Director

Detlef Weigel

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Detlef Weigel

I started out as a developmental biologist, but over the past two decades years, my lab has come to focus more and more on questions of evolution. We investigate these both from a genomic perspective and starting from phenotypes, primarily, but not exclusively in Arabidopsis thaliana. A relatively recent addition is a strong investment in plant-microbe interactions, including natural microbiomes.

Bio

- 2002 to present / Director / Max Planck Institute for Developmental Biology
- 1993 to 2002 / Assistant and Associate Professor / Salk Institute for Biological Studies, USA
- 1989 to 1993 / Postdoc / California Institute of Technology, USA
- 1988 to 1989 / Research Associate / Ludwig Maximilian University Munich, Germany
- 1986 to 1988 / PhD student / Max Planck Institute for Developmental Biology
- 1981 to 1986 / Diploma student / University of Cologne

Selected References

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

Chae E., Bomblies K., Kim S. T., Karelina D., Zaidem M., Ossowski S., Martin-Pizarro C., Laitinen R. A., Rowan B. A., Tenenboim H., Lechner S., Demar M., Habring-Muller A., Lanz C., Ratsch G. and Weigel D.
Cell (2014), 159(6) 1341-51.

Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

Todesco M., Balasubramanian S., Hu T. T., Traw M. B., Horton M., Epple P., Kuhns C., Sureshkumar S., Schwartz C., Lanz C., Laitinen R. A., Huang Y., Chory J., Lipka V., Borevitz J. O., Dangl J. L., Bergelson J., Nordborg M. and Weigel D.
Nature (2010), 465(7298) 632-6.

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana

Clark R. M., Schweikert G., Toomajian C., Ossowski S., Zeller G., Shinn P., Warthmann N., Hu T. T., Fu G., Hinds D. A., Chen H., Frazer K. A., Huson D. H., Scholkopf B., Nordborg M., Ratsch G., Ecker J. R. and Weigel D.
Science (2007), 317(5836) 338-42.

Integration of spatial and temporal information during floral induction in Arabidopsis

Wigge P. A., Kim M. C., Jaeger K. E., Busch W., Schmid M., Lohmann J. U. and Weigel D.
Science (2005), 309(5737) 1056-9.

Control of leaf morphogenesis by microRNAs

Palatnik J. F., Allen E., Wu X., Schommer C., Schwab R., Carrington J. C. and Weigel D.
Nature (2003), 425(6955) 257-63.

A molecular link between stem cell regulation and floral patterning in Arabidopsis

Lohmann J. U., Hong R. L., Hobe M., Busch M. A., Parcy F., Simon R. and Weigel D.
Cell (2001), 105(6) 793-803.

A genetic framework for floral patterning

Parcy F., Nilsson O., Busch M. A., Lee I. and Weigel D.
Nature (1998), 395(6702) 561-6.

A developmental switch sufficient for flower initiation in diverse plants

Weigel D. and Nilsson O.
Nature (1995), 377(6549) 495-500.

LEAFY controls floral meristem identity in Arabidopsis

Weigel D., Alvarez J., Smyth D. R., Yanofsky M. F. and Meyerowitz E. M.
Cell (1992), 69(5) 843-59.

The homeotic gene fork head encodes a nuclear protein and is expressed in the terminal regions of the Drosophila embryo

Weigel D., Jürgens G., Küttner F., Seifert E. and Jäckle H.
Cell (1989), 57(4) 645-58.

Contact

detlef.weigel@tuebingen.mpg.de

Evolutionary Genetics

Max Collenberg

Gene expression in hybrid plants.

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Max Collenberg

Phenotypic variation within species is often observed both at the morphological and the physiological level. While genetic variation contributes to structural alterations in proteins, differences in gene expression can provide an additional means of varying cellular composition and cell responses. I am using next generation sequencing to study the transcriptomes of several natural Arabidopsis thaliana accessions with full genome information, and also manually generated F1 hybrids. My main focus is on detecting cis and trans factors that contribute to differences in spatial and temporal expression, particularly those with roles in local adaptation such as to respond to pathogen pressures.

Research Topics

- Gene expression in hybrid plants

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013-2016 / MSc in Agricultural Biotechnology / University of Hohenheim, Germany
- 2010-2013 / BSc in Agricultural Biology / University of Hohenheim, Germany

Contact

max.collenberg@tuebingen.mpg.de

Moisés Expósito Alonso

Evolutionary rates and signatures. Experimental evolution. Spatial distribution of genetic variation.

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Moisés Expósito Alonso

How can some species thrive close to the Arctic circle as well as the Sahara Desert? And what are the consequences on genetic diversity? I address these questions with the cosmopolitan plant model, Arabidopsis thaliana. I combine genomic data from the 1001 Genomes Project with ecological experiments using seeds originating from all over the world. Specifically, I study how populations with low genetic diversity could colonise a large part of North America within only a few centuries, and what role de novo mutations played in that process. In the native species range, Eurasia, I investigate how different genotypes respond to challenging climatic conditions by performing common garden experiments at extreme altitudes or simulated drought. With these experiments, I aim to characterise the natural selection regimes that have acted on the different genetic variants, and how they can explain patterns of local adaptation as well as the geographic distribution of genetic diversity.

More information: https://moisesexpositoalonso.wordpress.com/

Research Topics

- Evolutionary rates and signatures
- Experimental evolution
- Spatial distribution of genetic variation

Bio

- 2014 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2014 / MSc in Quantitative Genetics and Genome Analysis / University of Edinburgh, UK
- 2008 to 2013 / BSc in Biology / Universities of Alicante and Sevilla, Spain

Selected References

The rate and potential relevance of new mutations in a colonizing plant lineage

Exposito-Alonso, M., Becker, C., Schuenemann, V. J., Reitter, E., Setzer, C., Slovak, R., Brachi, B., Hagmann, J., Grimm, D. G., Jiahui, C., Busch, W., Bergelson, J., Ness, R. W., Krause, J., Burbano, H. A., Weigel, D. PLoS Genet (2018), 14(2): e1007155.

Genomic basis and evolutionary potential for extreme drought adaptation in Arabidopsis thaliana

Exposito-Alonso, M., Vasseur, F., Ding, W., Wang, G., Burbano, H. A., Weigel, D.
Nat Ecol Evol (2018), 2: 352-358.

A rainfall-manipulation experiment with 517 Arabidopsis thaliana accessions

Exposito-Alonso, M., Rodríguez, R. G., Barragán, C., Capovilla, G., Chae, E., Devos, J., Dogan, E. S., Friedemann, C., Gross, C., Lang, P., Lundberg, D., Middendorf, V., Kageyama, J., Karasov, T., Kersten, S., Petersen, S., Rabbani, L., Regalado, J., Reinelt, L., Rowan, B., Seymour, D. K., Symenoidi, E., Schwab, R., Tran, D. T. N., Venkataramani, K. Van de Weyer, A.-L., Vasseur, F., Wang, G., Wedegärtner, R., Weiss, F., Wu, R., Xi, W., Zaidem, M., Zhu, W., García-Arenal, F., Burbano, H. A., Bossdorf, Ol, Weigel, D.
bioRxiv (2017)

1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana

1001 Genomes Consortium
Cell (2016), 166(2) 481-91.

Contact

moises.exposito-alonso@tuebingen.mpg.de

Alba Gonzalez

Co-evolution of Arabidopsis and its oomycete pathogen Hyaloperonospora.

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Alba Gonzalez

Co-evolution of pathogens and their host shape the diversity of both partners. In contrast to many well-studied crops, wild plant populations usually provide extensive genetic diversity to counteract pathogen pressure. My work focusses on the other side of the coin: using Arabidopsis thaliana and its natural pathogen Hyaloperonospora arabidopsidis (Hpa), I use genetic, genomic, and molecular tools to characterize how plant diversity shapes that of its pathogen. In combination with directed infection assays, association of phenotype and genotype will help me pinpoint genomic regions involved in pathogen adaptation.

Research Topics

- Co-evolution of Arabidopsis and its oomycete pathogen Hyaloperonospora

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2016 / Research internship / Max Planck Institute for Developmental Biology
- 2015 to 2016 / Research Assistant / University of Utah, USA
- 2009 to 2015 / BSc in Biology / University of Malaga, Spain

Contact

alba.gonzalez@tuebingen.mpg.de

Julia Hildebrandt

Next Generation Sequencing. PacBio Sequel.

