Claude Becker

Genomics and epigenomics of plant-plant and plant-environment interactions

The Becker group is currently accepting applications for PhD positions. We are looking for motivated people with a background in plant molecular biology, genomics and/or metagenomics. Skills in bioinformatics are a plus. PhD candidates should apply via the Vienna Biocenter PhD programme.

Research focus

Plants experience a tremendous pressure to rapidly adapt to their environment and to cope with changing conditions. Growing in more or less dense plant communities, they moreover have to compete with their neighbours for limited resources, such as nutrients, water, light and space.

Our lab studies the molecular effects of phytotoxic compounds that are released by certain plant species, a process known as allelopathy. We have recently presented the first molecular mode of action of an allelochemical that is produced by some major crop species and have shown that it inhibits the growth of target plants by affecting chromatin configuration. We are interested in learning how plants adapt to such adverse, phytotoxic environments, and what role plant-associated microorganisms might play in allelopathy between plants. We employ biochemical, molecular, genomic and metagenomic approaches to investigate the mode of action of allelochemicals, to identify genetic determinants of adaptive traits, and to characterise the allelopathy–promoting or –inhibiting properties of bacteria and fungi. Our goal is a better understanding at the molecular, genetic and organismal level of these fundamental processes, which contribute to shaping both natural and agricultural plant communities. 

Selected publications

Daccord N, Celton JM, Linsmith G, et al. (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49(7):1099-106.

Hagmann J, Becker C (2017) Assessing Distribution and Variation of Genome-Wide DNA Methylation Using Short-Read Sequencing. Methods Mol Biol. 1610:61-72.

Seymour D and Becker C (2017) The causes and consequences of DNA methylome variation in plants. Curr Opin Plant Biol 36:56-63.

Catoni M, Griffiths J, Becker C, et al. (2017) DNA sequence properties that predict susceptibility to epiallelic switching. EMBO J 36(5):617-28.

Kawakatsu T, Huang SS, Jupe F, et al. (2016) Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions. Cell 166(2):492-505.

Wibowo A, Becker C, Marconi G, et al. (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. Elife e13546.

Liu C, Wang C, Wang G, et al. (2016) Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution. Genome Res 26(8):1057-68.

Venturelli S, Petersen S, ... , Becker C (2016) Allelochemicals of the phenoxazinone class act at physiologically relevant concentrations. Plant Signal Behav 11(5):e1176818.

Rigal M, Becker C, Pélissier T, et al. (2016) Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids. Proc Natl Acad Sci USA 113(14):E2083-92.

Venturelli S, Belz RG,..., Becker C (2015) Plants Release Precursors of Histone Deacetylase Inhibitors to Suppress Growth of Competitors. Plant Cell 27(11):3175-89.

Willing EM, Rawat V, Mandáková T, et al. (2015) Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nat Plants 1:14023.

Hagmann J, Becker C, Müller J, et al. (2015) Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage. PLoS Genet 11(1):e1004920.

Wang C, Liu C, Roqueiro D, et al. (2015) Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res 25(2):246-56.

Seymour DK, Koenig D, Hagmann J, et al. (2014) Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization. PLoS Genet 10(11):e1004785.

Manavella PA, Koenig D, Rubio-Somoza I, et al. (2013) Tissue-specific silencing of Arabidopsis SU(VAR)3-9 HOMOLOG8 by miR171a. Plant Physiol 161(2):805-12.

Becker C, Weigel D (2012) Epigenetic variation: origin and transgenerational inheritance. Curr Opin Plant Biol 15(5):562-7.

Becker C, Hagmann J, Müller J, et al. (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480(7376):245-9.

Gregor Mendel Institute of
Molecular Plant Biology GmbH

Dr. Bohr-Gasse 3
1030 Vienna, Austria

T: +43 1 79044-9000
F: +43 1 79044-9001
E: office(at)