Plant-Microbe Co-Evolution


Group Interests

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Only with highly diverse immune gene repertoires can plant populations cope with myriad pathogen pressures. In Capsella, we have documented intense selection for immune gene diversity. At the same time, a near-clonal A. thaliana lineage has successfully spread throughout North America, populating a wide variety of habitats in the presence of its major microbial pathogens, Hyaloperonospora arabidopsidis and Albugo laibachii. Using wild isolates collected on field trips, we are addressing the molecular evolution of both host and pathogens using genome-sequencing based approaches, and use pathogen testing to reveal whether the uniform A. thaliana lineage is less adapted to local pathogen strains than accessions from the species’ native range.

Another major effort in this direction is to understand how microbes shape the immune gene repertoire of A. thaliana. We are using natural populations to establish the links that exist between microbiome composition and genetic diversity of the host. This will be a crucial step in identifying causal agents that drive differentiation of the plant immune system in the wild. In addition, we are using local A. thaliana populations from stands around Tübingen to investigate the dynamics of plant pathogen spread in natural host populations, taking into account that pre-existing microbiomes might alter host susceptibility.

  • Microbiome analyses in natural plant populations
  • Molecular co-evolution of Arabidopsis and its pathogens
  • Effect of microbiome composition on plant colonization by pathogens

Collaboration Partners



Allelochemicals of the phenoxazinone class act at physiologically relevant concentrations

Venturelli S., Petersen S., Langenecker T., Weigel D., Lauer U. M. and Becker C.
Plant Signal Behav
(2016), 11(5) e1176818.

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids

Rigal M., Becker C., Pelissier T., Pogorelcnik R., Devos J., Ikeda Y., Weigel D. and Mathieu O.
Proc Natl Acad Sci U S A
(2016), 113(14) 2083-92.

Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors

Venturelli S., Belz R. G., Kamper A., Berger A., von Horn K., Wegner A., Bocker A., Zabulon G., Langenecker T., Kohlbacher O., Barneche F., Weigel D., Lauer U. M., Bitzer M. and Becker C.
Plant Cell
(2015), 27(11) 3175-89.

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

Karlsson P., Christie M. D., Seymour D. K., Wang H., Wang X., Hagmann J., Kulcheski F. and Manavella P. A.
Proc Natl Acad Sci U S A
(2015), 112(45) 14096-101.

Chromatin in 3D: progress and prospects for plants

Liu C. and Weigel D.
Genome Biol
(2015), 16(1) 170.

THO2, a core member of the THO/TREX complex, is required for microRNA 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.
Plant J
(2015), 82(6) 1018-29.

Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage

Hagmann J., Becker C., Muller J., Stegle O., Meyer R. C., Wang G., Schneeberger K., Fitz J., Altmann T., Bergelson J., Borgwardt K. and Weigel D.
PLoS Genet
(2015), 11(1) e1004920.

Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

Wang C., Liu C., Roqueiro D., Grimm D., Schwab R., Becker C., Lanz C. and Weigel D.
Genome Res
(2015), 25(2) 246-56.

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

Smith L. M., Burbano H. A., Wang X., Fitz J., Wang G., Ural-Blimke Y. and Weigel D.
Plant J
(2015), 81(4) 597-610.

Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization

Seymour D. K., Koenig D., Hagmann J., Becker C. and Weigel D.
PLoS Genet
(2014), 10(11) e1004785.

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

Rubio-Somoza I., Zhou C. M., Confraria A., Martinho C., von Born P., Baena-Gonzalez E., Wang J. W. and Weigel D.
Curr Biol
(2014), 24(22) 2714-9.

Artificial microRNAs for specific gene silencing in rice

Warthmann N., Ossowski S., Schwab R. and Weigel D.
Methods Mol Biol
(2013), 956 131-49.

Coordination of flower maturation by a regulatory circuit of three microRNAs

Rubio-Somoza I. and Weigel D.
PLoS Genet
(2013), 9(3) e1003374.

Tissue-specific silencing of Arabidopsis SU(VAR)3-9 HOMOLOG8 by miR171a

Manavella P. A., Koenig D., Rubio-Somoza I., Burbano H. A., Becker C. and Weigel D.
Plant Physiol
(2013), 161(2) 805-12.

Transposon variants and their effects on gene expression in Arabidopsis

Wang X., Weigel D. and Smith L. M.
PLoS Genet
(2013), 9(2) e1003255.

Epialleles in plant evolution

Weigel D. and Colot V.
Genome Biol
(2012), 13(10) 249.

Epigenetic variation: origin and transgenerational inheritance

Becker C. and Weigel D.
Curr Opin Plant Biol
(2012), 15(5) 562-7.

Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1

Manavella P. A., Hagmann J., Ott F., Laubinger S., Franz M., Macek B. and Weigel D.
(2012), 151(4) 859-70.