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Julia Hildebrandt

My work focuses on challenges associated to Next Generation Sequencing. Apart from operating the instruments and preparing Illumina sequencing libraries with standard protocols, I am establishing and advancing new high-throughput home-made protocols that may also involving robotics. I am also in charge of our new instrument, the PacBio Sequel, which we are setting up as a long-read platform at the institute.

Research Topics

- Next Generation Sequencing
- PacBio Sequel

Bio

- 2015 to present / Technical Staff / Max Planck Institute for Developmental Biology
- 2009 to 2014 / PhD in Evolutionary Biology / Max Planck Institute for Developmental Biology
- 2005 to 2009 / Diploma in Biology / University of Tübingen, Germany

Selected References

Reproductive biology of Onchocerca ochengi, a nodule forming filarial nematode in zebu cattle

Hildebrandt, J. C., Eisenbarth, A., Renz, A., Streit, A.
Vet Parasitol (2014), 205(1-2), 318-329

Molecular evidence of 'Siisa form', a new genotype related to Onchocerca ochengi in cattle from North Cameroon

Eisenbarth, A., Ekale, D., Hildebrandt, J. C., Achukwi, M. D., Streit, A., Renz, A.
Acta Trop (2013), 127(3), 261-264

Single worm genotyping demonstrates that Onchocerca ochengi females simultaneously produce progeny sired by different males

Hildebrandt, J. C., Eisenbarth, A., Renz, A., Streit, A.
Parasitol Res (2012), 111(5), 2217-21

Contact

julia.hildebrandt@tuebingen.mpg.de

Patricia Lang

Genetic diversity trailing global change. Natural variation in microRNA pathways.

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Patricia Lang

I am interested in different aspects of adaptation and evolution, from small- (molecules) to large-scale (populations) processes. To complete my skill repertoire for looking at this big picture of evolution, I am now, after a molecular biology PhD on biogenesis and function of miRNAs, doing a Postdoc in ancient genetics and evolution. My project focuses on the effects of global change on genetic variation in plants - where, how and with which outcome do plants react (adapt?) to environmental changes? To address these questions, I am developing RAD sequencing and analysis methods for five non-model plant species, to process ~1000 contemporary and ~300 up to ~200 years old historic samples I collected in forests and herbaria. The project is part of the German Biodiversity Exploratories, a large scale, long-term DFG-funded effort for biodiversity and ecosystem research.

For more information: https://patricialmlang.wordpress.com/

Research Topics

- Genetic diversity trailing global change
- Natural variation in microRNA pathways

Bio

- 2017 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2012 to 2016 / PhD student / Max Planck Institute for Developmental Biology
- 2010 to 2012 / MSc in Plant and Forest Biotechnology / Umeå Plant Science Center, Sweden
- 2007 to 2010 / BSc in Biology / Würzburg University, Germany and Umeå University, Sweden

Selected References

A role for the F-box protein HAWAIIAN SKIRT in plant microRNA function

Lang P.L.M.*, Christie, M.D.*, Dogan, E.S., Schwab, R., Hagmann, J., Van de Weyer, A.-L., Scacchi, E. and Weigel, D., Plant Physiol. (2017) (*equal contribution)

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

Karlsson, P., Christie, M.D., Seymour, D., Wang, H., Wang, X., Hagmann, J., Kulcheski, F.R. and Manavella, P.A., Proc Natl Acad Sci USA (2015)

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

Francisco-Mangilet A. G.*, Karlsson P.*, Kim M.-H., Eo H. J., Oh S. A., Kim J. H., Kulcheski F. R., Park S. K. and Manavella P. A. The Plant Journal (2015) (*equal contribution)

Contact

patricia.lang@tuebingen.mpg.de

Christa Lanz

DNA sequencing and all associated challenges.

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Christa Lanz

I’m heading the Genome Center at the institute. Apart from making sure all our instruments run smoothly and continuously, establishing and advancing protocols for Next Generation Sequencing libraries is my prime focus. Over the last years, I have experienced the tremendous advancement in sequencing technologies, and moved from classical Sanger sequencing to highly parallelized short-read sequencing on a series of Illumina instruments. Our latest acquisition, the Pacbio Sequel, adds single-molecule long-read sequencing to our repertoire and, as the other instruments before, gives us the possibility to master numerous exciting challenges.

Research Topics

- DNA sequencing and all associated challenges

Bio

- 2000 to present / Technical Staff / Genome Center, Max Planck Institute for Developmental Biology
- 1990 to 2000 / Technician / Max Planck Institute for Biology
- 1986 to 1989 / PhD in Biology / University of Tübingen , Germany
- 1979 to 1986 / Diploma in Biology / University of Tübingen, Germany
- 1977 to 1979 / MTA education / Hygiene Institute, Tübingen, Germany

Selected References

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

Bolger, A., Scossa, F., Bolger, M. E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sorensen, I., Lichtenstein, G., Fich, E. A., Conte, M., Keller, H., Schneeberger, K., Schwacke, R., Ofner, I., Vrebalov, J., Xu, Y., Osorio, S., Aflitos, S. A., Schijlen, E., Jimenez-Gomez, J. M., Ryngajllo, M., Kimura, S., Kumar, R., Koenig, D., Headland, L. R., Maloof, J. N., Sinha, N., van Ham, R. C., Lankhorst, R. K., Mao, L., Vogel, A., Arsova, B., Panstruga, R., Fei, Z., Rose, J. K., Zamir, D., Carrari, F., Giovannoni, J. J., Weigel, D., Usadel, B., Fernie A. R.
Nat Genet (2014), 46(9), 1034-8

Species-wide genetic incompatibility analysis identifies immune genes as hotspots of deleterious epistasis

Chae, E., Bomblies, K., Kim, S.-T., Karelina, D., Zaidem, M., Ossowski, S., Martin Pizarro, C., Laitinen, R. A. E., Rowan, B. A., Tenenboim, H., Lechner, S., Demar, M., Habring-Müller, A., Lanz, C., Rätsch, G., Weigel, D.
Cell (2014), 159(6), 1341-51

Whole-genome sequencing of multiple Arabidopsis thaliana population

Cao, J., Schneeberger, K., Ossowski, S., Gunther, T., Bender, S., Fitz, J., Koenig, D., Lanz, C., Stegle, O., Lippert, C., Wang, X., Ott, F., Muller, J., Alonso-Blanco, C., Borgwardt, K., Schmid, K. J., Weigel, D.
Nat Gen (2011), 43(10), 956-63

Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

Hanikenne, M., Talke, I. N., Haydon, M. J., Lanz, C., Nolte, A., Motte, P., Kroymann, J., Weigel, D., Krämer, U.
Nature (2008), 453(7193), 391-5

A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective

Rendulic, S., Jagtap, P., Rosinus, A., Eppinger, M., Baar, C., Lanz, C., Keller, H., Lambert, C., Evans, K. J., Goesmann, A., Meyer, F., Sockett, R. E., Schuster, S. C.
Science (2004), 303(5658), 689-92

Contact

christa.lanz@tuebingen.mpg.de

Ulrich Lutz

GxG interactions. Flowering time variation. Herbicide resistance.

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Ulrich Lutz

I am interested in deciphering the genetic basis of adaptation and phenotypic plasticity of flowering time of plants, especially in response to changing environmental conditions. I use natural variation as a resource of genetic diversity to identify new alleles of known genes to better understand gene function, regulation, and interaction. Employing CRISPR/Cas9 technology, I investigate GxG interaction by testing a deleterious genetic deletion in a large set of natural Arabidopsis genetic backgrounds. I also work on herbicide resistance of Alopecurus myosuroides (black-grass), a plant species classified as a weed. Several next generation sequencing technologies and methods are applied to study the dynamics of resistance dispersion and the population structure of local and nationwide samples.

Research Topics

- GxG interactions. Flowering time variation. Herbicide resistance

Bio

- 2017 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2011 to 2016 / PhD student / Plant Systems Biology / Technical University of Munich (TUM), Germany
- 2010 to 2011 / Diploma thesis / Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
- 2005 to 2011 / Studies of Agricultural Biotechnology, University of Hohenheim, Germany

Selected References

Natural haplotypes of FLM non-coding sequences fine-tune flowering time in ambient spring temperatures in Arabidopsis.

Lutz, U., Nussbaumer, T., Spannagl, M., Dienter, J., Mayer, K. F., Schwechheimer C.
eLIFE (2017), e22114

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M.

