, will be presented by the CEO of Bayer, Werner Wenning, in Berlin on February 12, 2010. Weigel is being cited both for his efforts to understand how plants adapt to the environment, and for his work on microRNAs. The entire Weigel lab will participate in the award ceremony!

For more information, visit this website.

Nino Shervashidze wins NIPS 2009 Award

Posted on November 23, 2009

Nino Shervashidze, PhD student in Karsten Borgwardt's group, has won the Outstanding Student Paper Award. read more

Her work was selected from 1105 articles submitted at NIPS, the premier conference in Machine Learning. In her paper, Nino presents a novel algorithm for efficiently comparing large networks. This was not possible before with current state-of-the-art methods (reference: Shervashidze, Borgwardt: Fast subtree kernels on graphs, NIPS 2009).

Weigel leads citation ranking in plant and developmental biology

Posted on October 30, 2009

The trade magazine Laborjournal regularly publishes rankings comparing the citation records of scientists from the German speaking countries (Austria, Germany, Switzerland). read more

Across publications that appeared from 2003 to 2006, Detlef Weigel ranked first, by a considerable margin, among both plant biologists (as of 5/2009) and developmental biologists (as of 10/09).

In addition to Weigel, 7 current or former members of the department are among the 50 most highly cited developmental biologists!

See

Developmental biology ranking (10/2009)

Plant biology ranking (05/2009)

 

 

GenomeMapper short read tool published in Genome Biology

Posted on October 17, 2009

Current short read analysis strategies use only a single reference, ignoring previously identified variants. read more

We have developed a graph mapping approach, that allows simultaneous mapping against all known variants, and thereby greatly increases the number of polymorphisms discovered.Simultaneous alignment of short reads against multiple genomes.

Schneeberger K, Hagmann J, Ossowski S, Warthmann N, Gesing S, Kohlbacher O, Weigel D.

Genome Biol. 2009 Sep 17;10(9):R98. [Epub ahead of print]

miR156/SPL paper published in Cell

Posted on September 07, 2009

Jia-wei's paper, reporting the discovery of a new pathway that allows Arabidopsis thaliana to flower in the absence of inductive long days, has just been published in Cell read more

Back to back with a paper from the Poethig lab, on which Jia-wei is also a co-author and which reports additional roles for miR156-regulated SPL transcription factors.

Wang, J, Czech, B, and Weigel, D (2009).
miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana.
Cell, 138(4):738-49.

Wu, G, Park, MY, Conway, SR, Wang, J, Weigel, D, and Poethig, RS (2009).
The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis.
Cell, 138(4):750-9.

Identify an EMS lesion in one week--SHOREmap paper published!

Posted on September 07, 2009

Traditional strategies for identification of causal mutations involve two discrete steps: recombinant genotyping and candidate gene sequencing. read more

To dramatically speed up identification of causative point mutations and small deletions, we provide the software package SHOREmap (http://1001genomes.org/downloads/shore.html), an extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants.

Schneeberger, K, Ossowski, S, Lanz, C, Juul, T, Petersen, AH, Nielsen, KL, Jorgensen, J, Weigel, D, and Andersen, SU (2009).
SHOREmap: simultaneous mapping and mutation identification by deep sequencing.
Nat Methods, 6(8):550-1.

Sabbatical visitor Rod Wing wins prestigious Humboldt Award

Posted on September 06, 2009

Rod is spending a year-long sabbatical in the Department, with the aim of developing new strategies for comparative genomics in both rice and Brassicaceae. read more

Professor Rod Wing, Director of the Arizona Genomics Institute at the University of Arizona, has won a prestigious Humboldt Research Award from the Alexander von Humboldt Foundation. The award is granted to academics whose fundamental discoveries, new theories, or insights have had a significant impact on their own discipline and who are expected to continue producing cutting-edge achievements in future.

PNAS paper on rice varation published

Posted on July 14, 2009

We were part of a large international collaboration that used Perlegen ultra-high density microarrays to interrogate 20 diverse landraces and modern varieties of rice. read more

This work resulted in the first rice HapMap and laid the foundation for large-scale genetic characterization of a much larger set of rice varieties.

AENEAS and TRANSNET funded

Posted on May 22, 2009

Two new collaborative projects have recently been funded, read more

The EU project AENEAS--Acquired environmental epigenetics advances: from Arabidopsis to maize, and the BMBF-GABI project TRANSNET--Transcriptional networks and their evolution in the Brassicaceae.

AENEAS is led by Serena Varotto (Padova), and includes Vincenzo Rossi (Milano), José Gutierrez-Marcos (Warwick), Jurek Paszkowski (Geneva), Caroline Dean (Norwich), David Baulcombe (Cambridge), and Wyatt Paul (BIOGEMMA).

TRANSNET is led by George Coupland (Cologne), and includes Javier Paz-Ares and Pilar Carbonero (Madrid), Vincent Colot (Evry), Alexander Kel (BIOBASE), and Hadi Quesneville (Versailles).

Detlef Weigel elected to National Academy of Sciences

Posted on April 29, 2009

Detlef Weigel, a naturalized US citizen, was elected to the National Academy of Sciences at their 146th Annual Meeting in Washington, DC. read more

The National Academy of Sciences is the US' most prestigious scientific organization, and election to membership in the academy is considered one of the highest honors that can be accorded a US scientist or engineer.

Among the other scientists elected this year is Timothy Berners-Lee, credited with inventing the internet.

Science paper on triplet repeats published

Posted on March 24, 2009

Triplet repeat expansions cause many human genetic diseases. Until now, no naturally occurring triplet repeat associated genetic defects were known from other multicellular species. read more

We have identified such a case in Arabidopsis thaliana, which provides a convenient genetic model to study the origin of such triplet expansions as well as their distribution in natural populations.

 

See the paper by Sridevi Sureshkumar, Marco Todesco et al. in Science.

PNAS paper on Capsella speciation published

Posted on March 24, 2009

Self-compatible Capsella rubella and -incompatible C. grandiflora are two closely related and crossable species. read more

Remarkably, we have now found, in collaboration with other groups from the ERA-PG ARelatives consortium, that C. rubella apparently originated from C. grandiflora only a few tens of thousands of years ago. Allelic diversity patterns in the two species suggest that C. rubella was probably founded by a single individual, as published in PNAS. How phenotypic diversity is distributed in this species, and how it originated, are interesting questions for future research.