Life implies change. And this holds true for genes as well. Organisms require a flexible genome in order to adapt to changes in the local environment.
Christian Schlötterer and his team from the Institute for Population Genetics at the University of Veterinary Medicine, Vienna study the genomes of entire populations. The scientists want to know why individuals differ from each other and how these differences are encoded in the DNA.
Christian Schlötterer and his colleagues are searching for variation in the genomes of fruitflies.
Photo: Michael Bernkopf / Vetmeduni Vienna
In two review papers published in the journals Nature Reviews Genetics and Heredity, they discuss why DNA sequencing of entire groups can be an efficient and cost-effective way to answer these questions.
DNA analysis has become increasingly efficient and cost-effective since the human genome was first fully sequenced in the year 2001. Sequencing a complete genome, however, still costs around US$1,000. Sequencing the genetic code of hundreds of individuals would therefore be very expensive and time-consuming. In particular for non-human studies, researchers very quickly hit the limit of financial feasibility.
Sequencing groups instead of individuals
The solution to this problem is pool sequencing (Pool-Seq). Schlötterer and his team sequence entire groups of fruit flies (Drosophila melanogaster) at once instead of carrying out many individual sequencing reactions. While the resulting genetic information cannot be attributed to a single individual, the complete data set still provides important genetic information about the entire population.
In the two publications, Schlötterer and colleagues discuss the breadth of questions that can be addressed by Pool-Seq.
Searching for the building blocks of evolution
In order to understand how organisms react to changes in the local environment, the genomes of entire populations can be analysed using Pool-Seq, before and after changed conditions. To do so, the researchers use the method of evolve and resequence (E&R). Schlötterer received an ERC Advanced Grant for this approach in 2012. E&R is a method in which the DNA of a group of individuals is sequenced. After exposing the descendents of this group for several generations to a certain stress, such as high temperature, extreme cold or UV radiation, and the evolved group is then sequenced again. A comparison of the two data sets uncovers genes that have changed in response to the selective stress. The approach makes it possible, for example, to filter out the genes that are involved in a darker pigmentation in response to UV radiation.
“Using this principle, we can perform evolution experiments at high speed. We are using this method to address a broad range of questions, ranging from the identification of genes which influence aging, or genes protecting against diseases and finally to understand the genetic changes which reduce the impact of climate change,” Schlötterer explains.
Uncovering the genetics of aging and disease resistance
The evolve-and-resequence approach also makes it also possible to filter out the genes that regulate aging. This process involves selecting flies from a population, repeatedly over generations, that reach an especially old age. Several generations later, the researchers then compare the genomes of the “Methuselah” flies with those from normally aging flies in order to extract the genes that are involved in the aging process. This method also works to locate genes that provide resistance against certain diseases.
Bioinformatician and co-author, Robert Kofler, explains: “We are dealing with genetic change processes and are searching for variations in the genomes. The variations can help us to understand how evolution works.”
Population geneticists trained in Vienna
Schlötterer heads the “Vienna Graduate School of Population Genetics” hosted by the University of Veterinary Medicine, Vienna. The doctoral program fills the gap between theoretical and experimental population genetics. 22 PhD students are currently conducting research in Vienna in the field of theoretical and experimental population genetics, bioinformatics, and statistics. http://www.popgen-vienna.at
The article „Sequencing pools of individuals – mining genome-wide polymorphism data without big funding” by Christian Schlötterer, Taymond Tobler, Robert Kofler and Viola Nolte was published in the journal Nature Reviews Genetics. DOI:10.1038/nrg3803
The article “Combining experimental evolution with next-generation sequencing: a powerful tool to study adaptation from standing genetic variation” by Christian Schlötterer, Robert Kofler, E. Versace, Raymond Tobler and S. U. Franssen was published in the journal Heredity. DOI:HDY.2014.86
About the University of Veterinary Medicine, Vienna
The University of Veterinary Medicine, Vienna in Austria is one of the leading academic and research institutions in the field of Veterinary Sciences in Europe. About 1,300 employees and 2,300 students work on the campus in the north of Vienna which also houses five university clinics and various research sites. Outside of Vienna the university operates Teaching and Research Farms. http://www.vetmeduni.ac.at
Prof. Christian Schlötterer
Institute of Population Genetics
University of Veterinary Medicine Vienna (Vetmeduni Vienna)
T +43 1 25077-4300
Science Communication / Public Relations
University of Veterinary Medicine Vienna (Vetmeduni Vienna)
T +43 1 25077-1153
Dr. Susanna Kautschitsch | idw - Informationsdienst Wissenschaft
Predicting a protein's behavior from its appearance
10.12.2019 | Ecole Polytechnique Fédérale de Lausanne
Could dark carbon be hiding the true scale of ocean 'dead zones'?
10.12.2019 | University of Plymouth
Graphene, a two-dimensional structure made of carbon, is a material with excellent mechanical, electronic and optical properties. However, it did not seem suitable for magnetic applications. Together with international partners, Empa researchers have now succeeded in synthesizing a unique nanographene predicted in the 1970s, which conclusively demonstrates that carbon in very specific forms has magnetic properties that could permit future spintronic applications. The results have just been published in the renowned journal Nature Nanotechnology.
Depending on the shape and orientation of their edges, graphene nanostructures (also known as nanographenes) can have very different properties – for example,...
Using a clever technique that causes unruly crystals of iron selenide to snap into alignment, Rice University physicists have drawn a detailed map that reveals...
University of Texas and MIT researchers create virtual UAVs that can predict vehicle health, enable autonomous decision-making
In the not too distant future, we can expect to see our skies filled with unmanned aerial vehicles (UAVs) delivering packages, maybe even people, from location...
With ultracold chemistry, researchers get a first look at exactly what happens during a chemical reaction
The coldest chemical reaction in the known universe took place in what appears to be a chaotic mess of lasers. The appearance deceives: Deep within that...
Abnormal scarring is a serious threat resulting in non-healing chronic wounds or fibrosis. Scars form when fibroblasts, a type of cell of connective tissue, reach wounded skin and deposit plugs of extracellular matrix. Until today, the question about the exact anatomical origin of these fibroblasts has not been answered. In order to find potential ways of influencing the scarring process, the team of Dr. Yuval Rinkevich, Group Leader for Regenerative Biology at the Institute of Lung Biology and Disease at Helmholtz Zentrum München, aimed to finally find an answer. As it was already known that all scars derive from a fibroblast lineage expressing the Engrailed-1 gene - a lineage not only present in skin, but also in fascia - the researchers intentionally tried to understand whether or not fascia might be the origin of fibroblasts.
Fibroblasts kit - ready to heal wounds
03.12.2019 | Event News
15.11.2019 | Event News
15.11.2019 | Event News
10.12.2019 | Architecture and Construction
10.12.2019 | Information Technology
10.12.2019 | Life Sciences