Lutz, U., Posé, D., Pfeifer, M., Gundlach, H., Hagmann, J., Wang, C., Weigel, D., Mayer, K. F., Schmid, M., Schwechheimer C.
PLoS Genet. (2015), 11(10):e1005588

A set of Columbia-0-specific single nucleotide polymorphism markers for the genetic analysis of natural variation in Arabidopsis thaliana.

Lutz, U., Schwechheimer C.
bioRxiv preprint (2017), doi: 10.1101/153197

Contact

ulrich.lutz@tuebingen.mpg.de

Manuela Neumann

Flowering time regulation in Arabidopsis. INTACT technology.

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Manuela Neumann

I am currently on maternity leave - back at the bench in 2017.

Research Topics

- Flowering time regulation in Arabidopsis
- INTACT technology

Bio

- 2010 to present / Technician / Max Planck Institute for Developmental Biology
- 2010 / Lab Assistant / Helmholtz Centre for Infection Research, Brunswick, Germany
- 2007 to 2010 / Vocational education / Helmholtz Centre for Infection Research, Brunswick, Germany

Contact

manuela.neumann@tuebingen.mpg.de

Fernando Rabanal

Evolution and regulation of ribosomal RNA genes. Herbicide resistance.

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Fernando Rabanal

Research Topics

- Evolution and regulation of ribosomal RNA genes
- Herbicide resistance

Bio

- 2017 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2010 to 2017 / PhD in Molecular Biology / Gregor Mendel Institute (GMI), Austria
- 2005 to 2009 / BSc in Genomic Sciences / National Autonomous University of Mexico (UNAM)

Selected References

Epistatic and allelic interactions control expression of ribosomal RNA gene clusters in Arabidopsis thaliana.

Rabanal, F. A., Mandáková, T., Soto-Jiménez, L. M., Greenhalgh, R., Parrott, D. L., Lutzmayer S., Steffen, J. G., Nizhynska, V., Mott, R., Lysak, M. A., Clark, R. M. and Nordborg, M.
Genome Biol. (2017), 18(1):75

Unstable Inheritance of 45S rRNA Genes in Arabidopsis thaliana.

Rabanal, F. A., Nizhynska, V., Mandáková, T., Novikova, P. Y., Lysak, M. A., Mott, R. and Nordborg, M.
G3 (Bethesda) (2017), 7(4): 1201-1209

1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana.

1001 Genomes Consortium
Cell (2016), 166(2): 481-91

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden.

Long, Q., Rabanal, F. A., Meng, D., Huber, C. D., Farlow, A., Platzer, A., Zhang, Q., Vilhjálmsson, B. J., Korte, A., Nizhynska, V., Vronin, V., Korte, P., Sedman, L., Mandáková, T., Lysak, M. A., Seren, Ü., Hellmann, I. and Nordborg, M.
Nat Genet (2013), 45(8): 884-90

Contact

fernando.rabanal@tuebingen.mpg.de

Gautam Shirsekar

Co-evolution in natural A. thaliana – oomycete pathosystems.

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Gautam Shirsekar

I am a plant pathologist interested in understanding co-evolutionary patterns in host-pathogen interactions. In the long-term I intend to apply the knowledge I acquire for development of durable and sustainable crop disease management strategies. In the Weigel lab, I am studying phenotypic and molecular evolution in North American A. thaliana and co-existing oomycete pathogens H. arabidopsidis (downy mildew) and A. candida (white rust) populations. Important questions are whether new pathogen recognition capabilities in the host more often evolve through mutation or introgression from divergent lineages, and whether virulence factors in the pathogens are co-evolving in response.

Research Topics

- Co-evolution in natural A. thaliana – oomycete pathosystems

Bio

- 2013 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2013 / PhD in Plant Pathology / The Ohio State University, USA
- 2002 to 2006 / Senior Research Fellow / Regional Station, Indian Agricultural Research Institute, India
- 2002 / MSc in Plant Pathology / Konkan Agricultural University, India
- 2000 / BSc in Agriculture / Konkan Agricultural University, India

Selected References

Identification and characterization of suppressor mutants of spl11- mediated cell death in rice

Shirsekar G. S., Vega-Sanchez M. E., Bordeos A., Baraoidan M., Swisshelm A., Fan J., Park C. H., Leung H. and Wang G. L.
Mol Plant Microbe Interact (2014), 27(6) 528-36.

The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice

Park C. H*., Chen S*., Shirsekar G*., Zhou B*., Khang C. H., Songkumarn P., Afzal A. J., Ning Y., Wang R., Bellizzi M., Valent B. and Wang G. L.
Plant Cell (2012), 24(11) 4748-62. (*equal contribution)

The U-Box E3 ligase SPL11/PUB13 is a convergence point of defense and flowering signaling in plants

Liu J., Li W., Ning Y., Shirsekar G., Cai Y., Wang X., Dai L., Wang Z., Liu W. and Wang G. L.
Plant Physiol (2012), 160(1) 28-37.

Contact

gautam.shirsekar@tuebingen.mpg.de

Thanvi Srikant

DNA methylation. Epigenetics.

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Thanvi Srikant

I just started my PhD - more information will follow shortly

Research Topics

- DNA methylation
- Epigenetics

Bio

- 2017 to present / PhD student / Max Planck Institute for Developmental Biology

Contact

thanvi.srikant@tuebingen.mpg.de

Efthymia Symeonidi

GxG interactions. Diversity in flowering and immunity genetic architectures.

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Efthymia Symeonidi

I am interested in natural genetic variation, which is found in all organisms, but often particularly obvious in plants. Two paradigms for extreme phenotypic variation in a single plant species are flowering time and immune responses in Arabidopsis thaliana. I am taking a systematic approach to determine gene x gene (GxG) interactions, by testing the effects of the same genetic mutation on a diverse set of genetic backgrounds. To this end, I am using CRISPR/Cas9 technology to knock out the flowering regulator FLOWERING LOCUS C (FLC) and the immune regulator ISOCHORISMATE SYNTHASE 1 (ICS1) in dozens of natural accessions.

Research Topics

- GxG interactions
- Diversity in flowering and immunity genetic architectures

Bio

- 2014 to present / PhD student / Max Planck Institute for Developmental Biology
- 2014 / MRes in Biomedical Sciences / University of Glasgow, UK
- 2013 / BSc in Biology / Aristotle University of Thessaloniki, Greece

Selected References

BRAF alterations in pediatric low grade gliomas and mixed neuronal-glial tumors

Dimitriadis E., Alexiou G. A., Tsotsou P., Simeonidi E., Stefanaki K., Patereli A., Prodromou N. and Pandis N.
J Neurooncol (2013), 113(3) 353-8.

Contact

efthymia.symeonidi@tuebingen.mpg.de

Bridgit Waithaka

Evolutionary genomics of herbicide-resistant weeds.

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Bridgit Waithaka

The evolution of herbicide-resistant weeds is a predictable consequence of natural selection. Although resistance alleles bestow a fitness advantage in the presence of herbicide, resistance may come at a fitness cost in the absence of herbicide selection. This would influence the spread of herbicide-resistance-conferring alleles in natural populations.
I am evaluating the costs associated with a prominent herbicide-resistant mutation in 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), the target enzyme of glyphosate, by modelling herbicide resistance in A. thaliana using CRISPR-Cas9 technology. High resolution phenotyping and competition experiments are employed to assess fitness and changes in allele frequency.
In addition, I am conducting a genome-wide association study investigating the alleles underlying the differential response of A. thaliana accessions to varying glyphosate doses.

Research Topics

- Evolutionary genomics of herbicide-resistant weeds

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2015 / MSc in Forensic Science / Universidad de Córdoba, Spain; Instituto Superior de Ciências da Saúde Egas Moniz, Portugal; University of Lincoln, UK; John Jay College of Criminal Justice, USA
- 2011 to 2013 / Research technician / International Maize and Wheat Improvement Centre, CIMMYT, Nairobi, Kenya
- 2007 to 2010 / BSc in Biochemistry / University of Nairobi, Kenya

Contact

bridgit.waithaka@tuebingen.mpg.de

Frank Weiss

Plant Breeding.

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Frank Weiss

I am a trained gardener and help with plant care in various projects. Apart from the standard lab pet Arabidopsis thaliana, I am also in charge of other plant species that require more specialized growth conditions.

