Latest News

2016 Campus Soccer Tournament

Posted on June 24, 2016

Two incredibly good department teams participated in this year’s Campus Soccer Tournament read more

Absolute winner spirit - we keep practicing to become next year’s champions! 

Thanks to our numerous fans for believing in us, and thanks to the PhD reps for organizing a fun event!

Teams SWAT (Swift Weigel Attack Team) and Darwin’s Posse: 

Temporal patterns of damage and decay of DNA from herbaria specimens

Posted on June 22, 2016

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

Weiss, C. L., Schuenemann, V. J., Devos, J., Shirsekar, G., Reiter, E., Gould, B. A., Stinchcombe, J. R., Krause, J., Burbano, H. A.

Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66×10-4 per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.

First major phase of 1001 Genomes Project concluded

Posted on June 10, 2016

1135 genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana read more

The 1001 Genome Consortium

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

Epigenetic stress memory - elife paper with Gutierrez-Marcos lab

Posted on May 31, 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. read more

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.

Inducible epigenetic changes in eukaryotes are believed to enable rapid adaptation to environmental fluctuations. We have found distinct regions of the Arabidopsis genome that are susceptible to DNA (de)methylation in response to hyperosmotic stress. The stress-induced epigenetic changes are associated with conditionally heritable adaptive phenotypic stress responses. However, these stress responses are primarily transmitted to the next generation through the female lineage due to widespread DNA glycosylase activity in the male germline, and extensively reset in the absence of stress. Using the CNI1/ATL31 locus as an example, we demonstrate that epigenetically targeted sequences function as distantly-acting control elements of antisense long non-coding RNAs, which in turn regulate targeted gene expression in response to stress. Collectively, our findings reveal that plants use a highly dynamic maternal ‘short-term stress memory’ with which to respond to adverse external conditions. This transient memory relies on the DNA methylation machinery and associated transcriptional changes to extend the phenotypic plasticity accessible to the immediate offspring.

Congratulations, Dr. EunCheon Lim!

Posted on May 04, 2016

EunCheon successfully defended his PhD thesis entitled 'A large-scale computational framework for comparative analyses in population genetics and metagenomics' read more

Congratulations, EunCheon!

Congratulations, Dr. Danelle Seymour!

Posted on April 29, 2016

Danelle successfully defended her PhD thesis entitled 'On the Genetics and Genomics of Arabidopsis thaliana and its Relatives’ and received the exceptional summa cum laude grade. read more

Congratulations, Danelle!


Upcoming Events


SEB Brighton 2016

July 4-7
the Society of Experimental Biology, Brighton, UK

Hernán speaking about "Herbarium Genomics and Plant Evolution"


MiKo Talk Gil McVean

July 13, 3 pm
MPH Lecture Hall

Title: TBA


MiKo Talk Jeremy Burdon