Latest News

Detlef's latest talk

Posted on June 22, 2017

Curious about his keynote at the VIB Conference "At the Forefront of Plant Research"? read more

Check out his presentation on figshare!

Collaborative paper: Methylome and apple fruit development

Posted on June 13, 2017

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development read more

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Daccord et al.

Nature Genetics (2017) doi:10.1038/ng.3886

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

Biennial department retreat Bad Urach

Posted on May 28, 2017

We spent May 18-19 in Bad Urach read more

A great two days in Bad Urach, discussing not only exciting science, but also how we can improve ourselves as scientists, both individually and as a team.

With Mathieu lab: TE-related plant proteins in gene silencing

Posted on May 12, 2017

Latest paper: Arabidopsis proteins with a transposon-related domain act in gene silencing read more

Arabidopsis proteins with a transposon-related domain act in gene silencing

Yoko Ikeda, Thierry Pélissier, Pierre Bourguet, Claude Becker, Marie-Noëlle Pouch-Pélissier, Romain Pogorelcnik, Magdalena Weingartner, Detlef Weigel, Jean-Marc Deragon & Olivier Mathieu

Nature Communications 8, Article number: 15122 (2017) doi:10.1038/ncomms15122

Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein in TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation and short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 and MAIN define an alternative silencing pathway independent of DNA methylation and short interfering RNAs. Mutants for MAIL1 or MAIN exhibit release of silencing and appear to show impaired condensation of pericentromeric heterochromatin. Phylogenetic analysis suggests not only that MAIL1 and MAIN encode a retrotransposon-related plant mobile domain, but also that host plant mobile domains were captured by DNA transposons during plant evolution. Our results reveal a role for Arabidopsis proteins with a transposon-related domain in gene silencing.

RNA helicases and hybrid breakdown in A. thaliana

Posted on May 09, 2017

Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana read more

Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana

Björn Plötner, Markus Nurmi, Axel Fischer, Mutsumi Watanabe, Korbinian Schneeberger, Svante Holm, Neha Vaid, Mark Aurel Schöttler, Dirk Walther, Rainer Hoefgen, Detlef Weigel, Roosa A. E. Laitinen

Plant J. 2017 Apr 4. doi: 10.1111/tpj.13560

Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden). In addition to chlorosis, a fraction of the F2 plants have defects in leaf and embryo development and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major-effect loci, of which one, originating from Lov-5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in year 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in year 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes.

 

Sediment DNA revolutionizing ancient genetics

Posted on April 28, 2017

Targeted enrichment of sediment DNA revolutionizing ancient genetics read more

Neandertal and Denisovan DNA from Pleistocene sediments

Viviane Slon, Charlotte HopfeClemens L. Weiß, Hernán A. Burbano, Svante Pääbo, Matthias Meyer

Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found.

 

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Upcoming Events

Jul
03

SMBE 2017


Jul
18

GRC Ecological & Evolutionary Genomics

July 16-21, 2017
Biddeford, ME, USA

Hernán Burbano speaking about "Genomic Estimation of Complex Traits Reveals Ancient Maize Adaptation to Temperate North America"


Sep
12

IMPRS PhD Student Symposium

September 11-14
in Göttingen, Germany

Detlef speaking at International Horizons in Molecular Biology Symposium: "Genetics and epigenetics of adaptation to the environment"