Research Topics

- Plant Breeding

Bio

- 2013 to present / Gardener / Max Planck Institute for Developmental Biology

Contact

frank.weiss@tuebingen.mpg.de

Anjar Wibowo

Impact of tissue-specific regeneration and stress priming in different A.thaliana accession and different plant species.

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Anjar Wibowo

Heritable phenotypic variation in plants is mostly due to differences in DNA sequence. A number of studies have, however, shown that epigenetic changes can also result in phenotypic alteration. Furthermore, it was suggested that epigenetic diversity could positively impact on a population’s productivity, as well as tolerance against environmental stresses.

I am developing a novel methodology for the robust production of epigenetically stable plant variants, in order to increase epigenetic and phenotypic diversity. Special focus is on the propagation of otherwise tissue-specific epigenomes, as well as on natural Arabidopsis accessions. High throughput phenotyping and sequencing methods will be applied to characterize the resulting plant variants.

Research Topics

- Impact of tissue-specific regeneration and stress priming in different A.thaliana accession and different plant species

Bio

- 2016 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2011 to 2016 / PhD in Life Sciences / University of Warwick, UK
- 2009 to 2011 / MSc in Bioscience / King Abdullah University of Science and Technology, Saudi Arabia
- 2004 to 2009 / BSc in Science / Gadjah Mada University, Indonesia

Selected References

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

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.
Elife. (2016), e13546

Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana

Belfield, E. J., Gan, X., Mithani, A., Brown, C., Jiang, C., Franklin, K., Alvey, E., Wibowo, A., Jung, M., Bailey, K., Kalwani, S., Ragoussis, J., Mott, R., Harberd, N. P.
Genome Res. (2012), 22(7):1306-15

De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks

Mahfouz, M. M., Li, L., Shamimuazzaman, M., Wibowo, A., Fang, X., Zhu, J. K.
Proc Natl Acad Sci U S A. (2011), 108(6):2623.8

Contact

anjar.wibowo@tuebingen.mpg.de

To Top

Genome Informatics

Haim Ashkenazy

Contact

haim.ashkenazy@tuebingen.mpg.de

Felix Bemm

Complete genome assemblies for Arabidopsis species. Complete genome assemblies for A. thaliana accessions. Integration of short and long read sequencing technologies.

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Felix Bemm

I am broadly interested in comparative genomics. I am currently spearheading efforts to produce very high quality genome assemblies for most species in the genus Arabidopsis, and for several dozen of A. thaliana accessions. Both collections of genome assemblies will greatly leverage the resources available from the 1001 Genomes project. Most importantly, we will be able to make much stronger inferences about the extremely diverse and variable regions of the genome.

Research Topics

- Complete genome assemblies for Arabidopsis species
- Complete genome assemblies for A. thaliana accessions
- Integration of short and long read sequencing technologies

Bio

- 2014 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2011 to 2014 / PhD in Bioinformatics / University of Würzburg, Germany
- 2005 - 2011 / Diploma in Biology / University of Würzburg, Germany

Selected References

1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana

1001 Genomes Consortium
Cell (2016), 166(2) 481-91.

Integration of trap- and root-derived nitrogen nutrition of carnivorous Dionaea muscipula

Gao P., Loeffler T. S., Honsel A., Kruse J., Krol E., Scherzer S., Kreuzer I., Bemm F., Buegger F., Burzlaff T., Hedrich R. and Rennenberg H.
New Phytol (2015), 205(3) 1320-9.

The protein composition of the digestive fluid from the venus flytrap sheds light on prey digestion mechanisms

Schulze W. X., Sanggaard K. W., Kreuzer I., Knudsen A. D., Bemm F., Thogersen I. B., Brautigam A., Thomsen L. R., Schliesky S., Dyrlund T. F.,Escalante-Perez M., Becker D., Schultz J., Karring H., Weber A., Hojrup P., Hedrich R. and Enghild J. J.
Mol Cell Proteomics (2012), 11(11) 1306-19.

A kinome of 2600 in the ciliate Paramecium tetraurelia

Bemm F., Schwarz R., Forster F. and Schultz J.
FEBS Lett (2009), 583(22) 3589-92.

Contact

felix.bemm@tuebingen.mpg.de

Ilja Bezrukov

Automated Phenotyping. Pipelines for processing of short and long read sequencing data.

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Ilja Bezrukov

Research Topics

- Automated Phenotyping
- Pipelines for processing of short and long read sequencing data

Bio

- 2016 to present / Staff scientist / Max Planck Institute for Developmental Biology
- 2014 to 2015 / Researcher / Werner Siemens Imaging Center, Tübingen, Germany
- 2008 to 2014 / PhD student / Werner Siemens Imaging Center and Max Planck Institute for Intelligent Systems, Tübingen, Germany
- 2007 / Research assistant / Department of Medical Informatics, Aachen, Germany
- 2006 / Diploma in Computer Science / RWTH Aachen University, Germany

Selected References

Quantitative Evaluation of Segmentation- and Atlas-Based Attenuation Correction for PET/MR on Pediatric Patients

Bezrukov, I., Schmidt, H., Gatidis, S., Mantlik, F., Schafer, J. F., Schwenzer, N. and Pichler, B. J.
J Nucl Med (2015), 56(7):1067-74

MR-based attenuation correction methods for improved PET quantification in lesions within bone and susceptibility artifact regions

Bezrukov, I., Schmidt, H., Mantlik, F., Schwenzer, N., Brendle, C., Schölkopf, B. and Pichler, B.
J Nucl Med (2013), 54(10):1768-74

MRI-based attenuation correction for whole-body PET/MRI: quantitative evaluation of segmentation- and atlas-based methods

Hofmann, M., Bezrukov, I., Mantlik, F., Aschoff, P., Steinke, F., Beyer, T., Pichler, B. J. and Schölkopf, B.
J Nucl Med (2011), 52(9):1392-9 (*equal contribution)

Contact

ilja.bezrukov@tuebingen.mpg.de

Oliver Deusch

Plant-microbiome-interaction. Comparative genomics of phyllosphere bacteria.

Oliver Deusch

I am a bioinformatician with a wide range of interests, having worked in areas such as plant and organelle evolution, bacterial genomics, genome and transcriptome assembly and companion animal microbiome. I have research experience in both industry and academia and also work for local biotech startup CeMeT GmbH.

Research Topics

- Plant-microbiome-interaction
- Comparative genomics of phyllosphere bacteria

Bio

- 2018 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2018 to present / Scientific Head of Bioinformatics / CeMeT GmbH, Tübingen
- 2011 to 2017 / Bioinformatician / Mars Petcare, Melton Mowbray, UK
- 2010 to 2011 / Postdoc / Massey University, Palmerston North, New Zealand
- 2005 to 2009 / PhD in Biology / Düsseldorf University, Germany
- 1998 to 2005 / Diplom in Biology / Düsseldorf University, Germany

Selected References

Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens

Deusch, O., O'Flynn, C., Colyer, A., Morris, P., Allaway, D., Jones, P. G., Swanson, K. S.
PLoS One (2014), 9(7):e101021

A cross-sectional survey of bacterial species in plaque from client owned dogs with healthy gingiva, gingivitis or mild periodontitis

Davis, I. J., Wallis, C., Deusch, O., Colyer, A., Milella, L., Loman, N., Harris, S.
PLoS One (2013), 8(12):e83158

Cutoffs and k-mers: implications from a transcriptome study in allopolyploid plants

Gruenheit, N., Deusch, O., Esser, C., Becker, M., Voelckel, C., Lockhart, P.
BMC Genomics (2012), 13:92

Genes of cyanobacterial origin in plant nuclear genomes point to a heterocyst-forming plastid ancestor

Deusch, O., Landan, G., Roettger, M., Gruenheit, N., Kowallik, K. V., Allen, J. F., Martin, W., Dagan, T.
Mol Biol Evol (2008), 25(4):748-61

Contact

oliver.deusch@tuebingen.mpg.de

Christian Kubica

Patterns of structural variation in genomes.

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Christian Kubica

I am a PhD student in the department.

Research Topics

- Patterns of structural variation in genomes

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2012 to 2016 / MSc in Genome-Based Systems Biology / Bielefeld University, Germany
- 2009 to 2012 / BSc in Biosciences / Münster University, Germany

Contact

christian.kubica@tuebingen.mpg.de

Anna-Lena Van de Weyer

Array enrichment for targeted NGS analyses. Species-wide spectrum of NB-LRR (NLR) genes.

