Latest News

Congrats Danelle: Dissertation Award of Teufel Foundation

Posted on July 17, 2017

Danelle received today the dissertation award of the Reinhold-und-Maria-Teufel-Stiftung. read more

Danelle Seymour defended her PhD thesis on "Exploring the genetics and genomics of Arabidopsis thaliana and its relatives" last year. The dissertation award of the Reinhold-und-Maria-Teufel-Stiftung, which includes a personal purse of €5,000, recognizes the outstanding quality of her work. Congratulations, Danelle!

Danelle is currently a postdoc at UC Irvine, with Brandon Gaut.

On bioRxiv: Segregation distortion in Arabidopsis thaliana

Posted on July 10, 2017

The genetic architecture of recurrent segregation distortion in Arabidopsis thaliana read more

The genetic architecture of recurrent segregation distortion in Arabidopsis thaliana

Danelle K. Seymour, Eunyoung Chae, Burak I. Ariöz, Daniel Koenig, Detlef Weigel

doi.org/10.1101/158527

The equal probability of transmission of alleles from either parent during sexual reproduction is a central tenet of genetics and evolutionary biology. Yet, there are many cases where this rule is violated. Such violations limit intraspecific gene flow and can facilitate the formation of genetic barriers, a first step in speciation. Biased transmission of alleles, or segregation distortion, can result from a number of biological processes including epistatic interactions between incompatible loci, gametic selection, and meiotic drive. Examples of these phenomena have been identified in many species, implying that they are universal, but comprehensive species-wide studies of segregation distortion are lacking. We have performed a species-wide screen for distorted allele frequencies in over 500 segregating populations of Arabidopsis thaliana using reduced-representation genome sequencing. Biased transmission of alleles was evident in up to a quarter of surveyed populations. Most populations exhibited distortion at only one genomic region, with some regions being repeatedly affected in multiple populations. Our results begin to elucidate the species-level architecture of biased transmission of genetic material in A. thaliana, and serve as a springboard for future studies into the basis of intraspecific genetic barriers.

On bioRxiv: Arabidopsis genome assembled with one Nanopore flowcell

Posted on July 05, 2017

Arabidopsis thaliana genome assembly with a single Oxford Nanopore flow cell read more

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

Todd P. Michael, Florian Jupe, Felix Bemm, Stanley T. Motley, Justin P. Sandoval, Olivier Loudet, Detlef Weigel, VJoseph R. Ecker

doi.org/10.1101/149997

While many evolutionary questions can be answered by short read re-sequencing, presence/absence polymorphisms of genes and/or transposons have been largely ignored in large-scale intraspecific evolutionary studies. To enable the rigorous analysis of such variants, multiple high quality and contiguous genome assemblies are essential. Similarly, while genome assemblies based on short reads have made genomics accessible for non-reference species, these assemblies have limitations due to low contiguity. Long-read sequencers and long-read technologies have ushered in a new era of genome sequencing where the lengths of reads exceed those of most repeats. However, because these technologies are not only costly, but also time and compute intensive, it has been unclear how scalable they are. Here we demonstrate a fast and cost effective reference assembly for an Arabidopsis thaliana accession using the USB-sized Oxford Nanopore MinION sequencer and typical consumer computing hardware (4 Cores, 16Gb RAM). We assemble the accession KBS-Mac-74 into 62 contigs with an N50 length of 12.3 Mb covering 100% (119 Mb) of the non-repetitive genome. We demonstrate that the polished KBS-Mac-74 assembly is highly contiguous with BioNano optical genome maps, and of high per-base quality against a likewise polished Pacific Biosciences long-read assembly. The approach we implemented took a total of four days at a cost of less than 1,000 USD for sequencing consumables including instrument depreciation.

 

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.

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Upcoming Events

Aug
19

5th ICBPI 2017


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"


Sep
13

MiKo Talk Jochen Wolf

September 13, 3 pm
MPH Lecture Hall

Title: "TBA"