Yves Van de Peer leads the Bioinformatics and Evolutionary Genomics (BEG) Division. The BEG division is a center of excellence in the field of gene and genome annotation and in the field of comparative and evolutionary genomics.
Nowadays, BEG is considered a genome analysis powerhouse specialized in the study of the structure and evolution of plant genomes. Because of our unique expertise and experience in gene prediction, genome annotation, and genome analysis, our research group has been, and still is, involved in many international genome projects and works closely together with international genome sequencing centers such as the DOE Joint Genome Institute (USA), Genoscope (France), and BGI (China). In the past years, BEG has been heavily involved in analyzing and studying the genomes of the poplar tree, grape, apple, tomato, potato, Arabodopsis lyrata, Eucalyptus grandis, Medicago, the orchids Phalaenopsis equestris and Dendrobium catenatum, the sea grass Zostera marina, several green and brown algae, several fungi that are associated with plants, and different kinds of mites and other arthropods that are pests to plants. In total, our contribution to these important genome projects describing analyses of complete genomes that serve a very wide community of scientists has already led to more than 25 highly cited papers in the highest impact journals such as PNAS, Nature, Nature Genetics, and Science.
Also in the field of genome evolution and gene and genome duplications, we have obtained a world-renowned reputation. We have been the first to link whole genome duplications with the origin of the angiosperms, coined ‘an abominable mystery’ by Charles Darwin, and more recently we have provided exciting evidence that whole genome duplications probably play a role in avoiding extinctions. Most flowering plants have been shown to be ancient polyploids that have undergone one or more whole genome duplications early in their evolution. Furthermore, many different plant lineages seem to have experienced an additional, more recent genome duplication. Starting from paralogous genes lying in duplicated segments or identified in large expressed sequence tag collections, we recently dated these youngest duplication events through penalized likelihood phylogenetic tree inference and could show that a majority of these independent genome duplications are clustered in time and seem to coincide with the Cretaceous–Paleogene (K/Pg) boundary. Therefore, we proposed that polyploidization may have contributed to the survival and propagation of several plant lineages during or following the K/Pg extinction event. Although we published a first study on the possible correlation between WGDs and periods of environmental upheaval in 2009, we recently revisited this hypothesis and confirmed our previous results, based on more than 40 genomes and using the most sophisticated evolutionary models available. We are now planning to use both evolutionary experiments with unicellular green algae as well as evolutionary robotics to get more insights into the mechanisms and adaptive capabilities of polyploid organisms in dynamically changing environments.
The genome of the seagrass Zostera marina reveals angiosperm adaptation to the seaOlsen J* Rouzé P Verhelst B Lin Y Bayer T Collen J Dattolo E De Paoli E Dittami S Maumus F Michel G Kersting A Lauritano C Lohaus R Töpel M Tonon T Vanneste K Amirebrahimi M Brakel J Boström C Chovatia M Grimwood J Jenkins J Jueterbock A Mraz A Stam W Tice H Bornberg-Bauer E Green P Pearson G Procaccini G Duarte C Schmutz J Reusch T* Van De Peer Y*NATURE, 530, 331-5, 2016* These authors contributed equally The genome sequence of the orchid Phalaenopsis equestrisCai J* Liu X* Vanneste K* Proost S* Tsai W* Liu K* Chen L He Y Xu Q Bian C Zheng Z Sun F Liu W Hsiao Y Pan Z Hsu C Yang Y Hsu Y Chuang Y Dievart A Dufayard J Xu X Wang Y Wang J Xiao X Zhao X Du R Zhang G Wang M Su Y Xie G Liu G Li L Huang L Luo Y Chen H Van De Peer Y Liu ZNATURE GENETICS, 47, 65-72, 2015* These authors contributed equally The genome of Eucalyptus grandisMyburg A, Grattapaglia D, Tuskan G, Hellsten U, Hayes R, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein D, Dubchak I, Poliakov A, Mizrachi E, Kullan A, Hussey S, Pinard D, Van Der Merwe K, Singh P, Van Jaarsveld I, Silva-Junior O, Togawa R, Pappas M, Faria D, Sansaloni C, Petroli C, Yang