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Anna-Lena Van de Weyer

I am interested in using computational biology to decipher the molecular mechanisms leading to genetic diversity, adaptive evolution and speciation. My first project focuses on natural variation in resistance (R) genes of Arabidopsis thaliana. The main class of R-genes encodes nucleotide binding site-leucine rich repeat (NLR/NB-LRR) proteins and mediates the effector triggered immunity (ETI) in plants. My work will aid to understand how variation in these genes helps plants to resist pathogen pressures.

Research Topics

- Array enrichment for targeted NGS analyses
- Species-wide spectrum of NB-LRR (NLR) genes

Bio

- 2014 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2014 / Research Assistant / University of Würzburg, Germany
- 2011 to 2013 / MA in Biology / University of Würzburg, Germany
- 2008 to 2011 / BA in Biology / University of Würzburg, Germany

Contact

anna-lena.vd.weyer@tuebingen.mpg.de

Yoav Voichek

I just started - more information will follow shortly.

Bio

- 2018 to present / Postdoc / Max Planck Institute for Developmental Biology

Contact

Yoav.Voichek@tuebingen.mpg.de

To Top

Plant Microbe Co-Evolution

Dino Jolic

De novo genome and metagenome assembly. Plant-microbe interactions. Adaptation to climate change.

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Dino Jolic

I'm interested in DNA sequencing technologies and their application to answer questions about the underlying sequence variation of genetic diversity in plants. My main focus lies with investigating the spatio-temporal and genetic variation of Arabidopsis thaliana and its leaf microbial communities in local populations. In a separate project, I'm involved in a collaboration with the Tielbörger and Schlötterer labs, being responsible for the genome sequencing and assembly of Biscutella didyma, which is studied for its adaptability to environmental change in a combined ecological-genomic approach. Finally, I'm experimenting with new long-read sequencers to establish their performance on plant genomes.

Research Topics

- De novo genome and metagenome assembly
- Plant-microbe interactions
- Adaptation to climate change

Bio

- 2011 to present / PhD student / Max Planck Institute for Developmental Biology
- 2011 / MSc in Computational Biology / University of Zagreb, Croatia
- 2009 / BSc in Molecular Biology / University of Zagreb, Croatia

Contact

dino.jolic@tuebingen.mpg.de

Talia Karasov

Microbial evolution. Plant evolutionary genomics. Plant pathogen interactions.

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Talia Karasov

Successful pathogen colonization of a host requires not only that the pathogen successfully surpass the host immune system, but also that it survive and proliferate in the presence of other microbes. My research focuses on the evolution of pathogen and plant in the context of a larger microbial community.

Research Topics

- Microbial evolution
- Plant evolutionary genomics
- Plant pathogen interactions

Bio

- 2015 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2015 / PhD in Genetics, Genomics & Systems Biology / University of Chicago, USA
- 2008 / BSc in Biological Sciences / Stanford University, USA

Selected References

The long-term maintenance of a resistance polymorphism through diffuse interactions

Karasov T. L., Kniskern J. M., Gao L., DeYoung B. J., Ding J., Dubiella U., Lastra R. O., Nallu S., Roux F., Innes R. W., Barrett L. G., Hudson R. R.and Bergelson J. Nature (2014), 512(7515) 436-40.

Genomic variability as a driver of plant-pathogen coevolution?

Karasov T. L., Horton M. W. and Bergelson J.
Curr Opin Plant Biol (2014), 18 24-30.

Evidence that adaptation in Drosophila is not limited by mutation at single sites

Karasov T., Messer P. W. and Petrov D. A.
PLoS Genet (2010), 6(6) e1000924.

Contact

talia.karasov@tuebingen.mpg.de

Sonja Kersten

Metagenomics. Plant-Microbe Interactions. Immune Response Analysis in A. thaliana.

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Sonja Kersten

I am a trained plant breeder working as a technical and scientific assistant. My work concerns plant-microbe interactions in local populations. In one project, we sequence A. thaliana rosette microbiomes to study factors influencing the composition of these microbial communities. In a second, I assess phenotypic diversity of immune responses in North American A. thaliana populations challenged with Albugo candida and Hyaloperonospora arabidopsidis.

Research Topics

- Metagenomics
- Plant-Microbe Interactions
- Immune Response Analysis in A. thaliana

Bio

- 2014 to present / Technical and Scientific Assistant / Max Planck Institute for Developmental Biology
- 2011 to 2013 / MSc in Crop Sciences and Plant Breeding / University of Hohenheim, Germany
- 2008 to 2011 / BSc in Agricultural Sciences / University of Hohenheim, Germany

Contact

sonja.kersten@tuebingen.mpg.de

Derek Lundberg

Map distribution of microbial genotypes onto that of plant genotypes in a wild field. Associate plant and microbial genotypes in nature while tracking plant growth and transcriptional output. Test predictions about the microbial community and fitness using targeted genome engineering of locally adapted plants.

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Derek Lundberg

Nature exposes plants to large communities of microbes that are also interacting amongst themselves. Because maintaining an immune system is costly, successful plants must streamline their defense capabilities. I am investigating the influence of locally-adapted plant genetic variation on the colonization of wild microbes in the field. This will help understand the pressures that drive the evolution of the plant immune system, and to identify plant genes and key microbes that significantly contribute to microbial colonization patterns.

Research Topics

- Map distribution of microbial genotypes onto that of plant genotypes in a wild field
- Associate plant and microbial genotypes in nature while tracking plant growth and transcriptional output
- Test predictions about the microbial community and fitness using targeted genome engineering of locally adapted plants

Bio

- 2014 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2007 to 2014 / PhD in Genetics and Molecular Biology / University of North Carolina, Chapel Hill, USA
- 2002 to 2006 / BSc in Biology / University of North Carolina, Chapel Hill, USA

Selected References

Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

Wagner M. R., Lundberg D. S., Coleman-Derr D., Tringe S. G., Dangl J. L. and Mitchell-Olds T.
Ecol Lett (2014), 17(6) 717-26.

Practical innovations for high-throughput amplicon sequencing

Lundberg D. S., Yourstone S., Mieczkowski P., Jones C. D. and Dangl J. L.
Nat Methods (2013), 10(10) 999-1002.

Defining the core Arabidopsis thaliana root microbiome

Lundberg D. S., Lebeis S. L., Paredes S. H., Yourstone S., Gehring J., Malfatti S., Tremblay J., Engelbrektson A., Kunin V., del Rio T. G., Edgar R. C., Eickhorst T., Ley R. E., Hugenholtz P., Tringe S. G. and Dangl J. L.
Nature (2012), 488(7409) 86-90.

Contact

derek.lundberg@tuebingen.mpg.de

Fiona Paul

Pathodopsis. Geographical patterns of microbial diversity on Arabidopsis. Plant-microbe co-evolution.

Fiona Paul

I just started my PhD - more information following shortly

Research Topics

- Pathodopsis
- Geographical patterns of microbial diversity on Arabidopsis
- Plant-microbe co-evolution

Bio

- 2018 to present / PhD student / Max Planck Institute for Developmental Biology
- 2014 to 2017 / MSc Ecology and Evolution / Goethe-University Frankfurt, Germany
- 2011 to 2014 / BSc Biological Sciences / Münster University, Germany

Contact

fiona.paul@tuebingen.mpg.de

Julian Regalado

Classification of plant microbiome samples. GPU computational tools.

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Julian Regalado

My main research focuses on bioinformatics, computational biology, and algorithm development. Currently, I am working with metagenomics to understand the plant microbiome, aiming to develop new ways to analyze microbial communities using machine learning and empirical inference techniques. A special tool I am interested in is the use of GPU computation for massively parallel algorithms. This way complex problems can be approached without the use of sophisticated IT infrastructure. Other interests include next generation sequencing technology, and plantpathogen evolution.

Research Topics

- Classification of plant microbiome samples
- GPU computational tools

Bio

- 2014 to present / PhD student / Max Planck Institute for Developmental Biology
- 2010 to 2014 / BSc in Genomic Sciences / National Autonomous University of Mexico
- 2013 to 2014 / Internship / Cold Spring Harbor Laboratory, USA
- 2012 to 2013 / Internship / Winter Genomics Bioinformatics Solutions, Mexico
- 2012 to 2013 / Teaching Assistant / National Autonomous University of Mexico

Contact

julian.regalado@tuebingen.mpg.de

Or Shalev

Genetic factors determining the specificity of plant-microbe interactions.