MIGS: miRNA-induced gene silencing

Felippes F. F., Wang J. W. and Weigel D.
Plant J
(2012), 70(3) 541-7.

Plant secondary siRNA production determined by microRNA-duplex structure

Manavella P. A., Koenig D. and Weigel D.
Proc Natl Acad Sci U S A
(2012), 109(7) 2461-6.

Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana

de Felippes F. F., Ott F. and Weigel D.
Nucleic Acids Res
(2011), 39(7) 2880-9.

MicroRNA networks and developmental plasticity in plants

Rubio-Somoza I. and Weigel D.
Trends Plant Sci
(2011), 16(5) 258-64.

miRNA control of vegetative phase change in trees

Wang J. W., Park M. Y., Wang L. J., Koo Y., Chen X. Y., Weigel D. and Poethig R. S.
PLoS Genet
(2011), 7(2) e1002012.

Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor

Gou J. Y., Felippes F. F., Liu C. J., Weigel D. and Wang J. W.
Plant Cell
(2011), 23(4) 1512-22.

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Becker C., Hagmann J., Muller J., Koenig D., Stegle O., Borgwardt K. and Weigel D.
(2011), 480(7376) 245-9.

A collection of target mimics for comprehensive analysis of microRNA function in Arabidopsis thaliana

Todesco M., Rubio-Somoza I., Paz-Ares J. and Weigel D.
PLoS Genet
(2010), 6(7) e1001031.

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

Laubinger S., Zeller G., Henz S. R., Buechel S., Sachsenberg T., Wang J. W., Ratsch G. and Weigel D.
Proc Natl Acad Sci U S A
(2010), 107(41) 17466-73.

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

Wollmann H., Mica E., Todesco M., Long J. A. and Weigel D.
(2010), 137(21) 3633-42.

Small RNAs in flower development

Wollmann H. and Weigel D.
Eur J Cell Biol
(2010), 89(2-3) 250-7.

Structure determinants for accurate processing of miR172a in Arabidopsis thaliana

Werner S., Wollmann H., Schneeberger K. and Weigel D.
Curr Biol
(2010), 20(1) 42-8.

miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana

Wang J. W., Czech B. and Weigel D.
(2009), 138(4) 738-49.

Regulation and functional specialization of small RNA-target nodes during plant development

Rubio-Somoza I., Cuperus J. T., Weigel D. and Carrington J. C.
Curr Opin Plant Biol
(2009), 12(5) 622-7.

Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173

Felippes F. F. and Weigel D.
(2009), 10(3) 264-70.

Control of jasmonate biosynthesis and senescence by miR319 targets

Schommer C., Palatnik J. F., Aggarwal P., Chetelat A., Cubas P., Farmer E. E., Nath U. and Weigel D.
PLoS Biol
(2008), 6(9) e230.

Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana

Wang J. W., Schwab R., Czech B., Mica E. and Weigel D.
Plant Cell
(2008), 20(5) 1231-43.

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

Laubinger S., Sachsenberg T., Zeller G., Busch W., Lohmann J. U., Ratsch G. and Weigel D.
Proc Natl Acad Sci U S A
(2008), 105(25) 8795-800.

Evolution of Arabidopsis thaliana microRNAs from random sequences

Felippes F. F., Schneeberger K., Dezulian T., Huson D. H. and Weigel D.
(2008), 14(12) 2455-9.

Gene silencing in plants using artificial microRNAs and other small RNAs

Ossowski S., Schwab R. and Weigel D.
Plant J
(2008), 53(4) 674-90.

Highly specific gene silencing by artificial miRNAs in rice

Warthmann N., Chen H., Ossowski S., Weigel D. and Herve P.
PLoS One
(2008), 3(3) e1829.

Sequence and expression differences underlie functional specialization of Arabidopsis microRNAs miR159 and miR319

Palatnik J. F., Wollmann H., Schommer C., Schwab R., Boisbouvier J., Rodriguez R., Warthmann N., Allen E., Dezulian T., Huson D., Carrington J. C. and Weigel D.
Dev Cell
(2007), 13(1) 115-25.

Target mimicry provides a new mechanism for regulation of microRNA activity

Franco-Zorrilla J. M., Valli A., Todesco M., Mateos I., Puga M. I., Rubio-Somoza I., Leyva A., Weigel D., Garcia J. A. and Paz-Ares J.
Nat Genet
(2007), 39(8) 1033-7.

Highly specific gene silencing by artificial microRNAs in Arabidopsis

Schwab R., Ossowski S., Riester M., Warthmann N. and Weigel D.
Plant Cell
(2006), 18(5) 1121-33.

Specific effects of microRNAs on the plant transcriptome

Schwab R., Palatnik J. F., Riester M., Schommer C., Schmid M. and Weigel D.
Dev Cell
(2005), 8(4) 517-27.

Control of leaf morphogenesis by microRNAs

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