X, Ranjan P, Tschaplinski T, Ye C, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente H, Saidi N, Cassan-Wang H, Dunand C, Hefer C, Bornberg-Bauer E, Kersting A, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd A, Liston A, Spatafora J, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Kulheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel S, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones R, Steane D, Vaillancourt R, Potts B, Joubert F, Barry K, Pappas G, Strauss S, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar D, Schmutz JNATURE, 509, 356-62, 2014 Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulationsLin Y, Boone M, Meuris L, Lemmens I, Van Roy N, Soete A, Reumers J, Moisse M, Plaisance S, Drmanac R, Chen J, Speleman F, Lambrechts D, Van de Peer Y, Tavernier J, Callewaert NNature Communications, 5, 4767, 2014 The Norway spruce genome sequence and conifer genome evolutionNystedt B, Street N, Wetterbom A, Zuccolo A, Lin Y, Scofield D, Vezzi F, Delhomme N, Giacomello S, Alexeyenko A, Vicedomini R, Sahlin K, Sherwood E, Elfstrand M, Gramzow L, Holmberg K, Hallman J, Keech O, Klasson L, Koriabine M, Kucukoglu M, Kaller M, Luthman J, Lysholm F, Niittyla T, Olson A, Rilakovic N, Ritland C, Rossello J, Sena J, Svensson T, Talavera-Lopez C, Theissen G, Tuominen H, Vanneste K, Wu Z, Zhang B, Zerbe P, Arvestad L, Bhalerao R, Bohlmann J, Bousquet J, Garcia Gil R, Hvidsten T, De Jong P, Mackay j, Morgante M, Ritland K, Sundberg B, Thompson S, Van de Peer Y, Andersson B, Nilsson O, Ingvarsson P, Lundeberg J, Jansson SNATURE, 497, 579-84, 2013
13/05/2016 - A recent genome study of the seagrass Zostera marina, published by an international
team of 35 researchers in early 2016, may prove to lay the foundations for a range of
functional ecological studies. Yves Van de Peer is happy to give a full account.
18/02/2016 - This study reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants.
20/04/2015 - The lab of Yves Van de Peer (VIB Department of Plant Systems Biology) can add an extra genome paper to its long list.
27/06/2013 - ”This exceptional grant will allow me to think out of the box (ERC projects have to be high risk-high gain) and explore less obvious ways of addressing major questions in evolutionary biology.
27/06/2013 - Sofie Van Landeghem from the group of Yves Van de Peer at the VIB Department of Plant Systems Biology, UGent together with the group of Dirk Inzé, director of PSB, digged into the wealth of information hidden in the biomolecular literature mine.
30/05/2012 - The Tomato Genome Consortium (TGC), a group of over 300 scientists from thirteen countries, has sequenced the genomes of the domesticated tomato and its wild ancestor, Solanum pimpinellifolium.
24/11/2011 - An international team of scientists - including VIB-UGent - has succeeded in deciphering the genome of the spider mite.
15/09/2011 - Thomas Abeel, VIB Department of Plant Systems Biology, UGent, is one of the winners in the first iDEA (Illumina’s Data Excellence Award) Challenge
18/03/2011 - The DREAM is the most important benchmark for the comparison of computational models used in systems biology. Among all the top labs, their test was unanimously rated the overall best performer based on a number of gold standard data sets.
30/08/2010 - An international team of scientists – including Yves Van de Peer of
VIB (Vlaams Instituut voor Biotechnologie) and Ghent University – have cracked the genetic
code of the apple.
20/03/2010 - 150 years after Darwin published his theory of evolution, VIB researchers connected to Ghent University have discovered that DNA duplications have given plants an evolutionary advantage.
03/03/2008 - VIB researchers have succeeded in unravelling the genetic code of Laccaria bicolor. This new information will lead to a better understanding of how fungi help trees to grow and how together they can be indicators of climate change.
15/09/2006 - Scientists has succeeded in unraveling the first tree genome − that of the poplar. Moreover, their research indicates that the poplar has about 45,000 genes
10/02/2004 - The genes that people and fish have in common are the result of duplications of the entire DNA sometime in the distant past, VIB research has shown.
Yves Van de Peer
PhD: Univ. of Antwerp, Antwerp, Belgium, 1995
VIB Group leader since 2002
VIB Division Coordinator since 2003