‹ ›

Or Shalev

Plants serve as a rich habitat for microbes. Numerous macro and micro niches, both inside the plant and on its surface, allow a diverse set of microbes to thrive and propagate.
Using Arabidopsis thaliana and the wide-spread gram-negative bacterium Pseudomonas syringae as a model system, I aim to understand the interaction of host and microbe genotypes, and thus the selectivity of colonization. I am investigating both pathogenic and mutualistic Pseudomonas strains, and use genomic tools to decipher the dynamics of gene repertoires enabling or preventing plant colonization - both from a plant and a microbe perspective.

Research Topics

- Genetic factors determining the specificity of plant-microbe interactions

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2016 / MSc in Plant Science / Hebrew University, Israel
- 2013 to 2014 / Student exchange semester / Göttingen University, Germany
- 2010 to 2013 / BSc in Agroecology and Biotechnology / Hebrew University, Israel

Selected References

Pseudozyma aphidis Induces Salicylic-Acid-Independent Resistance to Clavibacter michiganensis in Tomato Plants

Barda, O., Shalev, O., Alster, S., Buxdorf, K., Gafni, A. and Levy, M.
Plant Disease (2015), 99(5): 621-626

Contact

or.shalev@tuebingen.mpg.de

To Top

Hybrid performance and fitness tradeoffs

Ana-Cristina Barragan Lopez

Hybrid incompatibility. Evolution of immune receptors. Arabidopsis arenosa.

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Ana-Cristina Barragan Lopez

The combination of two genomes in hybrid plants can lead to detrimental effects, often caused by interaction of incompatible immune genes. NLR-type immune receptors play major roles in this interaction, and to gain a better understanding of the molecular mechanisms involved in their activation, I am investigating the complexity and variability of NLR-type immune receptor gene clusters in Arabidopsis thaliana. I also study the Arabidopsis arenosa to find out whether hybrid incompatibility is more or less prevalent in this naturally outcrossing species, compared to the closely related selfer Arabidopsis thaliana.

Research Topics

- Hybrid incompatibility
- Evolution of immune receptors
- Arabidopsis arenosa

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2013 to 2016 / MSc in Plant Molecular Biology / University of Tübingen, Germany
- 2010 to 2013 / BSc in Biology / University of Tübingen, Germany

Contact

cristina.barragan@tuebingen.mpg.de

Monika Demar

I'm a research technician in the department.

Contact

monika.demar@tuebingen.mpg.de

Anette Habring

Hybrid incompatibility. Evolution of disease resistance.

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Anette Habring

My work as a technician in the group focuses on molecular and plant projects aimed at identifying hybrid incompatibilities and characterizing the underlying causal genes. I have been coordinating the generation and maintenance of the 80x80 diallel of Arabiodopsis thalinana accessions. Furthermore, I am generating molecular tools for the analysis of RPW8, and RPP8, two of the genes we are analyzing more closely now. Aside from research, I am lab safety person and have several organizational tasks that help the department run smoothly.

Research Topics

- Hybrid incompatibility
- Evolution of disease resistance

Bio

- 2002 to present / Technician / Dept. of Molecular Biology, Max Planck Institute for Developmental Biology
- 2001 to 2002 / Technichan / Dept. of Cell Biology, Max Planck Institute for Developmental Biology
- 1991 to 2001 / Technichan / Dept. of Biochemistry, Max Planck Institute for Developmental Biology
- 1986 to 1991 / Technician / Friedrich Miescher Laboratory, Tübingen, Germamy

Selected References

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

Chae E., Bomblies K., Kim S. T., Karelina D., Zaidem M., Ossowski S., Martin-Pizarro C., Laitinen R. A., Rowan B. A., Tenenboim H., Lechner S.,Demar M., Habring-Muller A., Lanz C., Ratsch G. and Weigel D.
Cell (2014), 159(6) 1341-51.

Contact

anette.habring@tuebingen.mpg.de

Lei Li

Biochemical characterization of immune protein complexes. Plant-pathogen interaction. Hybrid incompatibility.

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Lei Li

Plants have evolved sophisticated mechanisms to recognize non-self molecules, allowing them to deploy effective immune reactions against a myriad of pathogens. Resistance protein plays an important role in the process of pathogen defense, autoimmunity, and hybrid incompatibility. My research focuses on the activation mechanism of plant resistance proteins.

Research Topics

- Biochemical characterization of immune protein complexes
- Plant-pathogen interaction
- Hybrid incompatibility

Bio

- 2016 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2010 to 2015 / PhD in Genetics / Chinese Academy of Sciences, Beijing, China
- 2006 to 2010 / BSc in Biotechnology / Northwest A&F University, Yangling, China

Selected References

Activation-Dependent Destruction of a Co-receptor by a Pseudomonas syringae Effector Dampens Plant Immunity

Li, L.*, Kim, P.*, Yu, L.*, Cai, G., Chen, S., Alfano, J. R., Zhou, J. M.
Cell Host Microbe. (2014), 20(4):504-14.

The FLS2-associated kinase BIK1 directly phosphorylates the NADPH oxidase RbohD to control plant immunity

Li, L.*, Li, M.*, Zhou, Z., Liang, X., Liu, Z., Cai, G., Gao, L., Zhang, X., Wang, Y., Chen, S., Zhou, J. M.
Cell Host Microbe. (2014), 15(3):329-38.

Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex

Sun, Y.*, Li, L.*, Macho, A. P., Han, Z., Hu, Z., Zipfel, C., Zhou, J. M., Chai, J.
Science. (2013), 342(6158):624-8.

Contact

lei.li@tuebingen.mpg.de

Josip Perkovic

‹ ›

Josip Perkovic

I'm a technician in the department.

Contact

josip.perkovic@tuebingen.mpg.de

Rui Wu

Evolution of the NLR repertoire and autoimmunity. Genome editing for targeted modification of NLR genes.

‹ ›

Rui Wu

Resistance (R) loci with nucleotide binding/leucine rich repeat (NB-LRR or NLR) domains have been identified as the major causal genes for hybrid necrosis, which presents an extreme example of the trade-off between plant growth and the activation of immune system. My interest focuses on these three questions: 1) How NLR proteins, including the entire NLR family, lead to different degrees of hybrid necrosis at a cellular and biochemical level; 2) how they contribute to fitness under natural conditions; and 3) how this is reflected in their extreme sequence variation.

Research Topics

- Evolution of the NLR repertoire and autoimmunity
- Genome editing for targeted modification of NLR genes

Bio

- 2014 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2011 to 2014 / Pre-doctoral Fellow / Carnegie Institute for Science, Stanford, USA
- 2009 to 2011 / Junior Research Fellow / Temasek Lifesciences Laboratory, Singapore
- 2010 to 2014 / PhD / National University of Singapore
- 2006 to 2009 / MSc in Genetics / Northeast Normal University, China
- 2002 to 2006 / Diploma in Biology / Northeast Normal University, China

Selected References

A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis

Geng Y*., Wu R*., Wee C*. W., Xie F., Wei X., Chan P. M., Tham C., Duan L. and Dinneny J. R.
Plant Cell (2013), 25(6) 2132-54 (*equal contribution).

Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids

Wang X*., Wu R*., Lin X., Bai Y., Song C., Yu X., Xu C., Zhao N., Dong Y. and Liu B.
BMC Plant Biol (2013), 13 77 (*equal contribution).

Inter-species grafting caused extensive and heritable alterations of DNA methylation in Solanaceae plants

Wu R., Wang X., Lin Y., Ma Y., Liu G., Yu X., Zhong S. and Liu B.
PLoS One (2013), 8(4) e61995.

Contact

rui.wu@tuebingen.mpg.de

Wei Yuan

The molecular mechanism of heterosis.

‹ ›

Wei Yuan

I am a plant population geneticist being trained to exploit state-of-the-art molecular, genomics, and statistical tools to address evolutionary questions. My current research focus is on hybrid plants, and I use systematically acquired growth trajectories and transcriptome profiles from Arabidopsis thaliana hybrids and their parents to apply GWAS, TWAS, and eQTL analyses that will allow me uncover the relationship between genetic variation (available from the 1001 Genomes resource) and hybrid phenotype. My research will systematically evaluate whether heterosis is mainly dictated by overall heterozygosity in hybrid genomes, or rather by the expression/interactions of a core set of genes.

Research Topics

- The molecular mechanism of heterosis

Bio

- 2016 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2016 / PhD in Biology / New York University, USA
- 2009 / BSc in Plant Biology/ China Agricultural University, China

Selected References

Extreme QTL mapping of germination speed in Arabidopsis thaliana

Yuan, W., Flowers, J. M., Sahraie, D. J., Ehrenreich, I. M., Purugganan, M. D.
Molecluar Ecology (2016), 25(17):4177-96.

Cryptic genetic variation for Arabidopsis thaliana seed germination speed in a novel salt stress environment

Yuan, W., Flowers, J. M., Sahraie, D. J., Ehrenreich, I. M., Purugganan, M. D.
G3 (2016), 6(10):3129-38.

Contact

wei.yuan@tuebingen.mpg.de

Wangsheng Zhu

Natural modifiers of a natural ACD6 allele. Modulation of immune response in natural populations.

‹ ›

Wangsheng Zhu

I am interested in understanding genetic and molecular mechanisms involved in trade-off between growth and defense in plants. To this end, I am dissecting genetic variation in Arabidopsis thaliana accessions adapted to distinct geographical regions across the world. Combining genome wide association analysis (GWAS), quantitative genetic analysis and genome editing (CRISPR/Cas9 system), I am aiming to understand the way plants optimize their fitness in response to resource limitation and environment fluctuation.

Research Topics

- Natural modifiers of a natural ACD6 allele
- Modulation of immune response in natural populations

Bio

- 2014 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2014 / PhD / Monash University, Australia
- 2008 / M.Phil. / Donghua University, China
- 2005 / BA / Hua Zhong Agriculture University, China

Selected References

Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid

Zhu W.*, Hu, B., Becker, C., Dogan, E. S., Berendzen, K. W., Weigel, D. and Liu C*.
Genome Biology (2017). 18(1):157 (*equal contribution)

easyGWAS: A Cloud Based Platform for Comparing the Results of Genome-Wide Association Studies

Grimm, D. G., Roqueiro, D., Salomé, P. A., Kleeberger, S., Greshake, B., Zhu, W., Liu, C., Lippert, C., Stegle, O., Schölkopf B., Weigel, D., Borgwardt, K. M.
The Plant Cell (2017). 29(1): 5-19.

Genetic architecture of natural variation in thermal responses of Arabidopsis thaliana

Sanchez-Bermajo E.*, Zhu W.*, Tasset C., Eimer H., Sureshkumar S., Singh R., Sundaramoorthi V., Colling L. and Balasubramanian S.
Plant Physiol (2015). 169: 647-659 (*equal contribution)

Natural variation identifies ICARUS1, a universal gene required for cell proliferation and growth at high temperatures in Arabidopsis

Zhu W*., Ausin I*., Seleznev A., Méndez-Vigno B., Picó F. X., Sureshkumar S., Sundaramoorthi V., Bulach D., Powell D., Seemann T., Alonso-Blanco C. and Balasubramanian S.
PLoS Genet (2015), 11(5) e1005085. (*equal contribution)

Contact

wangsheng.zhu@tuebingen.mpg.de

To Top

Ancient Genomics and Evolution

Hernán Burbano

The dynamics of past plant-pathogen epidemics. Identification and timing of key events in crop domestication. Colonization of new ecological niches by invasive or introduced species.

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Hernán Burbano

I am very interested in evolutionary biology and chose genomics to study the forces and processes that influence evolution. I combine the use of modern and historic samples from both herbaria and archaeological remains. My group performs computational analysis of large datasets resulting from high-throughput DNA sequencing with a special emphasis on the particularities of DNA retrieved from historic samples: ancient DNA (aDNA). I have been extensively involved in the study of hominid evolution and currently focus mainly on plant and plant-pathogen evolution.

Research Topics

- The dynamics of past plant-pathogen epidemics
- Identification and timing of key events in crop domestication
- Colonization of new ecological niches by invasive or introduced species

Bio

- 2014 to present / Project Leader Ancient Genomics and Evolution / Max Planck Institute for Developmental Biology
- 2012 to 2014 / Postdoc / Max Planck Institute for Developmental Biology
- 2012 / PhD in Evolutionary Genetics / Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- 2006 / MSc in Biology/ Universidad Nacional de Colombia, Bogotá, Colombia
- 2002 / Veterinarian / Universidad Nacional de Colombia, Bogotá, Colombia

Selected References

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

Weiss, C. L., Schuenemann, V.J., Devos, J., Shirsekar, G., Reiter, E. Gould, B.A., Stinchcombe, J.R., Krause J., Burbano, H.A.
R Soc Open Sci (2016), 3(6) 160239

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

Weiss, C. L., Dannemann, M., Pruefer K., Burbano H. A.
eLife (2015), 4.

Mining herbaria for plant pathogen genomes: back to the future

Yoshida K., Burbano H. A*., Krause J., Thines M., Weigel D*. and Kamoun S*.
PLoS Pathog (2014), 10(4) e1004028. (*equal contribution)

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

Yoshida K., Schuenemann V. J., Cano L. M., Pais M., Mishra B., Sharma R., Lanz C., Martin F. N., Kamoun S., Krause J., Thines M., Weigel D. and Burbano H. A.
Elife (2013), 2 e00731.

Targeted investigation of the Neandertal genome by array-based sequence capture

Burbano H. A., Hodges E., Green R. E., Briggs A. W., Krause J., Meyer M., Good J. M., Maricic T., Johnson P. L., Xuan Z., Rooks M., Bhattacharjee A., Brizuela L., Albert F. W., de la Rasilla M., Fortea J., Rosas A., Lachmann M., Hannon G. J. and Paabo S.
Science (2010), 328(5979) 723-5.

Contact

hernan.burbano@tuebingen.mpg.de

Katrin Fritschi

‹ ›

Katrin Fritschi

I am currently on maternity leave - back at the bench in 2018.

Contact

katrin.fritschi@tuebingen.mpg.de

Patricia Lang

Genetic diversity trailing global change. Natural variation in microRNA pathways.

‹ ›

Patricia Lang

I am interested in different aspects of adaptation and evolution, from small- (molecules) to large-scale (populations) processes. To complete my skill repertoire for looking at this big picture of evolution, I am now, after a molecular biology PhD on biogenesis and function of miRNAs, doing a Postdoc in ancient genetics and evolution. My project focuses on the effects of global change on genetic variation in plants - where, how and with which outcome do plants react (adapt?) to environmental changes? To address these questions, I am developing RAD sequencing and analysis methods for five non-model plant species, to process ~1000 contemporary and ~300 up to ~200 years old historic samples I collected in forests and herbaria. The project is part of the German Biodiversity Exploratories, a large scale, long-term DFG-funded effort for biodiversity and ecosystem research.

For more information: https://patricialmlang.wordpress.com/

Research Topics

- Genetic diversity trailing global change
- Natural variation in microRNA pathways

Bio

- 2017 to present / Postdoc / Max Planck Institute for Developmental Biology
- 2012 to 2016 / PhD student / Max Planck Institute for Developmental Biology
- 2010 to 2012 / MSc in Plant and Forest Biotechnology / Umeå Plant Science Center, Sweden
- 2007 to 2010 / BSc in Biology / Würzburg University, Germany and Umeå University, Sweden

Selected References

A role for the F-box protein HAWAIIAN SKIRT in plant microRNA function

Lang P.L.M.*, Christie, M.D.*, Dogan, E.S., Schwab, R., Hagmann, J., Van de Weyer, A.-L., Scacchi, E. and Weigel, D., Plant Physiol. (2017) (*equal contribution)

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

Karlsson, P., Christie, M.D., Seymour, D., Wang, H., Wang, X., Hagmann, J., Kulcheski, F.R. and Manavella, P.A., Proc Natl Acad Sci USA (2015)

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

Francisco-Mangilet A. G.*, Karlsson P.*, Kim M.-H., Eo H. J., Oh S. A., Kim J. H., Kulcheski F. R., Park S. K. and Manavella P. A. The Plant Journal (2015) (*equal contribution)

Contact

patricia.lang@tuebingen.mpg.de

Sergio Latorre

Ancient genomics. Evolution of methylation in key plant species. Dynamics of host - pathogen interactions through history.

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Sergio Latorre

Historical and ancient samples, such as dried plants in herbaria, can tell us about the genetic makeup of a species at the time of collection and allow us to directly study, rather than infer, changes in DNA sequences over historical time spans. Advances in sequencing technologies and extraction methods have allowed us to interrogate not only very small amounts of material, but also epigenetic modifications on the DNA, such as cytosine methylation. I am analyzing those methylation patterns in ancient and modern plant samples to study changes across recent history, which will allow us to investigate the evolution of epigenetically controlled traits.

Research Topics

- Ancient genomics
- Evolution of methylation in key plant species
- Dynamics of host - pathogen interactions through history

Bio

- 2016 to present / PhD student / Max Planck Institute for Developmental Biology
- 2014 / MSc in Microbiology / Universidad Nacional de Colombia
- 2010 / Agronomic Engineer / Universidad Nacional de Colombia

Selected References

Environmental occurrence of arsenic in Colombia: a review.

Alonso, D. L*., Latorre, S*., Castillo, E., Brandão, P.F.
Environmental Pollution (2014). 186: 272-281. (*equal contribution)

Contact

sergio.latorre@tuebingen.mpg.de

Kelly Swarts

Computational biology and methods development. Quantitative genetics. Plant archaeogenomis.

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Kelly Swarts

Domesticated plants and animals are the culmination of intensive selection processes by which humans and associated organisms co-adapt to their mutually changing social and natural environment. I integrate archaeological inference with novel and established quantitative and population genetic analyses in diverse modern and ancient populations to understand how historical processes shape trait architecture and the distribution of modern diversity in maize (Zea mays ssp. mays). Ancient samples not only provide ‘snapshots’ of past diversity, but they anchor inference in cultural and environmental context. These data help us to understand the long-term impacts of evolutionary, environmental and cultural change, and inform a way forward for integrating novel germplasm and selection regimes in modern breeding.

Research Topics

- Computational biology and methods development
- Quantitative genetics
- Plant archaeogenomis

Bio

- 2016 to present / NSF Postdoctoral Fellow / Max Planck Institute for Developmental Biology
- 2011 to 2016 / PhD in Plant Breeding and Genetics / Cornell University
- 2010 to 2011 / Volunteer in Chandler Laboratory / University of Arizona
- 2008 to 2010 / Archaeologist (supervisor) based in Tucson, AZ
- 2006 to 2008 / M.A. in Archaeology / Northern Arizona University
- 2005 to 2006 / Archaeologist based in Tucson, AZ
- 2001 to 2005 / B.S. in Biology and Anthropology / University of Michigan-Ann Arbor

Selected References

Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America.

Swarts, K., Gutaker, R. M., Benz, B., Blake, M. Bukowski, R. Holland, et al.
Science (2017), 357(6350):512-515

A Study of Allelic Diversity Underlying Flowering-Time Adaptation in Maize Landraces .

Navarro Romero, J. A., Wilcox, M., Bugueno, J., Romay, M.C., Swarts, K., Trachsel, S., Preciado, E. et al.
Nat Genet (2017), 49(6):970

Novel Methods to Optimize Genotypic Imputation for Low-Coverage, Next-Generation Sequence Data in Crop Plants.

Swarts K., Li, H., Romero Navarro, J. A., An, D., Romay, M. C., Hearne, S., Acharya, C. Glaubitz, J. C., Mitchell, S., Elshire, R. J. et al.
The Plant Genome (2014), 7,0.

Contact

kelly.swarts@tuebingen.mpg.de

Clemens Weiss

Analyses of ancient DNA retrieved from herbarium specimens. Co-evolution of plants and their pathogens, combining ancient and modern DNA from infected plant samples.

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Clemens Weiss

I am interested in using Next Generation Sequencing (NGS) to address questions regarding the co-evolution of plants and their pathogens. The sequencing of ancient DNA (aDNA) is especially powerful in this regard, since it enables us to look back into the genomes of pathogens that triggered past epidemics. Desiccated plants that are stored in herbaria provide a great resource, since they sometimes also carry infectious organisms, and I am using herbarium samples to understand host pathogen interactions on a genomic level, over a timescale of several hundred years.

Research Topics

- Analyses of ancient DNA retrieved from herbarium specimens
- Co-evolution of plants and their pathogens, combining ancient and modern DNA from infected plant samples

Bio

- 2014 to present / PhD student / Max Planck Institute for Developmental Biology
- 2012 to 2014 / MSc in Biochemistry / University of Würzburg, Germany
- 2009 to 2012 / BSc in Biochemistry / University of Würzburg, Germany

Selected References

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

Weiss, C. L., Schuenemann, V.J., Devos, J., Shirsekar, G., Reiter, E. Gould, B.A., Stinchcombe, J.R., Krause J., Burbano, H.A.
R Soc Open Sci (2016), 3(6) 160239

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

Weiss, C. L., Dannemann, M., Pruefer K., Burbano H. A.
eLife (2015), 4.

Contact

clemens.weiss@tuebingen.mpg.de

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WeigelWorld scientists

Director

Detlef Weigel

Detlef Weigel

Bio

Selected References

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Evolutionary Genetics

Max Collenberg Gene expression in hybrid plants.

Max Collenberg

Research Topics

Bio

Contact

Moisés Expósito Alonso Evolutionary rates and signatures. Experimental evolution. Spatial distribution of genetic variation.

Moisés Expósito Alonso

Research Topics

Bio

Selected References

Contact

Alba Gonzalez Co-evolution of Arabidopsis and its oomycete pathogen Hyaloperonospora.

Alba Gonzalez

Research Topics

Bio

Contact

Julia Hildebrandt Next Generation Sequencing. PacBio Sequel.

Julia Hildebrandt

Research Topics

Bio

Selected References

Contact

Patricia Lang Genetic diversity trailing global change. Natural variation in microRNA pathways.

Patricia Lang

Research Topics

Bio

Selected References

Contact

Christa Lanz DNA sequencing and all associated challenges.

Christa Lanz

Research Topics

Bio

Selected References

Contact

Ulrich Lutz GxG interactions. Flowering time variation. Herbicide resistance.

Ulrich Lutz

Research Topics

Bio

Selected References

Contact

Manuela Neumann Flowering time regulation in Arabidopsis. INTACT technology.

Manuela Neumann

Research Topics

Bio

Contact

Fernando Rabanal Evolution and regulation of ribosomal RNA genes. Herbicide resistance.

Fernando Rabanal

Research Topics

Bio

Selected References

Contact

Gautam Shirsekar Co-evolution in natural A. thaliana – oomycete pathosystems.

Gautam Shirsekar

Research Topics

Bio

Selected References

Identification and characterization of suppressor mutants of spl11- mediated cell death in rice

The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice

The U-Box E3 ligase SPL11/PUB13 is a convergence point of defense and flowering signaling in plants

Contact

Thanvi Srikant DNA methylation. Epigenetics.

Thanvi Srikant

Research Topics

Bio

Contact

Efthymia Symeonidi GxG interactions. Diversity in flowering and immunity genetic architectures.

Efthymia Symeonidi

Research Topics

Bio

Selected References

Contact

Bridgit Waithaka Evolutionary genomics of herbicide-resistant weeds.

Max Collenberg

Gene expression in hybrid plants.

Moisés Expósito Alonso

Evolutionary rates and signatures. Experimental evolution. Spatial distribution of genetic variation.

Alba Gonzalez

Co-evolution of Arabidopsis and its oomycete pathogen Hyaloperonospora.

Julia Hildebrandt

Next Generation Sequencing. PacBio Sequel.

Patricia Lang

Genetic diversity trailing global change. Natural variation in microRNA pathways.

Christa Lanz

DNA sequencing and all associated challenges.

Ulrich Lutz

GxG interactions. Flowering time variation. Herbicide resistance.

Manuela Neumann

Flowering time regulation in Arabidopsis. INTACT technology.

Fernando Rabanal

Evolution and regulation of ribosomal RNA genes. Herbicide resistance.

Gautam Shirsekar

Co-evolution in natural A. thaliana – oomycete pathosystems.

Thanvi Srikant

DNA methylation. Epigenetics.

Efthymia Symeonidi

GxG interactions. Diversity in flowering and immunity genetic architectures.

Bridgit Waithaka

Evolutionary genomics of herbicide-resistant weeds.

Frank Weiss

Plant Breeding.

Anjar Wibowo

Impact of tissue-specific regeneration and stress priming in different A.thaliana accession and different plant species.

Felix Bemm

Complete genome assemblies for Arabidopsis species. Complete genome assemblies for A. thaliana accessions. Integration of short and long read sequencing technologies.

Ilja Bezrukov

Automated Phenotyping. Pipelines for processing of short and long read sequencing data.